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Bergamasco MI, Vanyai HK, Garnham AL, Geoghegan ND, Vogel AP, Eccles S, Rogers KL, Smyth GK, Blewitt ME, Hannan AJ, Thomas T, Voss AK. Increasing histone acetylation improves sociability and restores learning and memory in KAT6B-haploinsufficient mice. J Clin Invest 2024; 134:e167672. [PMID: 38557491 PMCID: PMC10977983 DOI: 10.1172/jci167672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/26/2024] [Indexed: 04/04/2024] Open
Abstract
Mutations in genes encoding chromatin modifiers are enriched among mutations causing intellectual disability. The continuing development of the brain postnatally, coupled with the inherent reversibility of chromatin modifications, may afford an opportunity for therapeutic intervention following a genetic diagnosis. Development of treatments requires an understanding of protein function and models of the disease. Here, we provide a mouse model of Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS) (OMIM 603736) and demonstrate proof-of-principle efficacy of postnatal treatment. SBBYSS results from heterozygous mutations in the KAT6B (MYST4/MORF/QFK) gene and is characterized by intellectual disability and autism-like behaviors. Using human cells carrying SBBYSS-specific KAT6B mutations and Kat6b heterozygous mice (Kat6b+/-), we showed that KAT6B deficiency caused a reduction in histone H3 lysine 9 acetylation. Kat6b+/- mice displayed learning, memory, and social deficits, mirroring SBBYSS individuals. Treatment with a histone deacetylase inhibitor, valproic acid, or an acetyl donor, acetyl-carnitine (ALCAR), elevated histone acetylation levels in the human cells with SBBYSS mutations and in brain and blood cells of Kat6b+/- mice and partially reversed gene expression changes in Kat6b+/- cortical neurons. Both compounds improved sociability in Kat6b+/- mice, and ALCAR treatment restored learning and memory. These data suggest that a subset of SBBYSS individuals may benefit from postnatal therapeutic interventions.
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Affiliation(s)
- Maria I. Bergamasco
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Hannah K. Vanyai
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Alexandra L. Garnham
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Niall D. Geoghegan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Adam P. Vogel
- Centre for Neurosciences of Speech, University of Melbourne, Parkville, Victoria, Australia
- Redenlab Inc., Melbourne, Australia
| | - Samantha Eccles
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Kelly L. Rogers
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Marnie E. Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Anthony J. Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
| | - Anne K. Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology and
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Blewitt ME. Mary Lyon and the birth of X-inactivation research. Nat Rev Genet 2024; 25:6. [PMID: 37704716 DOI: 10.1038/s41576-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Affiliation(s)
- Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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3
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Short KM, Tortelote GG, Jones LK, Diniz F, Edgington-Giordano F, Cullen-McEwen LA, Schröder J, Spencer A, Keniry A, Polo JM, Bertram JF, Blewitt ME, Smyth IM, El-Dahr SS. The molecular and cellular anatomy of a fetal programming defect - the impact of low protein diet on the developing kidney. bioRxiv 2023:2023.12.04.569988. [PMID: 38106143 PMCID: PMC10723346 DOI: 10.1101/2023.12.04.569988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Low nephron number correlates with the development of hypertension and chronic kidney disease later in life. While intrauterine growth restriction caused by maternal low protein diet (LPD) is thought to be a significant cause of reduced nephron endowment in impoverished communities, its influence on the cellular and molecular processes which drive nephron formation are poorly understood. We conducted a comprehensive characterization of the impact of LPD on kidney development using tomographic and confocal imaging to quantify changes in branching morphogenesis and the cellular and morphological features of nephrogenic niches across development. These analyses were paired with single-cell RNA sequencing to dissect the transcriptional changes that LPD imposes during renal development. Differences in the expression of genes involved in metabolism were identified in most cell types we analyzed, yielding imbalances and shifts in cellular energy production. We further demonstrate that LPD impedes branching morphogenesis and significantly reduces the number of pretubular aggregates - the initial precursors to nephron formation. The most striking observation was that LPD changes the developmental trajectory of nephron progenitor cells, driving the formation of a partially committed cell population which likely reflects a failure of cells to commit to nephron formation and which ultimately reduces endowment. This unique profile of a fetal programming defect demonstrates that low nephron endowment arises from the pleiotropic impact of changes in branching morphogenesis and nephron progenitor cell commitment, the latter of which highlights a critical role for nutrition in regulating the cell fate decisions underpinning nephron endowment. Significance Statement While a mother's diet and behavior can negatively impact the number of nephrons in the kidneys of her offspring, the root cellular and molecular drivers of these deficits have not been rigorously explored. In this study we use advanced imaging and gene expression analysis in mouse models to define how a maternal low protein diet, analogous to that of impoverished communities, results in reduced nephron endowment. We find that low protein diet has pleiotropic effects on metabolism and the normal programs of gene expression. These profoundly impact the process of branching morphogenesis necessary to establish niches for nephron generation and change cell behaviors which regulate how and when nephron progenitor cells commit to differentiation.
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4
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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5
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Borger JG, Ng AP, Anderton H, Ashdown GW, Auld M, Blewitt ME, Brown DV, Call MJ, Collins P, Freytag S, Harrison LC, Hesping E, Hoysted J, Johnston A, McInneny A, Tang P, Whitehead L, Jex A, Naik SH. Artificial intelligence takes center stage: exploring the capabilities and implications of ChatGPT and other AI-assisted technologies in scientific research and education. Immunol Cell Biol 2023; 101:923-935. [PMID: 37721869 DOI: 10.1111/imcb.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
The emergence of large language models (LLMs) and assisted artificial intelligence (AI) technologies have revolutionized the way in which we interact with technology. A recent symposium at the Walter and Eliza Hall Institute explored the current practical applications of LLMs in medical research and canvassed the emerging ethical, legal and social implications for the use of AI-assisted technologies in the sciences. This paper provides an overview of the symposium's key themes and discussions delivered by diverse speakers, including early career researchers, group leaders, educators and policy-makers highlighting the opportunities and challenges that lie ahead for scientific researchers and educators as we continue to explore the potential of this cutting-edge and emerging technology.
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Affiliation(s)
- Jessica G Borger
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Ashley P Ng
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Holly Anderton
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - George W Ashdown
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Megan Auld
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Marnie E Blewitt
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel V Brown
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Melissa J Call
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Peter Collins
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Saskia Freytag
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Leonard C Harrison
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Eva Hesping
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Jaci Hoysted
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Johnston
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew McInneny
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Phil Tang
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Lachlan Whitehead
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron Jex
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Shalin H Naik
- WEHI (Walter and Eliza Hall Institute of Medical Research), Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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6
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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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7
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Preston SP, Stutz MD, Allison CC, Nachbur U, Gouil Q, Tran BM, Duvivier V, Arandjelovic P, Cooney JP, Mackiewicz L, Meng Y, Schaefer J, Bader SM, Peng H, Valaydon Z, Rajasekaran P, Jennison C, Lopaticki S, Farrell A, Ryan M, Howell J, Croagh C, Karunakaran D, Schuster-Klein C, Murphy JM, Fifis T, Christophi C, Vincan E, Blewitt ME, Thompson A, Boddey JA, Doerflinger M, Pellegrini M. Epigenetic Silencing of RIPK3 in Hepatocytes Prevents MLKL-mediated Necroptosis From Contributing to Liver Pathologies. Gastroenterology 2022; 163:1643-1657.e14. [PMID: 36037995 DOI: 10.1053/j.gastro.2022.08.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND & AIMS Necroptosis is a highly inflammatory mode of cell death that has been implicated in causing hepatic injury including steatohepatitis/ nonalcoholic steatohepatitis (NASH); however, the evidence supporting these claims has been controversial. A comprehensive, fundamental understanding of cell death pathways involved in liver disease critically underpins rational strategies for therapeutic intervention. We sought to define the role and relevance of necroptosis in liver pathology. METHODS Several animal models of human liver pathology, including diet-induced steatohepatitis in male mice and diverse infections in both male and female mice, were used to dissect the relevance of necroptosis in liver pathobiology. We applied necroptotic stimuli to primary mouse and human hepatocytes to measure their susceptibility to necroptosis. Paired liver biospecimens from patients with NASH, before and after intervention, were analyzed. DNA methylation sequencing was also performed to investigate the epigenetic regulation of RIPK3 expression in primary human and mouse hepatocytes. RESULTS Identical infection kinetics and pathologic outcomes were observed in mice deficient in an essential necroptotic effector protein, MLKL, compared with control animals. Mice lacking MLKL were indistinguishable from wild-type mice when fed a high-fat diet to induce NASH. Under all conditions tested, we were unable to induce necroptosis in hepatocytes. We confirmed that a critical activator of necroptosis, RIPK3, was epigenetically silenced in mouse and human primary hepatocytes and rendered them unable to undergo necroptosis. CONCLUSIONS We have provided compelling evidence that necroptosis is disabled in hepatocytes during homeostasis and in the pathologic conditions tested in this study.
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Affiliation(s)
- Simon P Preston
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michael D Stutz
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Cody C Allison
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ueli Nachbur
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Bang Manh Tran
- Department of Infectious Diseases, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Valerie Duvivier
- Cardiovascular and Metabolic Disease Center for Therapeutic Innovation, SERVIER Group, Suresnes, France
| | - Philip Arandjelovic
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - James P Cooney
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Liana Mackiewicz
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Yanxiang Meng
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jan Schaefer
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stefanie M Bader
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Hongke Peng
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Zina Valaydon
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Pravin Rajasekaran
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Charlie Jennison
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sash Lopaticki
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Ann Farrell
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marno Ryan
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jess Howell
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catherine Croagh
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Denuja Karunakaran
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia; Monash Biomedicine Discovery Institute and Victorian Heart Institute, Monash University, Clayton, Victoria, Australia
| | - Carole Schuster-Klein
- Cardiovascular and Metabolic Disease Center for Therapeutic Innovation, SERVIER Group, Suresnes, France
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Theodora Fifis
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher Christophi
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Vincan
- Department of Infectious Diseases, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Victorian Infectious Disease Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexander Thompson
- Department of Gastroenterology, St. Vincent's Hospital, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justin A Boddey
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Marcel Doerflinger
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Marc Pellegrini
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
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8
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Keniry A, Jansz N, Hickey PF, Breslin KA, Iminitoff M, Beck T, Gouil Q, Ritchie ME, Blewitt ME. A method for stabilising the XX karyotype in female mESC cultures. Development 2022; 149:285125. [PMID: 36355065 PMCID: PMC10112917 DOI: 10.1242/dev.200845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022]
Abstract
Female mouse embryonic stem cells (mESCs) present differently from male mESCs in several fundamental ways; however, complications with their in vitro culture have resulted in an under-representation of female mESCs in the literature. Recent studies show that the second X chromosome in female, and more specifically the transcriptional activity from both of these chromosomes due to absent X chromosome inactivation, sets female and male mESCs apart. To avoid this undesirable state, female mESCs in culture preferentially adopt an XO karyotype, with this adaption leading to loss of their unique properties in favour of a state that is near indistinguishable from male mESCs. If female pluripotency is to be studied effectively in this system, it is crucial that high-quality cultures of XX mESCs are available. Here, we report a method for better maintaining XX female mESCs in culture that also stabilises the male karyotype and makes study of female-specific pluripotency more feasible.
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Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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9
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Wanigasuriya I, Kinkel SA, Beck T, Roper EA, Breslin K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME, Gouil Q. Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation. Epigenetics Chromatin 2022; 15:26. [PMID: 35843975 PMCID: PMC9290310 DOI: 10.1186/s13072-022-00458-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Embryonic development is dependent on the maternal supply of proteins through the oocyte, including factors setting up the adequate epigenetic patterning of the zygotic genome. We previously reported that one such factor is the epigenetic repressor SMCHD1, whose maternal supply controls autosomal imprinted expression in mouse preimplantation embryos and mid-gestation placenta. In mouse preimplantation embryos, X chromosome inactivation is also an imprinted process. Combining genomics and imaging, we show that maternal SMCHD1 is required not only for the imprinted expression of Xist in preimplantation embryos, but also for the efficient silencing of the inactive X in both the preimplantation embryo and mid-gestation placenta. These results expand the role of SMCHD1 in enforcing the silencing of Polycomb targets. The inability of zygotic SMCHD1 to fully restore imprinted X inactivation further points to maternal SMCHD1’s role in setting up the appropriate chromatin environment during preimplantation development, a critical window of epigenetic remodelling.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Ellise A Roper
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Heather J Lee
- The School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. .,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
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10
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Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME. NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PLoS Comput Biol 2021; 17:e1009524. [PMID: 34695109 PMCID: PMC8568149 DOI: 10.1371/journal.pcbi.1009524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/04/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental groups led us to develop the NanoMethViz R package. Our software can handle methylation output generated from a range of different methylation callers and manages large datasets using a compressed data format. To fully explore the methylation patterns in a dataset, NanoMethViz allows plotting of data at various resolutions. At the sample-level, we use dimensionality reduction to look at the relationships between methylation profiles in an unsupervised way. We visualize methylation profiles of classes of features such as genes or CpG islands by scaling them to relative positions and aggregating their profiles. At the finest resolution, we visualize methylation patterns across individual reads along the genome using the spaghetti plot and heatmaps, allowing users to explore particular genes or genomic regions of interest. In summary, our software makes the handling of methylation signal more convenient, expands upon the visualization options for nanopore data and works seamlessly with existing methylation analysis tools available in the Bioconductor project. Our software is available at https://bioconductor.org/packages/NanoMethViz.
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Affiliation(s)
- Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail: (SS); (MER)
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Marnie E. Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Dianne Cook
- Econometrics & Business Statistics, Monash University, Melbourne, Australia
| | - Peter F. Hickey
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Matthew E. Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail: (SS); (MER)
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11
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Drummond KD, Waring ML, Faulkner GJ, Blewitt ME, Perry CJ, Kim JH. Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence. Neurobiol Stress 2021; 15:100367. [PMID: 34337114 PMCID: PMC8313755 DOI: 10.1016/j.ynstr.2021.100367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
Impaired extinction of conditioned fear is associated with anxiety disorders. Common lifestyle factors, like isolation stress and exercise, may alter the ability to extinguish fear. However, the effect of and interplay between these factors on adolescent fear extinction, and the relevant underlying neural mechanisms are unknown. Here we examined the effects of periadolescent social isolation and physical activity on adolescent fear extinction in rats and explored neurogenesis as a potential mechanism. Isolation stress impaired extinction recall in male adolescents, an effect prevented by exercise. Extinction recall in female adolescents was unaffected by isolation stress. However, exercise disrupted extinction recall in isolated females. Extinction recall in isolated females was positively correlated to the number of immature neurons in the ventral hippocampus, suggesting that exercise affected extinction recall via neurogenesis in females. Pharmacologically suppressing cellular proliferation in isolated adolescents using temozolomide blocked the effect of exercise on extinction recall in both sexes. Together, these findings highlight sex-specific outcomes of isolation stress and exercise on adolescent brain and behavior, and highlights neurogenesis as a potential mechanism underlying lifestyle effects on adolescent fear extinction. Periadolescent isolation stress disrupted extinction recall in male adolescents. Running prevented isolation-induced extinction recall deficit in male adolescents. Exercise impaired extinction recall in isolated female adolescents. Exercise increased hippocampal neurogenesis, except in isolated males. Suppression of neurogenesis blocked exercise effects in isolated adolescents.
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Affiliation(s)
- Katherine D Drummond
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia.,Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Michelle L Waring
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, QLD, 4102, Australia.,Queensland Brain Institute, University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Marnie E Blewitt
- The Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christina J Perry
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia.,Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jee Hyun Kim
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia.,Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia.,IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia
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12
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Ah-Cann C, Wimmer VC, Weeden CE, Marceaux C, Law CW, Galvis L, Filby CE, Liu J, Breslin K, Willson T, Ritchie ME, Blewitt ME, Asselin-Labat ML. A functional genetic screen identifies aurora kinase b as an essential regulator of Sox9-positive mouse embryonic lung progenitor cells. Development 2021; 148:269134. [PMID: 34121118 DOI: 10.1242/dev.199543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022]
Abstract
Development of a branching tree in the embryonic lung is crucial for the formation of a fully mature functional lung at birth. Sox9+ cells present at the tip of the primary embryonic lung endoderm are multipotent cells responsible for branch formation and elongation. We performed a genetic screen in murine primary cells and identified aurora kinase b (Aurkb) as an essential regulator of Sox9+ cells ex vivo. In vivo conditional knockout studies confirmed that Aurkb was required for lung development but was not necessary for postnatal growth and the repair of the adult lung after injury. Deletion of Aurkb in embryonic Sox9+ cells led to the formation of a stunted lung that retained the expression of Sox2 in the proximal airways, as well as Sox9 in the distal tips. Although we found no change in cell polarity, we showed that loss of Aurkb or chemical inhibition of Aurkb caused Sox9+ cells to arrest at G2/M, likely responsible for the lack of branch bifurcation. This work demonstrates the power of genetic screens in identifying novel regulators of Sox9+ progenitor cells and lung branching morphogenesis.
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Affiliation(s)
- Casey Ah-Cann
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Verena C Wimmer
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Clare E Weeden
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Claire Marceaux
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Charity W Law
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville 3010, Australia
| | - Laura Galvis
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Caitlin E Filby
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Joy Liu
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Kelsey Breslin
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Tracy Willson
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Divison, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
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13
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Dong X, Tian L, Gouil Q, Kariyawasam H, Su S, De Paoli-Iseppi R, Prawer YDJ, Clark MB, Breslin K, Iminitoff M, Blewitt ME, Law CW, Ritchie ME. The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools. NAR Genom Bioinform 2021; 3:lqab028. [PMID: 33937765 PMCID: PMC8074342 DOI: 10.1093/nargab/lqab028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (‘sequins’) as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 was analysed using a mix of long-read specific tools for preprocessing together with established short-read RNA-seq methods for downstream analysis. We used limma-voom to perform differential gene expression analysis, and the novel FLAMES pipeline to perform isoform identification and quantification, followed by DRIMSeq and limma-diffSplice (with stageR) to perform differential transcript usage analysis. We compared results from the sequins dataset to the ground truth, and results of the mouse dataset to a previous short-read study on equivalent samples. Overall, our work shows that transcriptomic analysis of long-read nanopore data using long-read specific preprocessing methods together with short-read differential expression methods and software that are already in wide use can yield meaningful results.
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Affiliation(s)
- Xueyi Dong
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Luyi Tian
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Hasaru Kariyawasam
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Ricardo De Paoli-Iseppi
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yair David Joseph Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kelsey Breslin
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Megan Iminitoff
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Charity W Law
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
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14
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Tullett KM, Tan PS, Park HY, Schittenhelm RB, Michael N, Li R, Policheni AN, Gruber E, Huang C, Fulcher AJ, Danne JC, Czabotar PE, Wakim LM, Mintern JD, Ramm G, Radford KJ, Caminschi I, O'Keeffe M, Villadangos JA, Wright MD, Blewitt ME, Heath WR, Shortman K, Purcell AW, Nicola NA, Zhang JG, Lahoud MH. RNF41 regulates the damage recognition receptor Clec9A and antigen cross-presentation in mouse dendritic cells. eLife 2020; 9:63452. [PMID: 33264090 PMCID: PMC7710356 DOI: 10.7554/elife.63452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/18/2020] [Indexed: 11/22/2022] Open
Abstract
The dendritic cell receptor Clec9A facilitates processing of dead cell-derived antigens for cross-presentation and the induction of effective CD8+ T cell immune responses. Here, we show that this process is regulated by E3 ubiquitin ligase RNF41 and define a new ubiquitin-mediated mechanism for regulation of Clec9A, reflecting the unique properties of Clec9A as a receptor specialized for delivery of antigens for cross-presentation. We reveal RNF41 is a negative regulator of Clec9A and the cross-presentation of dead cell-derived antigens by mouse dendritic cells. Intriguingly, RNF41 regulates the downstream fate of Clec9A by directly binding and ubiquitinating the extracellular domains of Clec9A. At steady-state, RNF41 ubiquitination of Clec9A facilitates interactions with ER-associated proteins and degradation machinery to control Clec9A levels. However, Clec9A interactions are altered following dead cell uptake to favor antigen presentation. These findings provide important insights into antigen cross-presentation and have implications for development of approaches to modulate immune responses.
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Affiliation(s)
- Kirsteen M Tullett
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Peck Szee Tan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Hae-Young Park
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Nicole Michael
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Rong Li
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Antonia N Policheni
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Emily Gruber
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Alex J Fulcher
- Monash Micro Imaging Facility, Monash University, Clayton, Australia
| | - Jillian C Danne
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Justine D Mintern
- Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Georg Ramm
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Australia
| | - Kristen J Radford
- Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Irina Caminschi
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Meredith O'Keeffe
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.,Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia
| | - Mark D Wright
- Department of Immunology, Monash University, Melbourne, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - William R Heath
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Ken Shortman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mireille H Lahoud
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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15
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Wanigasuriya I, Gouil Q, Kinkel SA, Tapia Del Fierro A, Beck T, Roper EA, Breslin K, Stringer J, Hutt K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME. Smchd1 is a maternal effect gene required for genomic imprinting. eLife 2020; 9:55529. [PMID: 33186096 PMCID: PMC7665889 DOI: 10.7554/elife.55529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor Smchd1 as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice. We also found zygotic SMCHD1 had a dose-dependent effect on the imprinted expression of seven genes. Together, zygotic and maternal SMCHD1 regulate three classic imprinted clusters and eight other genes, including non-canonical imprinted genes. Interestingly, the loss of maternal SMCHD1 does not alter germline DNA methylation imprints pre-implantation or later in gestation. Instead, what appears to unite most imprinted genes sensitive to SMCHD1 is their reliance on polycomb-mediated methylation as germline or secondary imprints, therefore we propose that SMCHD1 acts downstream of polycomb imprints to mediate its function.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andrés Tapia Del Fierro
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ellise A Roper
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jessica Stringer
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Karla Hutt
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Heather J Lee
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
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16
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Chen K, Birkinshaw RW, Gurzau AD, Wanigasuriya I, Wang R, Iminitoff M, Sandow JJ, Young SN, Hennessy PJ, Willson TA, Heckmann DA, Webb AI, Blewitt ME, Czabotar PE, Murphy JM. Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues. Sci Signal 2020; 13:13/636/eaaz5599. [PMID: 32546545 DOI: 10.1126/scisignal.aaz5599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.
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Affiliation(s)
- Kelan Chen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alexandra D Gurzau
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ruoyun Wang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Megan Iminitoff
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Patrick J Hennessy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Denise A Heckmann
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia.,School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia
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17
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Lau KX, Mason EA, Kie J, De Souza DP, Kloehn J, Tull D, McConville MJ, Keniry A, Beck T, Blewitt ME, Ritchie ME, Naik SH, Zalcenstein D, Korn O, Su S, Romero IG, Spruce C, Baker CL, McGarr TC, Wells CA, Pera MF. Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. Nat Commun 2020; 11:2420. [PMID: 32415101 PMCID: PMC7229198 DOI: 10.1038/s41467-020-16214-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells. Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have distinct cell cycle, metabolic, DNA methylation, and ATAC-seq profiles.
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Affiliation(s)
- Kevin X Lau
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elizabeth A Mason
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joshua Kie
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joachim Kloehn
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Andrew Keniry
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Tamara Beck
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Marnie E Blewitt
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Shalin H Naik
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Daniela Zalcenstein
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Shian Su
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | | | | | | | - Christine A Wells
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Divisions of Cancer and Hematology and Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin F Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia. .,The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
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18
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MacPherson L, Anokye J, Yeung MM, Lam EYN, Chan YC, Weng CF, Yeh P, Knezevic K, Butler MS, Hoegl A, Chan KL, Burr ML, Gearing LJ, Willson T, Liu J, Choi J, Yang Y, Bilardi RA, Falk H, Nguyen N, Stupple PA, Peat TS, Zhang M, de Silva M, Carrasco-Pozo C, Avery VM, Khoo PS, Dolezal O, Dennis ML, Nuttall S, Surjadi R, Newman J, Ren B, Leaver DJ, Sun Y, Baell JB, Dovey O, Vassiliou GS, Grebien F, Dawson SJ, Street IP, Monahan BJ, Burns CJ, Choudhary C, Blewitt ME, Voss AK, Thomas T, Dawson MA. HBO1 is required for the maintenance of leukaemia stem cells. Nature 2020; 577:266-270. [PMID: 31827282 DOI: 10.1038/s41586-019-1835-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/12/2019] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs)1. Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.
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Affiliation(s)
- Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Juliana Anokye
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Miriam M Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul Yeh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Miriam S Butler
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Annabelle Hoegl
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kah-Lok Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marian L Burr
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tracy Willson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Jarny Choi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca A Bilardi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Hendrik Falk
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Nghi Nguyen
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Ming Zhang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Melanie de Silva
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Poh Sim Khoo
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Children's Cancer Institute, Kensington, New South Wales, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Regina Surjadi
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Janet Newman
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria, Australia
| | - David J Leaver
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Yuxin Sun
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Oliver Dovey
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian P Street
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Brendon J Monahan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Therapeutics CRC, Melbourne, Victoria, Australia
| | - Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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19
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Jansz N, Nesterova T, Keniry A, Iminitoff M, Hickey PF, Pintacuda G, Masui O, Kobelke S, Geoghegan N, Breslin KA, Willson TA, Rogers K, Kay GF, Fox AH, Koseki H, Brockdorff N, Murphy JM, Blewitt ME. Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway. Cell Rep 2019; 25:1912-1923.e9. [PMID: 30428357 DOI: 10.1016/j.celrep.2018.10.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023] Open
Abstract
We and others have recently reported that the SMC protein Smchd1 is a regulator of chromosome conformation. Smchd1 is critical for the structure of the inactive X chromosome and at autosomal targets such as the Hox genes. However, it is unknown how Smchd1 is recruited to these sites. Here, we report that Smchd1 localizes to the inactive X via the Xist-HnrnpK-PRC1 (polycomb repressive complex 1) pathway. Contrary to previous reports, Smchd1 does not bind Xist or other RNA molecules with any specificity. Rather, the localization of Smchd1 to the inactive X is H2AK119ub dependent. Following perturbation of this interaction, Smchd1 is destabilized, which has consequences for gene silencing genome-wide. Our work adds Smchd1 to the PRC1 silencing pathway for X chromosome inactivation.
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Affiliation(s)
- Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tatyana Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Osamu Masui
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Niall Geoghegan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Kelly Rogers
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Graham F Kay
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Haruhiko Koseki
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC 3010, Australia.
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20
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Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME. Using long-read sequencing to detect imprinted DNA methylation. Nucleic Acids Res 2019; 47:e46. [PMID: 30793194 PMCID: PMC6486641 DOI: 10.1093/nar/gkz107] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 02/01/2023] Open
Abstract
Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of ∼10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs.
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Affiliation(s)
- Scott Gigante
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Genetics, Yale University, 333 Cedar Street, New Haven CT 06510, USA
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
| | - Matthew Tinning
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Lavinia Gordon
- Australian Genome Research Facility, 305 Grattan Street, Melbourne VIC 3000, Australia
| | - Chris Woodruff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
| | - Terence P Speed
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,School of Mathematics and Statistics, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne VIC 3010, Australia.,School of Mathematics and Statistics, The University of Melbourne, Melbourne VIC 3010, Australia
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21
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Dion C, Roche S, Laberthonnière C, Broucqsault N, Mariot V, Xue S, Gurzau AD, Nowak A, Gordon CT, Gaillard MC, El-Yazidi C, Thomas M, Schlupp-Robaglia A, Missirian C, Malan V, Ratbi L, Sefiani A, Wollnik B, Binetruy B, Salort Campana E, Attarian S, Bernard R, Nguyen K, Amiel J, Dumonceaux J, Murphy JM, Déjardin J, Blewitt ME, Reversade B, Robin JD, Magdinier F. SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite. Nucleic Acids Res 2019; 47:2822-2839. [PMID: 30698748 PMCID: PMC6451109 DOI: 10.1093/nar/gkz005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS). By investigating why germline SMCHD1 mutations lead to these two different diseases, we uncovered a role for this factor in de novo methylation at the pluripotent stage. SMCHD1 is required for the dynamic methylation of the D4Z4 macrosatellite upon reprogramming but seems dispensable for methylation maintenance. We find that FSHD and BAMS patient's cells carrying SMCHD1 mutations are both permissive for DUX4 expression, a transcription factor whose regulation has been proposed as the main trigger for FSHD. These findings open new questions as to what is the true aetiology for FSHD, the epigenetic events associated with the disease thus calling the current model into question and opening new perspectives for understanding repetitive DNA sequences regulation.
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Affiliation(s)
- Camille Dion
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | | | - Natacha Broucqsault
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Agnieszka Nowak
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Claire El-Yazidi
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Morgane Thomas
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Andrée Schlupp-Robaglia
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France.,Centre de ressources biologiques, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Chantal Missirian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Valérie Malan
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Liham Ratbi
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Campus Göttingen, 37073 Göttingen, Germany
| | - Bernard Binetruy
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Jérôme Déjardin
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore.,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.,Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
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22
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de Greef JC, Krom YD, den Hamer B, Snider L, Hiramuki Y, van den Akker RFP, Breslin K, Pakusch M, Salvatori DCF, Slütter B, Tawil R, Blewitt ME, Tapscott SJ, van der Maarel SM. Smchd1 haploinsufficiency exacerbates the phenotype of a transgenic FSHD1 mouse model. Hum Mol Genet 2019; 27:716-731. [PMID: 29281018 DOI: 10.1093/hmg/ddx437] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 12/18/2017] [Indexed: 11/12/2022] Open
Abstract
In humans, a copy of the DUX4 retrogene is located in each unit of the D4Z4 macrosatellite repeat that normally comprises 8-100 units. The D4Z4 repeat has heterochromatic features and does not express DUX4 in somatic cells. Individuals with facioscapulohumeral muscular dystrophy (FSHD) have a partial failure of somatic DUX4 repression resulting in the presence of DUX4 protein in sporadic muscle nuclei. Somatic DUX4 derepression is caused by contraction of the D4Z4 repeat to 1-10 units (FSHD1) or by heterozygous mutations in genes responsible for maintaining the D4Z4 chromatin structure in a repressive state (FSHD2). One of the FSHD2 genes is the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene. SMCHD1 mutations have also been identified in FSHD1; patients carrying a contracted D4Z4 repeat and a SMCHD1 mutation are more severely affected than relatives with only a contracted repeat or a SMCHD1 mutation. To evaluate the modifier role of SMCHD1, we crossbred mice carrying a contracted D4Z4 repeat (D4Z4-2.5 mice) with mice that are haploinsufficient for Smchd1 (Smchd1MommeD1 mice). D4Z4-2.5/Smchd1MommeD1 mice presented with a significantly reduced body weight and developed skin lesions. The same skin lesions, albeit in a milder form, were also observed in D4Z4-2.5 mice, suggesting that reduced Smchd1 levels aggravate disease in the D4Z4-2.5 mouse model. Our study emphasizes the evolutionary conservation of the SMCHD1-dependent epigenetic regulation of the D4Z4 repeat array and further suggests that the D4Z4-2.5/Smchd1MommeD1 mouse model may be used to unravel the function of DUX4 in non-muscle tissues like the skin.
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Affiliation(s)
- Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lauren Snider
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yosuke Hiramuki
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rob F P van den Akker
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Miha Pakusch
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Bram Slütter
- Divisions of Biopharmaceutics & Drug Delivery Technology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,University of Melbourne, Melbourne, Australia
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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23
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Sanders MA, Chew E, Flensburg C, Zeilemaker A, Miller SE, Al Hinai AS, Bajel A, Luiken B, Rijken M, Mclennan T, Hoogenboezem RM, Kavelaars FG, Fröhling S, Blewitt ME, Bindels EM, Alexander WS, Löwenberg B, Roberts AW, Valk PJM, Majewski IJ. MBD4 guards against methylation damage and germ line deficiency predisposes to clonal hematopoiesis and early-onset AML. Blood 2018; 132:1526-1534. [PMID: 30049810 PMCID: PMC6172562 DOI: 10.1182/blood-2018-05-852566] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/18/2018] [Indexed: 02/07/2023] Open
Abstract
The tendency of 5-methylcytosine (5mC) to undergo spontaneous deamination has had a major role in shaping the human genome, and this methylation damage remains the primary source of somatic mutations that accumulate with age. How 5mC deamination contributes to cancer risk in different tissues remains unclear. Genomic profiling of 3 early-onset acute myeloid leukemias (AMLs) identified germ line loss of MBD4 as an initiator of 5mC-dependent hypermutation. MBD4-deficient AMLs display a 33-fold higher mutation burden than AML generally, with >95% being C>T in the context of a CG dinucleotide. This distinctive signature was also observed in sporadic cancers that acquired biallelic mutations in MBD4 and in Mbd4 knockout mice. Sequential sampling of germ line cases demonstrated repeated expansion of blood cell progenitors with pathogenic mutations in DNMT3A, a key driver gene for both clonal hematopoiesis and AML. Our findings reveal genetic and epigenetic factors that shape the mutagenic influence of 5mC. Within blood cells, this links methylation damage to the driver landscape of clonal hematopoiesis and reveals a conserved path to leukemia. Germ line MBD4 deficiency enhances cancer susceptibility and predisposes to AML.
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Affiliation(s)
- Mathijs A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edward Chew
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christoffer Flensburg
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Annelieke Zeilemaker
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sarah E Miller
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Adil S Al Hinai
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- National Genetic Center, Royal Hospital, Ministry of Health, Muscat, Sultanate of Oman
| | - Ashish Bajel
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Bram Luiken
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melissa Rijken
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tamara Mclennan
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Fröhling
- Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany; and
- Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marnie E Blewitt
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Eric M Bindels
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Warren S Alexander
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew W Roberts
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ian J Majewski
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
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24
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Chew E, Sanders MA, Flensburg C, Zeilemaker A, Miller SE, Hinai ASA, Bajel A, Luiken B, Rijken M, Mclennan T, Hoogenboezem RM, Kavelaars FG, Blewitt ME, Bindels EM, Alexander WS, Löwenberg B, Roberts AW, Majewski IJ, Valk PJ. Abstract 1366: MBD4 guards against DNA damage from methylcytosine deamination. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Spontaneous methylcytosine (5mC) deamination is a common source of cytosine to thymine (C>T) mutations. These mutations accumulate over time, serving as a “molecular clock” that tracks cellular age. MBD4 is a thymine glycosylase that recognises sites of 5mC deamination and initiates base excision repair.
Three patients (of whom 2 are siblings) with germline MBD4 loss of function (LOF) mutations developed acute myeloid leukemia (AML) at a young age (<35 years old). Whole exome (WES) and whole genome sequencing (WGS) showed an elevated C>T mutation rate ~33 times the average for AML. The mutations occurred nearly exclusively at CG dinucleotides. Reduced representation bisulfite sequencing showed the mutations occurred at previously methylated cytosines. The 3 AMLs had somatic C>T mutations in the same driver genes (DNMT3A and either IDH1 or IDH2), suggesting the methylation damage charts a recurrent path towards malignancy in the hematopoietic system.
MBD4 is inactivated in other cancers, although this appears to be a rare event. Nine of 10,638 cancers in the TCGA database had MBD4 LOF mutations. In a uveal melanoma and a glioblastoma multiforme, there was also loss of heterozygosity of the wild-type MBD4. These 2 cancers with MBD4 deficiency exhibit the same mutational signature, with a high C>T mutation rate at CG dinucleotides.
To verify the link between MBD4 and the 5mC damage signature, Mbd4-/- and Mbd4+/+ mouse bone marrow were cultured in semi-solid agar and WGS was performed on individual myeloid progenitor colonies. Mbd4-/- myeloid progenitor colonies displayed the same increase in C>T mutations at CG dinucleotides. This highlights the importance of MBD4 across species.
Mbd4 deficient mice offer a model system to investigate mutation acquisition and cancer pathogenesis. Work on the interaction of MBD4 with other leukaemia initiating genes is underway.
Citation Format: Edward Chew, Mathijs A. Sanders, Christoffer Flensburg, Annelieke Zeilemaker, Sarah E. Miller, Adil S. al Hinai, Ashish Bajel, Bram Luiken, Melissa Rijken, Tamara Mclennan, Remco M. Hoogenboezem, François G. Kavelaars, Marnie E. Blewitt, Eric M. Bindels, Warren S. Alexander, Bob Löwenberg, Andrew W. Roberts, Ian J. Majewski, Peter J. Valk. MBD4 guards against DNA damage from methylcytosine deamination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1366.
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Affiliation(s)
- Edward Chew
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | | | | | - Sarah E. Miller
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | | | - Bram Luiken
- 2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Melissa Rijken
- 2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tamara Mclennan
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | | | - Marnie E. Blewitt
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | | | - Bob Löwenberg
- 2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Andrew W. Roberts
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ian J. Majewski
- 1Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Peter J. Valk
- 2Erasmus University Medical Center, Rotterdam, Netherlands
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25
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Gurzau AD, Chen K, Xue S, Dai W, Lucet IS, Ly TTN, Reversade B, Blewitt ME, Murphy JM. FSHD2- and BAMS-associated mutations confer opposing effects on SMCHD1 function. J Biol Chem 2018; 293:9841-9853. [PMID: 29748383 DOI: 10.1074/jbc.ra118.003104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/03/2018] [Indexed: 01/01/2023] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (Smchd1) plays important roles in epigenetic silencing and normal mammalian development. Recently, heterozygous mutations in SMCHD1 have been reported in two disparate disorders: facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). FSHD2-associated mutations lead to loss of function; however, whether BAMS is associated with loss- or gain-of-function mutations in SMCHD1 is unclear. Here, we have assessed the effect of SMCHD1 missense mutations from FSHD2 and BAMS patients on ATP hydrolysis activity and protein conformation and the effect of BAMS mutations on craniofacial development in a Xenopus model. These data demonstrated that FSHD2 mutations only result in decreased ATP hydrolysis, whereas many BAMS mutations can result in elevated ATPase activity and decreased eye size in Xenopus Interestingly, a mutation reported in both an FSHD2 patient and a BAMS patient results in increased ATPase activity and a smaller Xenopus eye size. Mutations in the extended ATPase domain increased catalytic activity, suggesting critical regulatory intramolecular interactions and the possibility of targeting this region therapeutically to boost SMCHD1's activity to counter FSHD.
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Affiliation(s)
- Alexandra D Gurzau
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Kelan Chen
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Shifeng Xue
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore
| | - Weiwen Dai
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Isabelle S Lucet
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.,the Departments of Medical Biology and
| | - Thanh Thao Nguyen Ly
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore
| | - Bruno Reversade
- the Institute of Molecular and Cell Biology and.,Human Genetics and Embryology Laboratory, Institute of Medical Biology, A*STAR, Singapore.,the Department of Medical Genetics, Koç University School of Medicine (KUSoM), 34450 Sarıyer/Istanbul, Turkey.,the Department of Paediatrics, School of Medicine, National University of Singapore, Singapore, and.,Amsterdam Reproduction and Development, Academic Medical Centre and VU University Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Marnie E Blewitt
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, .,the Departments of Medical Biology and.,Genetics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - James M Murphy
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia, .,the Departments of Medical Biology and
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26
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Su S, Law CW, Ah-Cann C, Asselin-Labat ML, Blewitt ME, Ritchie ME. Glimma: interactive graphics for gene expression analysis. Bioinformatics 2018; 33:2050-2052. [PMID: 28203714 PMCID: PMC5870845 DOI: 10.1093/bioinformatics/btx094] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/12/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens of thousands of points. Details about certain genes or samples of interest are easily obscured in such dense summary displays. Incorporating interactivity into summary plots would enable additional information to be displayed on demand and facilitate intuitive data exploration. Results The open-source Glimma package creates interactive graphics for exploring gene expression analysis with a few simple R commands. It extends popular plots found in the limma package, such as multi-dimensional scaling plots and mean-difference plots, to allow individual data points to be queried and additional annotation information to be displayed upon hovering or selecting particular points. It also offers links between plots so that more information can be revealed on demand. Glimma is widely applicable, supporting data analyses from a number of well-established Bioconductor workflows ( limma , edgeR and DESeq2 ) and uses D3/JavaScript to produce HTML pages with interactive displays that enable more effective data exploration by end-users. Results from Glimma can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. Availability and Implementation The Glimma R package is available from http://bioconductor.org/packages/Glimma/ . Contact su.s@wehi.edu.au , law@wehi.edu.au or mritchie@wehi.edu.au.
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Affiliation(s)
- Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Charity W Law
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Casey Ah-Cann
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Marie-Liesse Asselin-Labat
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville 3010, Australia
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27
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Shields BJ, Keniry A, Blewitt ME, McCormack MP. Analysis of Histone Modifications in Acute Myeloid Leukaemia Using Chromatin Immunoprecipitation. Methods Mol Biol 2018; 1725:177-184. [PMID: 29322418 DOI: 10.1007/978-1-4939-7568-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chromatin Immunoprecipitation (ChIP) using antibodies specific for histone modifications is a powerful technique for assessing the epigenetic states of cell populations by either quantitative PCR (ChIP-PCR) or next generation sequencing analysis (ChIP-Seq). Here we describe the procedure for ChIP of histone marks in myeloid leukaemia cell lines and the subsequent purification of genomic DNA associated with repressive and activating histone modifications for further analysis. This procedure can be widely applied to a variety of histone marks to assess both activating and repressive modifications in the context of myeloid leukaemia.
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Affiliation(s)
- Benjamin J Shields
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew P McCormack
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia.
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Jansz N, Chen K, Murphy JM, Blewitt ME. The Epigenetic Regulator SMCHD1 in Development and Disease. Trends Genet 2017; 33:233-243. [PMID: 28222895 DOI: 10.1016/j.tig.2017.01.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/24/2017] [Indexed: 12/30/2022]
Abstract
It has very recently become clear that the epigenetic modifier SMCHD1 has a role in two distinct disorders: facioscapulohumoral muscular dystrophy (FSHD) and Bosma arhinia and micropthalmia (BAMS). In the former there are heterozygous loss-of-function mutations, while both gain- and loss-of-function mutations have been proposed to underlie the latter. These findings have led to much interest in SMCHD1 and how it works at the molecular level. We summarise here current understanding of the mechanism of action of SMCHD1, its role in these diseases, and what has been learnt from study of mouse models null for Smchd1 in the decade since the discovery of SMCHD1.
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Affiliation(s)
- Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia; The Department of Medical Biology, The University of Melbourne, Melbourne VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia; The Department of Medical Biology, The University of Melbourne, Melbourne VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia; The Department of Medical Biology, The University of Melbourne, Melbourne VIC, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne VIC, Australia; The Department of Medical Biology, The University of Melbourne, Melbourne VIC, Australia.
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29
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Yin D, Ritchie ME, Jabbari JS, Beck T, Blewitt ME, Keniry A. High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS). Genom Data 2016; 10:97-100. [PMID: 27766205 PMCID: PMC5065634 DOI: 10.1016/j.gdata.2016.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 09/29/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500. All sequencing data are deposited in the GEO database under accession number GSE87097.
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Affiliation(s)
- Danqing Yin
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jafar S Jabbari
- The Australian Genome Research Facility, Melbourne, Parkville, Victoria 3052, Australia
| | - Tamara Beck
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Andrew Keniry
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia
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30
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Gilan O, Lam EYN, Becher I, Lugo D, Cannizzaro E, Joberty G, Ward A, Wiese M, Fong CY, Ftouni S, Tyler D, Stanley K, MacPherson L, Weng CF, Chan YC, Ghisi M, Smil D, Carpenter C, Brown P, Garton N, Blewitt ME, Bannister AJ, Kouzarides T, Huntly BJP, Johnstone RW, Drewes G, Dawson SJ, Arrowsmith CH, Grandi P, Prinjha RK, Dawson MA. Functional interdependence of BRD4 and DOT1L in MLL leukemia. Nat Struct Mol Biol 2016; 23:673-81. [PMID: 27294782 DOI: 10.1038/nsmb.3249] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023]
Abstract
Targeted therapies against disruptor of telomeric silencing 1-like (DOT1L) and bromodomain-containing protein 4 (BRD4) are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukemogenic transcription programs remain unclear. Using quantitative proteomics, chemoproteomics and biochemical fractionation, we found that native BRD4 and DOT1L exist in separate protein complexes. Genetic disruption or small-molecule inhibition of BRD4 and DOT1L showed marked synergistic activity against MLL leukemia cell lines, primary human leukemia cells and mouse leukemia models. Mechanistically, we found a previously unrecognized functional collaboration between DOT1L and BRD4 that is especially important at highly transcribed genes in proximity to superenhancers. DOT1L, via dimethylated histone H3 K79, facilitates histone H4 acetylation, which in turn regulates the binding of BRD4 to chromatin. These data provide new insights into the regulation of transcription and specify a molecular framework for therapeutic intervention in this disease with poor prognosis.
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MESH Headings
- Acetylation
- Animals
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Clinical Trials as Topic
- Disease Models, Animal
- Female
- Gene Expression Regulation, Leukemic
- Histone-Lysine N-Methyltransferase
- Histones/genetics
- Histones/metabolism
- Humans
- Leukemia, Biphenotypic, Acute/genetics
- Leukemia, Biphenotypic, Acute/metabolism
- Leukemia, Biphenotypic, Acute/pathology
- Male
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Primary Cell Culture
- Protein Binding
- Proteomics/methods
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Dave Lugo
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | | | - Gerard Joberty
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Aoife Ward
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Meike Wiese
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sarah Ftouni
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dean Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kym Stanley
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Margherita Ghisi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Peter Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Neil Garton
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
- Cambridge Stem Cell Institute, Cambridge, UK
| | - Ricky W Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
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31
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Keniry A, Gearing LJ, Jansz N, Liu J, Holik AZ, Hickey PF, Kinkel SA, Moore DL, Breslin K, Chen K, Liu R, Phillips C, Pakusch M, Biben C, Sheridan JM, Kile BT, Carmichael C, Ritchie ME, Hilton DJ, Blewitt ME. Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing. Epigenetics Chromatin 2016; 9:16. [PMID: 27195021 PMCID: PMC4870784 DOI: 10.1186/s13072-016-0064-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/31/2016] [Indexed: 11/16/2022] Open
Abstract
Background
The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation in any species has remained largely unexplored. Results Here we report the first genomic analysis of H3K9 di- and tri-methylation on the inactive X: we find they are enriched at the intergenic, gene poor regions of the inactive X, interspersed between H3K27 tri-methylation domains found in the gene dense regions. Although H3K9 methylation is predominantly non-genic, we find that depletion of H3K9 methylation via depletion of H3K9 methyltransferase Set domain bifurcated 1 (Setdb1) during the establishment of X inactivation, results in failure of silencing for around 150 genes on the inactive X. By contrast, we find a very minor role for Setdb1-mediated H3K9 methylation once X inactivation is fully established. In addition to failed gene silencing, we observed a specific failure to silence X-linked long-terminal repeat class repetitive elements. Conclusions Here we have shown that H3K9 methylation clearly marks the murine inactive X chromosome. The role of this mark is most apparent during the establishment phase of gene silencing, with a more muted effect on maintenance of the silent state. Based on our data, we hypothesise that Setdb1-mediated H3K9 methylation plays a role in epigenetic silencing of the inactive X via silencing of the repeats, which itself facilitates gene silencing through alterations to the conformation of the whole inactive X chromosome. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0064-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Linden J Gearing
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Joy Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Aliaksei Z Holik
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Sarah A Kinkel
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Darcy L Moore
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ruijie Liu
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Catherine Phillips
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Miha Pakusch
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Julie M Sheridan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Benjamin T Kile
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Catherine Carmichael
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052 Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010 Australia.,Department of Genetics, University of Melbourne, Melbourne, VIC 3010 Australia
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32
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Liu R, Chen K, Jansz N, Blewitt ME, Ritchie ME. Transcriptional profiling of the epigenetic regulator Smchd1. Genom Data 2015; 7:144-7. [PMID: 26981392 PMCID: PMC4778621 DOI: 10.1016/j.gdata.2015.12.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/30/2015] [Indexed: 11/19/2022]
Abstract
Smchd1 is an epigenetic repressor with important functions in healthy cellular processes and disease. To elucidate its role in transcriptional regulation, we performed two independent genome-wide RNA-sequencing studies comparing wild-type and Smchd1 null samples in neural stem cells and lymphoma cell lines. Using an R-based analysis pipeline that accommodates observational and sample-specific weights in the linear modeling, we identify key genes dysregulated by Smchd1 deletion such as clustered protocadherins in the neural stem cells and imprinted genes in both experiments. Here we provide a detailed description of this analysis, from quality control to read mapping and differential expression analysis. These data sets are publicly available from the Gene Expression Omnibus database (accession numbers GSE64099 and GSE65747).
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Affiliation(s)
- Ruijie Liu
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kelan Chen
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Natasha Jansz
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marnie E. Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- Corresponding authors at: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.Molecular Medicine DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoria3052Australia
| | - Matthew E. Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
- Corresponding authors at: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.Molecular Medicine DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoria3052Australia
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33
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Keniry A, Gearing L, Jansz N, Liu J, Kinkel S, Breslin K, Moore D, Chen K, Pakusch M, Willson T, Kile B, Carmichael C, Ritchie M, Hilton D, Blewitt ME. Ihstone H3 lysine 9 methylation is involved not only in maintaining epigenetic silencing, but is essential for setting up gene silencing. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Res 2015; 43:e97. [PMID: 25925576 PMCID: PMC4551905 DOI: 10.1093/nar/gkv412] [Citation(s) in RCA: 315] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 04/17/2015] [Indexed: 12/30/2022] Open
Abstract
Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean-variance relationship of the log-counts-per-million using 'voom'. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source 'limma' package.
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Affiliation(s)
- Ruijie Liu
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Aliaksei Z Holik
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Natasha Jansz
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kelan Chen
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Huei San Leong
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marie-Liesse Asselin-Labat
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
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35
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Galvis LA, Holik AZ, Short KM, Pasquet J, Lun ATL, Blewitt ME, Smyth IM, Ritchie ME, Asselin-Labat ML. Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung. Development 2015; 142:1458-69. [PMID: 25790853 PMCID: PMC4392602 DOI: 10.1242/dev.122077] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/18/2015] [Indexed: 01/29/2023]
Abstract
Epigenetic mechanisms involved in the establishment of lung epithelial cell lineage identities during development are largely unknown. Here, we explored the role of the histone methyltransferase Ezh2 during lung lineage determination. Loss of Ezh2 in the lung epithelium leads to defective lung formation and perinatal mortality. We show that Ezh2 is crucial for airway lineage specification and alveolarization. Using optical projection tomography imaging, we found that branching morphogenesis is affected in Ezh2 conditional knockout mice and the remaining bronchioles are abnormal, lacking terminally differentiated secretory club cells. Remarkably, RNA-seq analysis revealed the upregulation of basal genes in Ezh2-deficient epithelium. Three-dimensional imaging for keratin 5 further showed the unexpected presence of a layer of basal cells from the proximal airways to the distal bronchioles in E16.5 embryos. ChIP-seq analysis indicated the presence of Ezh2-mediated repressive marks on the genomic loci of some but not all basal genes, suggesting an indirect mechanism of action of Ezh2. We found that loss of Ezh2 de-represses insulin-like growth factor 1 (Igf1) expression and that modulation of IGF1 signaling ex vivo in wild-type lungs could induce basal cell differentiation. Altogether, our work reveals an unexpected role for Ezh2 in controlling basal cell fate determination in the embryonic lung endoderm, mediated in part by repression of Igf1 expression. SUMMARY: The histone methyltransferase Ezh2 inhibits basal cell differentiation in the mouse lung by depositing repressive marks on the promoter region of basal cell genes and by repressing Igf1 expression.
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Affiliation(s)
- Laura A Galvis
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Aliaksei Z Holik
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kieran M Short
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Julie Pasquet
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Aaron T L Lun
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Marnie E Blewitt
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ian M Smyth
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Matthew E Ritchie
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Marie-Liesse Asselin-Labat
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3052, Australia
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Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E. An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol 2015; 14:R96. [PMID: 24025402 PMCID: PMC4053835 DOI: 10.1186/gb-2013-14-9-r96] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/06/2013] [Indexed: 12/28/2022] Open
Abstract
Background We have used a sensitized ENU mutagenesis screen to produce mouse lines that carry mutations in genes required for epigenetic regulation. We call these lines Modifiers of murine metastable epialleles (Mommes). Results We report a basic molecular and phenotypic characterization for twenty of the Momme mouse lines, and in each case we also identify the causative mutation. Three of the lines carry a mutation in a novel epigenetic modifier, Rearranged L-myc fusion (Rlf), and one gene, Rap-interacting factor 1 (Rif1), has not previously been reported to be involved in transcriptional regulation in mammals. Many of the other lines are novel alleles of known epigenetic regulators. For two genes, Rlf and Widely-interspaced zinc finger (Wiz), we describe the first mouse mutants. All of the Momme mutants show some degree of homozygous embryonic lethality, emphasizing the importance of epigenetic processes. The penetrance of lethality is incomplete in a number of cases. Similarly, abnormalities in phenotype seen in the heterozygous individuals of some lines occur with incomplete penetrance. Conclusions Recent advances in sequencing enhance the power of sensitized mutagenesis screens to identify the function of previously uncharacterized factors and to discover additional functions for previously characterized proteins. The observation of incomplete penetrance of phenotypes in these inbred mutant mice, at various stages of development, is of interest. Overall, the Momme collection of mouse mutants provides a valuable resource for researchers across many disciplines.
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Flensburg C, Kinkel SA, Keniry A, Blewitt ME, Oshlack A. A comparison of control samples for ChIP-seq of histone modifications. Front Genet 2014; 5:329. [PMID: 25309581 PMCID: PMC4174756 DOI: 10.3389/fgene.2014.00329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/03/2014] [Indexed: 11/13/2022] Open
Abstract
The advent of high-throughput sequencing has allowed genome wide profiling of histone modifications by Chromatin ImmunoPrecipitation (ChIP) followed by sequencing (ChIP-seq). In this assay the histone mark of interest is enriched through a chromatin pull-down assay using an antibody for the mark. Due to imperfect antibodies and other factors, many of the sequenced fragments do not originate from the histone mark of interest, and are referred to as background reads. Background reads are not uniformly distributed and therefore control samples are usually used to estimate the background distribution at any given genomic position. The Encyclopedia of DNA Elements (ENCODE) Consortium guidelines suggest sequencing a whole cell extract (WCE, or “input”) sample, or a mock ChIP reaction such as an IgG control, as a background sample. However, for a histone modification ChIP-seq investigation it is also possible to use a Histone H3 (H3) pull-down to map the underlying distribution of histones. In this paper we generated data from a hematopoietic stem and progenitor cell population isolated from mouse fetal liver to compare WCE and H3 ChIP-seq as control samples. The quality of the control samples is estimated by a comparison to pull-downs of histone modifications and to expression data. We find minor differences between WCE and H3 ChIP-seq, such as coverage in mitochondria and behavior close to transcription start sites. Where the two controls differ, the H3 pull-down is generally more similar to the ChIP-seq of histone modifications. However, the differences between H3 and WCE have a negligible impact on the quality of a standard analysis.
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Affiliation(s)
- Christoffer Flensburg
- Bioinformatics Group, Murdoch Childrens Research Institute Melbourne, VIC, Australia
| | - Sarah A Kinkel
- Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia
| | - Andrew Keniry
- Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia
| | - Marnie E Blewitt
- Division of Molecular Medicine, Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne Melbourne, VIC, Australia ; Department of Genetics, University of Melbourne Melbourne, VIC, Australia
| | - Alicia Oshlack
- Bioinformatics Group, Murdoch Childrens Research Institute Melbourne, VIC, Australia ; Department of Genetics, University of Melbourne Melbourne, VIC, Australia
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38
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Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, Wilcox S, O'Connor L, Dickins RA, Blewitt ME, Ritchie ME. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Res 2014; 3:95. [PMID: 24860646 PMCID: PMC4023662 DOI: 10.12688/f1000research.3928.2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows) with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.
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Affiliation(s)
- Zhiyin Dai
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Julie M Sheridan
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Linden J Gearing
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Darcy L Moore
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Sam Wormald
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Stephen Wilcox
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Liam O'Connor
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ross A Dickins
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, Wilcox S, O'Connor L, Dickins RA, Blewitt ME, Ritchie ME. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Res 2014. [PMID: 24860646 DOI: 10.12688/f1000research.3928.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, genes in the rows) with options for allowing mismatches and small shifts in sequence position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or generalized linear modeling that can handle complex experimental designs. A detailed users' guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.
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Affiliation(s)
- Zhiyin Dai
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Julie M Sheridan
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Linden J Gearing
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Darcy L Moore
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shian Su
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Sam Wormald
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Stephen Wilcox
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Liam O'Connor
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia ; Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ross A Dickins
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia ; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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McColl B, Kao BR, Lourthai P, Chan K, Wardan H, Roosjen M, Delagneau O, Gearing LJ, Blewitt ME, Svasti S, Fucharoen S, Vadolas J. An in vivo model for analysis of developmental erythropoiesis and globin gene regulation. FASEB J 2014; 28:2306-17. [PMID: 24443374 DOI: 10.1096/fj.13-246637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Expression of fetal γ-globin in adulthood ameliorates symptoms of β-hemoglobinopathies by compensating for the mutant β-globin. Reactivation of the silenced γ-globin gene is therefore of substantial clinical interest. To study the regulation of γ-globin expression, we created the GG mice, which carry an intact 183-kb human β-globin locus modified to express enhanced green fluorescent protein (eGFP) from the Gγ-globin promoter. GG embryos express eGFP first in the yolk sac blood islands and then in the aorta-gonad mesonephros and the fetal liver, the sites of normal embryonic hematopoiesis. eGFP expression in erythroid cells peaks at E9.5 and then is rapidly silenced (>95%) and maintained at low levels into adulthood, demonstrating appropriate developmental regulation of the human β-globin locus. In vitro knockdown of the epigenetic regulator DNA methyltransferase-1 in GG primary erythroid cells increases the proportion of eGFP(+) cells in culture from 41.9 to 74.1%. Furthermore, eGFP fluorescence is induced >3-fold after treatment of erythroid precursors with epigenetic drugs known to induce γ-globin expression, demonstrating the suitability of the Gγ-globin eGFP reporter for evaluation of γ-globin inducers. The GG mouse model is therefore a valuable model system for genetic and pharmacologic studies of the regulation of the β-globin locus and for discovery of novel therapies for the β-hemoglobinopathies.
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Affiliation(s)
- Bradley McColl
- 2Cell and Gene Therapy Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.
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Roosjen M, McColl B, Kao B, Gearing LJ, Blewitt ME, Vadolas J. Transcriptional regulators Myb and BCL11A interplay with DNA methyltransferase 1 in developmental silencing of embryonic and fetal β-like globin genes. FASEB J 2013; 28:1610-20. [PMID: 24371119 DOI: 10.1096/fj.13-242669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The clinical symptoms of hemoglobin disorders such as β-thalassemia and sickle cell anemia are significantly ameliorated by the persistent expression of γ-globin after birth. This knowledge has driven the discovery of important regulators that silence γ-globin postnatally. Improved understanding of the γ- to β-globin switching mechanism holds the key to devising targeted therapies for β-hemoglobinopathies. To further investigate this mechanism, we used the murine erythroleukemic (MEL) cell line containing an intact 183-kb human β-globin locus, in which the (G)γ- and β-globin genes are replaced by DsRed and eGFP fluorescent reporters, respectively. Following RNA interference (RNAi)-mediated knockdown of two key transcriptional regulators, Myb and BCL11A, we observed a derepression of γ-globin, measured by DsRed fluorescence and qRT-PCR (P<0.001). Interestingly, double knockdown of Myb and DNA methyltransferase 1 (DNMT1) resulted in a robust induction of ε-globin, (up to 20% of total β-like globin species) compared to single knockdowns (P<0.001). Conversely, double knockdowns of BCL11A and DNMT1 enhanced γ-globin expression (up to 90% of total β-like globin species) compared to single knockdowns (P<0.001). Moreover, following RNAi treatment, expression of human β-like globin genes mirrored the expression levels of their endogenous murine counterparts. These results demonstrate that Myb and BCL11A cooperate with DNMT1 to achieve developmental repression of embryonic and fetal β-like globin genes in the adult erythroid environment.
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Affiliation(s)
- Mark Roosjen
- 1Cell and Gene Therapy Group, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd., Parkville, VIC 3052, Australia.
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Leong HS, Chen K, Hu Y, Lee S, Corbin J, Pakusch M, Murphy JM, Majewski IJ, Smyth GK, Alexander WS, Hilton DJ, Blewitt ME. Epigenetic regulator Smchd1 functions as a tumor suppressor. Cancer Res 2012; 73:1591-9. [PMID: 23269277 DOI: 10.1158/0008-5472.can-12-3019] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
SMCHD1 is an epigenetic modifier of gene expression that is critical to maintain X chromosome inactivation. Here, we show in mouse that genetic inactivation of Smchd1 accelerates tumorigenesis in male mice. Loss of Smchd1 in transformed mouse embryonic fibroblasts increased tumor growth upon transplantation into immunodeficient nude mice. In addition, loss of Smchd1 in Eμ-Myc transgenic mice that undergo lymphomagenesis reduced disease latency by 50% relative to control animals. In premalignant Eμ-Myc transgenic mice deficient in Smchd1, there was an increase in the number of pre-B cells in the periphery, likely accounting for the accelerated disease in these animals. Global gene expression profiling suggested that Smchd1 normally represses genes activated by MLL chimeric fusion proteins in leukemia, implying that Smchd1 loss may work through the same pathways as overexpressed MLL fusion proteins do in leukemia and lymphoma. Notably, we found that SMCHD1 is underexpressed in many types of human hematopoietic malignancy. Together, our observations collectively highlight a hitherto uncharacterized role for SMCHD1 as a candidate tumor suppressor gene in hematopoietic cancers.
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Affiliation(s)
- Huei San Leong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
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43
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Lewis RS, Kolesnik TB, Kuang Z, D'Cruz AA, Blewitt ME, Masters SL, Low A, Willson T, Norton RS, Nicholson SE. TLR regulation of SPSB1 controls inducible nitric oxide synthase induction. J Immunol 2011; 187:3798-805. [PMID: 21876038 DOI: 10.4049/jimmunol.1002993] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The mammalian innate immune system has evolved to recognize foreign molecules derived from pathogens via the TLRs. TLR3 and TLR4 can signal via the TIR domain-containing adapter inducing IFN-β (TRIF), which results in the transcription of a small array of genes, including IFN-β. Inducible NO synthase (iNOS), which catalyzes the production of NO, is induced by a range of stimuli, including cytokines and microbes. NO is a potent source of reactive nitrogen species that play an important role in killing intracellular pathogens and forms a crucial component of host defense. We have recently identified iNOS as a target of the mammalian SPSB2 protein. The SOCS box is a peptide motif, which, in conjunction with elongins B and C, recruits cullin-5 and Rbx-2 to form an active E3 ubiquitin ligase complex. In this study, we show that SPSB1 is the only SPSB family member to be regulated by the same TLR pathways that induce iNOS expression and characterize the interaction between SPSB1 and iNOS. Through the use of SPSB1 transgenic mouse macrophages and short hairpin RNA knockdown of SPSB1, we show that SPSB1 controls both the induction of iNOS and the subsequent production of NO downstream of TLR3 and TLR4. Further, we demonstrate that regulation of iNOS by SPSB1 is dependent on the proteasome. These results suggest that SPSB1 acts through a negative-feedback loop that, together with SPSB2, controls the extent of iNOS induction and NO production.
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Affiliation(s)
- Rowena S Lewis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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44
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Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, Blewitt ME, Oshlack A, Majewski IJ. ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res 2011; 39:7415-27. [PMID: 21652639 PMCID: PMC3177187 DOI: 10.1093/nar/gkr416] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcriptional control is dependent on a vast network of epigenetic modifications. One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalysed and maintained by Polycomb Repressive Complex 2 (PRC2). Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear. We have used ChIP-seq to generate genome-wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription. Second, a peak of enrichment around the transcription start site (TSS) is commonly associated with ‘bivalent’ genes, where H3K4me3 also marks the TSS. Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied. The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation.
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Affiliation(s)
- Matthew D Young
- Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
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Roberts AR, Blewitt ME, Youngson NA, Whitelaw E, Chong S. Reduced dosage of the modifiers of epigenetic reprogramming Dnmt1, Dnmt3L, SmcHD1 and Foxo3a has no detectable effect on mouse telomere length in vivo. Chromosoma 2011; 120:377-85. [PMID: 21553025 PMCID: PMC3140923 DOI: 10.1007/s00412-011-0318-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/18/2011] [Indexed: 12/18/2022]
Abstract
Studies carried out in cultured cells have implicated modifiers of epigenetic reprogramming in the regulation of telomere length, reporting elongation in cells that were null for DNA methyltransferase DNA methyltransferase 1 (Dnmt1), both de novo DNA methyltransferases, Dnmt3a and Dnmt3b or various histone methyltransferases. To investigate this further, we assayed telomere length in whole embryos or adult tissue from mice carrying mutations in four different modifiers of epigenetic reprogramming: Dnmt1, DNA methyltransferase 3-like, structural maintenance of chromosomes hinge domain containing 1, and forkhead box O3a. Terminal restriction fragment analysis was used to compare telomere length in homozygous mutants, heterozygous mutants and wild-type littermates. Contrary to expectation, we did not detect overall lengthening in the mutants, raising questions about the role of epigenetic processes in telomere length in vivo.
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Affiliation(s)
- Amity R Roberts
- Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, QLD, Australia
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Ashe A, Morgan DK, Whitelaw NC, Bruxner TJ, Vickaryous NK, Cox LL, Butterfield NC, Wicking C, Blewitt ME, Wilkins SJ, Anderson GJ, Cox TC, Whitelaw E. A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development. Genome Biol 2008; 9:R182. [PMID: 19099580 PMCID: PMC2646286 DOI: 10.1186/gb-2008-9-12-r182] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2008] [Revised: 10/22/2008] [Accepted: 12/19/2008] [Indexed: 12/22/2022] Open
Abstract
An extended ENU screen for modifiers of transgene variegation identified four new modifiers, MommeD7-D10. Background Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain containing 1 (Smchd1), a novel modifier of epigenetic gene silencing; MommeD2 is a mutation in DNA methyltransferase 1 (Dnmt1); and MommeD4 is a mutation in Smarca 5 (Snf2h), a known chromatin remodeler. The identification of Dnmt1 and Smarca5 attest to the effectiveness of the screen design. Results We have now extended the screen and have identified four new modifiers, MommeD7-D10. Here we show that all ten MommeDs link to unique sites in the genome, that homozygosity for the mutations is associated with severe developmental abnormalities and that heterozygosity results in phenotypic abnormalities and reduced reproductive fitness in some cases. In addition, we have now identified the underlying genes for MommeD5 and MommeD10. MommeD5 is a mutation in Hdac1, which encodes histone deacetylase 1, and MommeD10 is a mutation in Baz1b (also known as Williams syndrome transcription factor), which encodes a transcription factor containing a PHD-type zinc finger and a bromodomain. We show that reduction in the level of Baz1b in the mouse results in craniofacial features reminiscent of Williams syndrome. Conclusions These results demonstrate the importance of dosage-dependent epigenetic reprogramming in the development of the embryo and the power of the screen to provide mouse models to study this process.
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Affiliation(s)
- Alyson Ashe
- Epigenetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Herston, Queensland 4006, Australia.
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Majewski IJ, Blewitt ME, de Graaf CA, McManus EJ, Bahlo M, Hilton AA, Hyland CD, Smyth GK, Corbin JE, Metcalf D, Alexander WS, Hilton DJ. Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity. PLoS Biol 2008; 6:e93. [PMID: 18416604 PMCID: PMC2292752 DOI: 10.1371/journal.pbio.0060093] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 03/04/2008] [Indexed: 12/16/2022] Open
Abstract
Polycomb group proteins are transcriptional repressors that play a central role in the establishment and maintenance of gene expression patterns during development. Using mice with an N-ethyl-N-nitrosourea (ENU)-induced mutation in Suppressor of Zeste 12 (Suz12), a core component of Polycomb Repressive Complex 2 (PRC2), we show here that loss of Suz12 function enhances hematopoietic stem cell (HSC) activity. In addition to these effects on a wild-type genetic background, mutations in Suz12 are sufficient to ameliorate the stem cell defect and thrombocytopenia present in mice that lack the thrombopoietin receptor (c-Mpl). To investigate the molecular targets of the PRC2 complex in the HSC compartment, we examined changes in global patterns of gene expression in cells deficient in Suz12. We identified a distinct set of genes that are regulated by Suz12 in hematopoietic cells, including eight genes that appear to be highly responsive to PRC2 function within this compartment. These data suggest that PRC2 is required to maintain a specific gene expression pattern in hematopoiesis that is indispensable to normal stem cell function. The chromatin environment that surrounds a gene heavily influences the gene's transcriptional activity. Specific modifications on histone tails serve as signposts for the basal transcriptional machinery, reflecting a cell's developmental history and identifying genes that should be actively transcribed and those that must be repressed. Polycomb group proteins are involved in large, multiprotein complexes that catalyse the post-translational modification of histones. The disruption of these complexes induces wholesale changes in gene expression, a scenario commonly seen in diseases such as cancer. We have investigated the role of Polycomb group proteins during blood cell formation: in stem cells, progenitor cells, and mature blood cells. Using a variety of functional assays, we demonstrate an important role for Polycomb group proteins in restricting the activity of hematopoietic stem cells. To define the molecular targets of the complex, we examined gene expression profiles in cells with impaired expression of Polycomb group proteins. This analysis identified a set of target genes within the hematopoietic compartment that was distinct from those defined in embryonic stem cells and fibroblasts. This study provides new insights into the role of these proteins during hematopoiesis, and suggests a novel mechanism by which they might contribute to leukaemia. Epigenetic modifications are central to the maintenance of cellular identity and are dynamically regulated during differentiation. We addressed the role of Polycomb group proteins during hematopoiesis and define a series of genes that are highly responsive to Polycomb dysfunction.
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Affiliation(s)
- Ian J Majewski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Carolyn A de Graaf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Edward J McManus
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Adrienne A Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Craig D Hyland
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jason E Corbin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Donald Metcalf
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- * To whom correspondence should be addressed. E-mail:
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Blewitt ME, Vickaryous NK, Paldi A, Koseki H, Whitelaw E. Dynamic reprogramming of DNA methylation at an epigenetically sensitive allele in mice. PLoS Genet 2006; 2:e49. [PMID: 16604157 PMCID: PMC1428789 DOI: 10.1371/journal.pgen.0020049] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 02/14/2006] [Indexed: 11/17/2022] Open
Abstract
There is increasing evidence in both plants and animals that epigenetic marks are not always cleared between generations. Incomplete erasure at genes associated with a measurable phenotype results in unusual patterns of inheritance from one generation to the next, termed transgenerational epigenetic inheritance. The Agouti viable yellow (A(vy)) allele is the best-studied example of this phenomenon in mice. The A(vy) allele is the result of a retrotransposon insertion upstream of the Agouti gene. Expression at this locus is controlled by the long terminal repeat (LTR) of the retrotransposon, and expression results in a yellow coat and correlates with hypomethylation of the LTR. Isogenic mice display variable expressivity, resulting in mice with a range of coat colours, from yellow through to agouti. Agouti mice have a methylated LTR. The locus displays epigenetic inheritance following maternal but not paternal transmission; yellow mothers produce more yellow offspring than agouti mothers. We have analysed the DNA methylation in mature gametes, zygotes, and blastocysts and found that the paternally and maternally inherited alleles are treated differently. The paternally inherited allele is demethylated rapidly, and the maternal allele is demethylated more slowly, in a manner similar to that of nonimprinted single-copy genes. Interestingly, following maternal transmission of the allele, there is no DNA methylation in the blastocyst, suggesting that DNA methylation is not the inherited mark. We have independent support for this conclusion from studies that do not involve direct analysis of DNA methylation. Haplo-insufficiency for Mel18, a polycomb group protein, introduces epigenetic inheritance at a paternally derived A(vy) allele, and the pedigrees reveal that this occurs after zygotic genome activation and, therefore, despite the rapid demethylation of the locus.
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Affiliation(s)
- Marnie E Blewitt
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales, Australia
| | - Nicola K Vickaryous
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales, Australia
| | | | - Haruhiko Koseki
- Developmental Genetics Group, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
| | - Emma Whitelaw
- School of Molecular and Microbial Biosciences, University of Sydney, New South Wales, Australia
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia
- * To whom correspondence should be addressed. E-mail:
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49
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Blewitt ME, Vickaryous NK, Hemley SJ, Ashe A, Bruxner TJ, Preis JI, Arkell R, Whitelaw E. An N-ethyl-N-nitrosourea screen for genes involved in variegation in the mouse. Proc Natl Acad Sci U S A 2005; 102:7629-34. [PMID: 15890782 PMCID: PMC1140414 DOI: 10.1073/pnas.0409375102] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed a sensitized screen to identify genes involved in gene silencing, using random N-ethyl-N-nitrosourea mutagenesis on mice carrying a variegating GFP transgene. The dominant screen has produced six mutant lines, including both suppressors and enhancers of variegation. All are semidominant and five of the six are homozygous embryonic lethal. In one case, the homozygous lethality depends on sex: homozygous females die at midgestation and display abnormal DNA methylation of the X chromosome, whereas homozygous males are viable. Linkage analysis reveals that the mutations map to unique chromosomal locations. We have studied the effect of five of the mutations on expression of an endogenous allele known to be sensitive to epigenetic state, agouti viable yellow. In all cases, there is an effect on penetrance, and in most cases, parent of origin and sex-specific effects are detected. This screen has identified genes that are involved in epigenetic reprogramming of the genome, and the behavior of the mutant lines suggests a common mechanism between X inactivation and transgene and retrotransposon silencing. Our findings raise the possibility that the presence or absence of the X chromosome in mammals affects the establishment of the epigenetic state at autosomal loci by acting as a sink for proteins involved in gene silencing. The study demonstrates the power of sensitized screens in the mouse not only for the discovery of novel genes involved in a particular process but also for the elucidation of the biology of that process.
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Affiliation(s)
- Marnie E Blewitt
- School of Molecular and Microbial Biosciences, University of Sydney, Butlin Avenue, New South Wales 2006, Australia
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Abstract
One's ultimate phenotype is the result of a combination of genotype and environment, and includes a poorly understood component termed "developmental noise". This "developmental noise", also known as "intangible variation", is rarely discussed even though it appears to make a significant contribution to the variance of quantitative traits within a species. The molecular basis of developmental noise remains unknown, but it appears to be established in embryonic development and to be retained for the life of the organism. We propose that the molecular basis of developmental noise is, at least in some instances, the epigenetic state of the genome. The stochastic nature of the establishment of epigenetic state, combined with its heritability during mitosis, provides all of the essential components for developmental noise.
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Affiliation(s)
- Marnie E Blewitt
- School of Molecular and Microbial Biosciences, University of Sydney, 2006 NSW, Australia
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