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Yin Z, Kang J, Cheng X, Gao H, Huo S, Xu H. Investigating Müller glia reprogramming in mice: a retrospective of the last decade, and a look to the future. Neural Regen Res 2025; 20:946-959. [PMID: 38989930 DOI: 10.4103/nrr.nrr-d-23-01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 07/12/2024] Open
Abstract
Müller glia, as prominent glial cells within the retina, plays a significant role in maintaining retinal homeostasis in both healthy and diseased states. In lower vertebrates like zebrafish, these cells assume responsibility for spontaneous retinal regeneration, wherein endogenous Müller glia undergo proliferation, transform into Müller glia-derived progenitor cells, and subsequently regenerate the entire retina with restored functionality. Conversely, Müller glia in the mouse and human retina exhibit limited neural reprogramming. Müller glia reprogramming is thus a promising strategy for treating neurodegenerative ocular disorders. Müller glia reprogramming in mice has been accomplished with remarkable success, through various technologies. Advancements in molecular, genetic, epigenetic, morphological, and physiological evaluations have made it easier to document and investigate the Müller glia programming process in mice. Nevertheless, there remain issues that hinder improving reprogramming efficiency and maturity. Thus, understanding the reprogramming mechanism is crucial toward exploring factors that will improve Müller glia reprogramming efficiency, and for developing novel Müller glia reprogramming strategies. This review describes recent progress in relatively successful Müller glia reprogramming strategies. It also provides a basis for developing new Müller glia reprogramming strategies in mice, including epigenetic remodeling, metabolic modulation, immune regulation, chemical small-molecules regulation, extracellular matrix remodeling, and cell-cell fusion, to achieve Müller glia reprogramming in mice.
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Affiliation(s)
- Zhiyuan Yin
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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2
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Jayakrishnan M, Havlová M, Veverka V, Regnard C, Becker P. Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers. Nucleic Acids Res 2024; 52:7627-7649. [PMID: 38813825 PMCID: PMC11260483 DOI: 10.1093/nar/gkae449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me3) marks active chromatin. The mark is interpreted by epigenetic readers that assist transcription and safeguard the integrity of the chromatin fiber. The chromodomain protein MSL3 binds H3K36me3 to target X-chromosomal genes in male Drosophila for dosage compensation. The PWWP-domain protein JASPer recruits the JIL1 kinase to active chromatin on all chromosomes. Unexpectedly, depletion of K36me3 had variable, locus-specific effects on the interactions of those readers. This observation motivated a systematic and comprehensive study of K36 methylation in a defined cellular model. Contrasting prevailing models, we found that K36me1, K36me2 and K36me3 each contribute to distinct chromatin states. A gene-centric view of the changing K36 methylation landscape upon depletion of the three methyltransferases Set2, NSD and Ash1 revealed local, context-specific methylation signatures. Set2 catalyzes K36me3 predominantly at transcriptionally active euchromatin. NSD places K36me2/3 at defined loci within pericentric heterochromatin and on weakly transcribed euchromatic genes. Ash1 deposits K36me1 at regions with enhancer signatures. The genome-wide mapping of MSL3 and JASPer suggested that they bind K36me2 in addition to K36me3, which was confirmed by direct affinity measurement. This dual specificity attracts the readers to a broader range of chromosomal locations and increases the robustness of their actions.
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Affiliation(s)
- Muhunden Jayakrishnan
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Havlová
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Catherine Regnard
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
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3
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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration. Epigenetics Chromatin 2024; 17:22. [PMID: 39033118 PMCID: PMC11264793 DOI: 10.1186/s13072-024-00547-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024] Open
Abstract
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains only partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of changes in chromatin modifications during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-h old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.
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Affiliation(s)
- Phu Duong
- Department of Biomedical Genetics, University of Rochester, Rochester, USA
| | | | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, USA.
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester, Rochester, USA.
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4
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Marquez-Molins J, Cheng J, Corell-Sierra J, Juarez-Gonzalez VT, Villalba-Bermell P, Annacondia ML, Gomez G, Martinez G. Hop stunt viroid infection induces heterochromatin reorganization. THE NEW PHYTOLOGIST 2024. [PMID: 39030826 DOI: 10.1111/nph.19986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
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Affiliation(s)
- Joan Marquez-Molins
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Jinping Cheng
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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5
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Atinbayeva N, Valent I, Zenk F, Loeser E, Rauer M, Herur S, Quarato P, Pyrowolakis G, Gomez-Auli A, Mittler G, Cecere G, Erhardt S, Tiana G, Zhan Y, Iovino N. Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos. EMBO J 2024; 43:2685-2714. [PMID: 38831123 PMCID: PMC11217351 DOI: 10.1038/s44318-024-00127-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.
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Affiliation(s)
- Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085, Freiburg im Breisgau, Germany
| | - Iris Valent
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Fides Zenk
- Brain Mind Institute, School of Life Sciences EPFL, SV3809, 1015, Lausanne, Switzerland
| | - Eva Loeser
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Shwetha Herur
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giorgos Pyrowolakis
- Centre for Biological signaling studies, University of Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Alejandro Gomez-Auli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Germano Cecere
- Institute Pasteur, Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, UMR3738, CNRS, 75724, Cedex 15, Paris, France
| | - Sylvia Erhardt
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
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6
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Stanton BZ, Pomella S. Epigenetic determinants of fusion-driven sarcomas: paradigms and challenges. Front Cell Dev Biol 2024; 12:1416946. [PMID: 38946804 PMCID: PMC11211607 DOI: 10.3389/fcell.2024.1416946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 05/14/2024] [Indexed: 07/02/2024] Open
Abstract
We describe exciting recent advances in fusion-driven sarcoma etiology, from an epigenetics perspective. By exploring the current state of the field, we identify and describe the central mechanisms that determine sarcomagenesis. Further, we discuss seminal studies in translational genomics, which enabled epigenetic characterization of fusion-driven sarcomas. Important context for epigenetic mechanisms include, but are not limited to, cell cycle and metabolism, core regulatory circuitry, 3-dimensional chromatin architectural dysregulation, integration with ATP-dependent chromatin remodeling, and translational animal modeling. Paradoxically, while the genetic requirements for oncogenic transformation are highly specific for the fusion partners, the epigenetic mechanisms we as a community have uncovered are categorically very broad. This dichotomy prompts the question of whether the investigation of rare disease epigenomics should prioritize studying individual cell populations, thereby examining whether the mechanisms of chromatin dysregulation are specific to a particular tumor. We review recent advances focusing on rhabdomyosarcoma, synovial sarcoma, alveolar soft part sarcoma, clear cell sarcoma, undifferentiated round cell sarcoma, Ewing sarcoma, myxoid/round liposarcoma, epithelioid hemangioendothelioma and desmoplastic round cell tumor. The growing number of groundbreaking discoveries in the field, motivated us to anticipate further exciting advances in the area of mechanistic epigenomics and direct targeting of fusion transcription factors in the years ahead.
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Affiliation(s)
- Benjamin Z. Stanton
- Nationwide Children’s Hospital, Center for Childhood Cancer Research, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Silvia Pomella
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
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7
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Katznelson A, Hernandez B, Fahning H, Zhang J, Burton A, Torres-Padilla ME, Plachta N, Zaret KS, McCarthy RL. Heterochromatin protein ERH represses alternative cell fates during early mammalian differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597604. [PMID: 38895478 PMCID: PMC11185749 DOI: 10.1101/2024.06.06.597604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
During development, H3K9me3 heterochromatin is dynamically rearranged, silencing repeat elements and protein coding genes to restrict cell identity. Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized in fission yeast and recently shown to be required for H3K9me3 maintenance in human fibroblasts, but its function during development remains unknown. Here, we show that ERH is required for proper segregation of the inner cell mass and trophectoderm cell lineages during mouse development by repressing totipotent and alternative lineage programs. During human embryonic stem cell (hESC) differentiation into germ layer lineages, ERH is crucial for silencing naïve and pluripotency genes, transposable elements, and alternative lineage genes. Strikingly, ERH depletion in somatic cells reverts the H3K9me3 landscape to an hESC state and enables naïve and pluripotency gene and transposable element activation during iPSC reprogramming. Our findings reveal a role for ERH in initiation and maintenance of developmentally established gene repression.
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8
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Keenan CR, Coughlan HD, Iannarella N, Tapia Del Fierro A, Keniry A, Johanson TM, Chan WF, Garnham AL, Whitehead LW, Blewitt ME, Smyth GK, Allan RS. Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription. Genome Res 2024; 34:556-571. [PMID: 38719473 PMCID: PMC11146594 DOI: 10.1101/gr.279119.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/03/2024] [Indexed: 06/05/2024]
Abstract
H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences of heterochromatin loss in cells deficient in both SUV39H1 and SUV39H2 (Suv39DKO), the major mammalian histone methyltransferase enzymes that catalyze heterochromatic H3K9me3 deposition. We reveal a paradoxical repression of protein-coding genes in Suv39DKO cells, with these differentially expressed genes principally in euchromatic (Tn5-accessible, H3K4me3- and H3K27ac-marked) rather than heterochromatic (H3K9me3-marked) or polycomb (H3K27me3-marked) regions. Examination of the three-dimensional (3D) nucleome reveals that transcriptomic dysregulation occurs in euchromatic regions close to the nuclear periphery in 3D space. Moreover, this transcriptomic dysregulation is highly correlated with altered 3D genome organization in Suv39DKO cells. Together, our results suggest that the nuclear lamina-tethering of Suv39-dependent H3K9me3 domains provides an essential scaffold to support euchromatic genome organization and the maintenance of gene transcription for healthy cellular function.
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Affiliation(s)
- Christine R Keenan
- 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
| | - Hannah D Coughlan
- 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
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Andres Tapia Del Fierro
- 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
| | - Andrew Keniry
- 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
| | - Timothy M Johanson
- 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
| | - Wing Fuk Chan
- 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
| | - Alexandra L Garnham
- 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
| | - Lachlan W Whitehead
- 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
- 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
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Rhys S Allan
- 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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9
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Zhong Z, Du J, Zhu X, Guan L, Hu Y, Zhang P, Wang H. Highly efficient conversion of mouse fibroblasts into functional hepatic cells under chemical induction. J Mol Cell Biol 2024; 15:mjad071. [PMID: 37996395 PMCID: PMC11121195 DOI: 10.1093/jmcb/mjad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/25/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Previous studies have shown that hepatocyte-like cells can be generated from fibroblasts using either lineage-specific transcription factors or chemical induction methods. However, these methods have their own deficiencies that restrict the therapeutic applications of such induced hepatocytes. In this study, we present a transgene-free, highly efficient chemical-induced direct reprogramming approach to generate hepatocyte-like cells from mouse embryonic fibroblasts (MEFs). Using a small molecule cocktail (SMC) as an inducer, MEFs can be directly reprogrammed into hepatocyte-like cells, bypassing the intermediate stages of pluripotent and immature hepatoblasts. These chemical-induced hepatocyte-like cells (ciHeps) closely resemble mature primary hepatocytes in terms of morphology, biological behavior, gene expression patterns, marker expression levels, and hepatic functions. Furthermore, transplanted ciHeps can integrate into the liver, promote liver regeneration, and improve survival rates in mice with acute liver damage. ciHeps can also ameliorate liver fibrosis caused by chronic injuries and enhance liver function. Notably, ciHeps exhibit no tumorigenic potential either in vitro or in vivo. Mechanistically, SMC-induced mesenchymal-to-epithelial transition and suppression of SNAI1 contribute to the fate conversion of fibroblasts into ciHeps. These results indicate that this transgene-free, chemical-induced direct reprogramming technique has the potential to serve as a valuable means of producing alternative hepatocytes for both research and therapeutic purposes. Additionally, this method also sheds light on the direct reprogramming of other cell types under chemical induction.
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Affiliation(s)
- Zhi Zhong
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Jiangchuan Du
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Xiangjie Zhu
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China
| | - Lingting Guan
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Yanyu Hu
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Peilin Zhang
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
| | - Hongyang Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- National Center for Liver Cancer, Naval Medical University, Shanghai 201805, China
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10
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Duong P, Rodriguez-Parks A, Kang J, Murphy PJ. CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration. RESEARCH SQUARE 2024:rs.3.rs-4189493. [PMID: 38645155 PMCID: PMC11030498 DOI: 10.21203/rs.3.rs-4189493/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Regenerative potential is governed by a complex process of transcriptional reprogramming, involving chromatin reorganization and dynamics in transcription factor binding patterns throughout the genome. The degree to which chromatin and epigenetic changes contribute to this process remains partially understood. Here we provide a modified CUT&Tag protocol suitable for improved characterization and interrogation of epigenetic changes during adult fin regeneration in zebrafish. Our protocol generates data that recapitulates results from previously published ChIP-Seq methods, requires far fewer cells as input, and significantly improves signal to noise ratios. We deliver high-resolution enrichment maps for H3K4me3 of uninjured and regenerating fin tissues. During regeneration, we find that H3K4me3 levels increase over gene promoters which become transcriptionally active and genes which lose H3K4me3 become silenced. Interestingly, these epigenetic reprogramming events recapitulate the H3K4me3 patterns observed in developing fin folds of 24-hour old zebrafish embryos. Our results indicate that changes in genomic H3K4me3 patterns during fin regeneration occur in a manner consistent with reactivation of developmental programs, demonstrating CUT&Tag to be an effective tool for profiling chromatin landscapes in regenerating tissues.
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11
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Woodworth MA, Lakadamyali M. Toward a comprehensive view of gene architecture during transcription. Curr Opin Genet Dev 2024; 85:102154. [PMID: 38309073 PMCID: PMC10989512 DOI: 10.1016/j.gde.2024.102154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
The activation of genes within the nucleus of eukaryotic cells is a tightly regulated process, orchestrated by a complex interplay of various physical properties and interacting factors. Studying the multitude of components and features that collectively contribute to gene activation has proven challenging due to the complexities of simultaneously visualizing the dynamic and transiently interacting elements that coalesce within the small space occupied by each individual gene. However, various labeling and imaging advances are now starting to overcome this challenge, enabling visualization of gene activation at different lengths and timescales. In this review, we aim to highlight these microscopy-based advances and suggest how they can be combined to provide a comprehensive view of the mechanisms regulating gene activation.
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Affiliation(s)
- Marcus A Woodworth
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024; 25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.
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Affiliation(s)
- Francesca Taglini
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Altos Labs, Cambridge Institute, Cambridge, UK
| | - Willow Rolls
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kamila Irena Musialik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Imperial College London, London, UK
| | - Heng Yang Lee
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Endocrine Oncology Research Group, Department of Surgery, The Royal College of Surgeons RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Yujie Zhang
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Mattia Marenda
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hannah Finan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Swiss Federal Institute of Technology, ETH Zürich, Institute of Molecular Health Sciences, Zürich, Switzerland
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Hazel Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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13
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Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A. Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. Cell Syst 2024; 15:109-133.e10. [PMID: 38335955 PMCID: PMC10940218 DOI: 10.1016/j.cels.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this subset remain unknown. We apply retrospective clone tracing to identify and characterize the rare human fibroblasts primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis increased the reprogramming efficiency. We provide evidence for a unified model in which cells can move into and out of the primed state over time, explaining how reprogramming appears deterministic at short timescales and stochastic at long timescales. Furthermore, inhibiting the activity of LSD1 enlarged the pool of cells that were primed for reprogramming. Thus, even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.
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Affiliation(s)
- Naveen Jain
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher J Cote
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Mellis
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connie L Jiang
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miles Arnett
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenli Yang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Liang Z, Solano A, Lou J, Hinde E. Histone FRET reports the spatial heterogeneity in nanoscale chromatin architecture that is imparted by the epigenetic landscape at the level of single foci in an intact cell nucleus. Chromosoma 2024; 133:5-14. [PMID: 38265456 PMCID: PMC10904561 DOI: 10.1007/s00412-024-00815-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Genome sequencing has identified hundreds of histone post-translational modifications (PTMs) that define an open or compact chromatin nanostructure at the level of nucleosome proximity, and therefore serve as activators or repressors of gene expression. Direct observation of this epigenetic mode of transcriptional regulation in an intact single nucleus, is however, a complex task. This is because despite the development of fluorescent probes that enable observation of specific histone PTMs and chromatin density, the changes in nucleosome proximity regulating gene expression occur on a spatial scale well below the diffraction limit of optical microscopy. In recent work, to address this research gap, we demonstrated that the phasor approach to fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between fluorescently labelled histones core to the nucleosome, is a readout of chromatin nanostructure that can be multiplexed with immunofluorescence (IF) against specific histone PTMs. Here from application of this methodology to gold standard gene activators (H3K4Me3 and H3K9Ac) versus repressors (e.g., H3K9Me3 and H3K27Me), we find that while on average these histone marks do impart an open versus compact chromatin nanostructure, at the level of single chromatin foci, there is significant spatial heterogeneity. Collectively this study illustrates the importance of studying the epigenetic landscape as a function of space within intact nuclear architecture and opens the door for the study of chromatin foci sub-populations defined by combinations of histone marks, as is seen in the context of bivalent chromatin.
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Affiliation(s)
- Zhen Liang
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
- Cancer and RNA Laboratory, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medicine, Melbourne Medical School, St Vincent's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth Hinde
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia.
- School of Physics, University of Melbourne, Melbourne, VIC, Australia.
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15
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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16
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Moyers BA, Partridge EC, Mackiewicz M, Betti MJ, Darji R, Meadows SK, Newberry KM, Brandsmeier LA, Wold BJ, Mendenhall EM, Myers RM. Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. Genome Res 2023; 33:1879-1892. [PMID: 37852782 PMCID: PMC10760452 DOI: 10.1101/gr.278205.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.
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Affiliation(s)
- Belle A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Michael J Betti
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Roshan Darji
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Barbara J Wold
- Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA
| | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
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17
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Jokl E, Mullan AF, Simpson K, Birchall L, Pearmain L, Martin K, Pritchett J, Raza S, Shah R, Hodson NW, Williams CJ, Camacho E, Zeef L, Donaldson I, Athwal VS, Hanley NA, Piper Hanley K. PAK1-dependent mechanotransduction enables myofibroblast nuclear adaptation and chromatin organization during fibrosis. Cell Rep 2023; 42:113414. [PMID: 37967011 DOI: 10.1016/j.celrep.2023.113414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/14/2023] [Accepted: 10/25/2023] [Indexed: 11/17/2023] Open
Abstract
Myofibroblasts are responsible for scarring during fibrosis. The scar propagates mechanical signals inducing a radical transformation in myofibroblast cell state and increasing profibrotic phenotype. Here, we show mechanical stress from progressive scarring induces nuclear softening and de-repression of heterochromatin. The parallel loss of H3K9Me3 enables a permissive state for distinct chromatin accessibility and profibrotic gene regulation. Integrating chromatin accessibility profiles with RNA expression provides insight into the transcription network underlying the switch in profibrotic myofibroblast states, emphasizing mechanoadaptive regulation of PAK1 as key drivers. Through genetic manipulation in liver and lung fibrosis, loss of PAK1-dependent signaling impairs the mechanoadaptive response in vitro and dramatically improves fibrosis in vivo. Moreover, we provide human validation for mechanisms underpinning PAK1-mediated mechanotransduction in liver and lung fibrosis. Collectively, these observations provide insight into the nuclear mechanics driving the profibrotic chromatin landscape in fibrosis, highlighting actomyosin-dependent mechanisms as potential therapeutic targets in fibrosis.
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Affiliation(s)
- Elliot Jokl
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Aoibheann F Mullan
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Kara Simpson
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Lindsay Birchall
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Laurence Pearmain
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Katherine Martin
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - James Pritchett
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Sayyid Raza
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
| | - Rajesh Shah
- Manchester University NHS Foundation Trust, Oxford Road, Manchester, UK
| | - Nigel W Hodson
- Core Facilities, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Craig J Williams
- Department of Materials, University of Manchester, Manchester, UK
| | - Elizabeth Camacho
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, University of Manchester, Manchester, UK
| | - Leo Zeef
- Core Facilities, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Ian Donaldson
- Core Facilities, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Varinder S Athwal
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK; Manchester University NHS Foundation Trust, Oxford Road, Manchester, UK
| | - Neil A Hanley
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK; Manchester University NHS Foundation Trust, Oxford Road, Manchester, UK; College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
| | - Karen Piper Hanley
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK; Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK.
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18
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Feng M, Wang J, Li K, Nakamura F. UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition. Biochem J 2023; 480:1659-1674. [PMID: 37818922 DOI: 10.1042/bcj20230208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Mechanotransduction and contact inhibition (CI) control gene expression to regulate proliferation, differentiation, and even tumorigenesis of cells. However, their downstream trans-acting factors (TAFs) are not well known due to a lack of a high-throughput method to quantitatively detect them. Here, we developed a method to identify TAFs on the cis-acting sequences that reside in open chromatin or DNaseI-hypersensitive sites (DHSs) and to detect nucleocytoplasmic shuttling TAFs using computational and experimental screening. The DHS-proteomics revealed over 1000 potential mechanosensing TAFs and UBE2A/B (Ubiquitin-conjugating enzyme E2 A) was experimentally identified as a force- and CI-dependent nucleocytoplasmic shuttling TAF. We found that translocation of YAP/TAZ and UBE2A/B are distinctively regulated by inhibition of myosin contraction, actin-polymerization, and CI depending on cell types. Next-generation sequence analysis revealed many downstream genes including YAP are transcriptionally regulated by ubiquitination of histone by UBE2A/B. Our results suggested a YAP-independent mechanotransduction and CI pathway mediated by UBE2A/B.
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Affiliation(s)
- Mingwei Feng
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiale Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Kangjing Li
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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19
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Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Nat Commun 2023; 14:6420. [PMID: 37828010 PMCID: PMC10570362 DOI: 10.1038/s41467-023-42094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5- and DNase I-inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
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Grants
- This research was supported by AMED-CREST and AMED-PRIME of the Japan Agency for Medical Research and Development (JP22gm1310004, JP22gm6110021), SECOM Science and Technology Foundation SECOM Science and Technology Foundation (for Y.K.), Platform Project for Supporting Drug Discovery and Life Science Research from AMED JP21am0101076 and (for H.K.), Research Support Project for Life Science and Drug Discovery from AMED JP22ama121009 (for H.K.), Japan Science and Technology Agency ERATO JPMJER1901 (for H.K.) and by KAKENHI grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan and the Japan Society for the Promotion of Science (JP21J14115 for N.K.; JP22K15033 for T.K.;16H06279, 20H03179, 21H00242 and 22H04687 for Y.K.; 20K07589 for S.W.; JP20H00449, JP18H05534 for H.K.; JP22H00431, JP16H06279 and JP22H04925 for Y.G.)
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Affiliation(s)
- Naohiro Kuwayama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Kishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rina Hirano
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kenta Echigoya
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Lingyan Fang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sugiko Watanabe
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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20
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Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L. Single-cell chromatin state transitions during epigenetic memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560616. [PMID: 37873344 PMCID: PMC10592931 DOI: 10.1101/2023.10.03.560616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
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Affiliation(s)
- Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Joydeb Sinha
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
| | - Derek Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Current address: Department of Discovery Oncology, Genentech, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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21
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Yin Y, Shen X. Noncoding RNA-chromatin association: Functions and mechanisms. FUNDAMENTAL RESEARCH 2023; 3:665-675. [PMID: 38933302 PMCID: PMC11197541 DOI: 10.1016/j.fmre.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 06/28/2024] Open
Abstract
Pervasive transcription of the mammalian genome produces hundreds of thousands of noncoding RNAs (ncRNAs). Numerous studies have suggested that some of these ncRNAs regulate multiple cellular processes and play important roles in physiological and pathological processes. Notably, a large subset of ncRNAs is enriched on chromatin and participates in regulating gene expression and the dynamics of chromatin structure and status. In this review, we summarize recent advances in the functional study of chromatin-associated ncRNAs and mechanistic insights into how these ncRNAs associate with chromatin. We also discuss the potential future challenges which still need to be overcome in this field.
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Affiliation(s)
- Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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22
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Zhu P, Hou C, Liu M, Chen T, Li T, Wang L. Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol. BMC Genomics 2023; 24:493. [PMID: 37641002 PMCID: PMC10464338 DOI: 10.1186/s12864-023-09600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid-liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. RESULTS By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. CONCLUSION This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems.
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Affiliation(s)
- Peiyu Zhu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Manlin Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
| | - Likun Wang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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23
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Fan K, Pfister E, Weng Z. Toward a comprehensive catalog of regulatory elements. Hum Genet 2023; 142:1091-1111. [PMID: 36935423 DOI: 10.1007/s00439-023-02519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 03/21/2023]
Abstract
Regulatory elements are the genomic regions that interact with transcription factors to control cell-type-specific gene expression in different cellular environments. A precise and complete catalog of functional elements encoded by the human genome is key to understanding mammalian gene regulation. Here, we review the current state of regulatory element annotation. We first provide an overview of assays for characterizing functional elements, including genome, epigenome, transcriptome, three-dimensional chromatin interaction, and functional validation assays. We then discuss computational methods for defining regulatory elements, including peak-calling and other statistical modeling methods. Finally, we introduce several high-quality lists of regulatory element annotations and suggest potential future directions.
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Affiliation(s)
- Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Edith Pfister
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA.
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24
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Lerner J, Katznelson A, Zhang J, Zaret KS. Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2. Cell Rep 2023; 42:112748. [PMID: 37405916 PMCID: PMC10529229 DOI: 10.1016/j.celrep.2023.112748] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Andrew Katznelson
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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25
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McCarthy RL, Zhang J, Zaret KS. Diverse heterochromatin states restricting cell identity and reprogramming. Trends Biochem Sci 2023; 48:513-526. [PMID: 36990958 PMCID: PMC10182259 DOI: 10.1016/j.tibs.2023.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.
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Affiliation(s)
- Ryan L McCarthy
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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26
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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27
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Kim T, Yoo J, Do S, Hwang DS, Park Y, Shin Y. RNA-mediated demixing transition of low-density condensates. Nat Commun 2023; 14:2425. [PMID: 37105967 PMCID: PMC10140143 DOI: 10.1038/s41467-023-38118-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Biomolecular condensates play a key role in organizing cellular reactions by concentrating a specific set of biomolecules. However, whether condensate formation is accompanied by an increase in the total mass concentration within condensates or by the demixing of already highly crowded intracellular components remains elusive. Here, using refractive index imaging, we quantify the mass density of several condensates, including nucleoli, heterochromatin, nuclear speckles, and stress granules. Surprisingly, the latter two condensates exhibit low densities with a total mass concentration similar to the surrounding cyto- or nucleoplasm. Low-density condensates display higher permeability to cellular protein probes. We find that RNA tunes the biomolecular density of condensates. Moreover, intracellular structures such as mitochondria heavily influence the way phase separation proceeds, impacting the localization, morphology, and growth of condensates. These findings favor a model where segregative phase separation driven by non-associative or repulsive molecular interactions together with RNA-mediated selective association of specific components can give rise to low-density condensates in the crowded cellular environment.
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Affiliation(s)
- Taehyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaeyoon Yoo
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, 34141, Republic of Korea
- Tomocube Inc, Daejeon, 34109, South Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.
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28
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Bersaglieri C, Santoro R. Methods for mapping 3D-chromosome architecture around nucleoli. Curr Opin Cell Biol 2023; 81:102171. [PMID: 37230037 DOI: 10.1016/j.ceb.2023.102171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/03/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The nucleolus is the largest subcompartment of the nucleus, known to be the place of ribosome biogenesis. Emerging evidence has started to implicate the nucleolus in the organization of chromosomes in the nucleus. Genomic domains contacting the nucleolus are defined as nucleolar associated domains (NADs) and are generally characterized by repressive chromatin states. However, the role of the nucleolus in genome architecture remains still not fully understood mainly because the lack of a membrane has challenged the establishment of methods for accurate identification of NADs. Here, we will discuss recent advances on methods to identify and characterize NADs, discuss their improvements relative to old methods, and highlight future perspectives.
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Affiliation(s)
- Cristiana Bersaglieri
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland.
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29
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Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023; 186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
Abstract
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
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Affiliation(s)
- Joel Rozowsky
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Kun Xiong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keyang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ana Berthel
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - Fabio Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Maxwell S Sun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Justin Chang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Christopher J F Cameron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sergey Aganezov
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Sora Chee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Gabriel Conte Cortez Martins
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cassidy Danyko
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carrie A Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel Farid
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Idan Gabdank
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vivian Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin C Hitz
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Melanie Kirsche
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bonita R Lam
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Khine Zin Lin
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, CHN
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Mudge
- European Bioinformatics Institute, Cambridge, Cambridgeshire, GB
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioann Popov
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Srividya Ramakrishnan
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joe Raymond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
| | - Alexandra Scavelli
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jacob M Schreiber
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fritz J Sedlazeck
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rachel M Sherman
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Minyi Shi
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Cricket Alicia Sloan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - J Seth Strattan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zhen Tan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Forrest Y Tanaka
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anna Vlasova
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain; Institute of Research in Biomedicine, Barcelona, Spain
| | - Jun Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Werner
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lu Yu
- Institute of Cancer Research, London, UK
| | - Christopher Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | | | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Morgan E Levine
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Alexander Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Jesse Gillis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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30
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Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A. Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527870. [PMID: 36798299 PMCID: PMC9934612 DOI: 10.1101/2023.02.10.527870] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Pluripotency can be induced in somatic cells by the expression of the four "Yamanaka" factors OCT4, KLF4, SOX2, and MYC. However, even in homogeneous conditions, usually only a rare subset of cells admit reprogramming, and the molecular characteristics of this subset remain unknown. Here, we apply retrospective clone tracing to identify and characterize the individual human fibroblast cells that are primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis led to increased reprogramming efficiency, identifying it as a barrier to reprogramming. Changing the frequency of reprogramming by inhibiting the activity of LSD1 led to an enlarging of the pool of cells that were primed for reprogramming. Our results show that even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.
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Affiliation(s)
- Naveen Jain
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher J Cote
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Mellis
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Connie L Jiang
- Genetics and Epigenetics Program, Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian P Dardani
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Sam Reffsin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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31
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Heo SJ, Thakur S, Chen X, Loebel C, Xia B, McBeath R, Burdick JA, Shenoy VB, Mauck RL, Lakadamyali M. Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. Nat Biomed Eng 2023; 7:177-191. [PMID: 35996026 PMCID: PMC10053755 DOI: 10.1038/s41551-022-00910-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
Changes in the micro-environment of fibrous connective tissue can lead to alterations in the phenotypes of tissue-resident cells, yet the underlying mechanisms are poorly understood. Here, by visualizing the dynamics of histone spatial reorganization in tenocytes and mesenchymal stromal cells from fibrous tissue of human donors via super-resolution microscopy, we show that physiological and pathological chemomechanical cues can directly regulate the spatial nanoscale organization and density of chromatin in these tissue-resident cell populations. Specifically, changes in substrate stiffness, altered oxygen tension and the presence of inflammatory signals drive chromatin relocalization and compaction into the nuclear boundary, mediated by the activity of the histone methyltransferase EZH2 and an intact cytoskeleton. In healthy cells, chemomechanically triggered changes in the spatial organization and density of chromatin are reversible and can be attenuated by dynamically stiffening the substrate. In diseased human cells, however, the link between mechanical or chemical inputs and chromatin remodelling is abrogated. Our findings suggest that aberrant chromatin organization in fibrous connective tissue may be a hallmark of disease progression that could be leveraged for therapeutic intervention.
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Affiliation(s)
- Su-Jin Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xingyu Chen
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudia Loebel
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Boao Xia
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Rowena McBeath
- Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jason A Burdick
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Vivek B Shenoy
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert L Mauck
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA.
- Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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32
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Alvarez V, Bandau S, Jiang H, Rios-Szwed D, Hukelmann J, Garcia-Wilson E, Wiechens N, Griesser E, Ten Have S, Owen-Hughes T, Lamond A, Alabert C. Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication. Cell Rep 2023; 42:111996. [PMID: 36680776 DOI: 10.1016/j.celrep.2023.111996] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA-bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative proteomics coupled to Nascent Chromatin Capture or isolation of Proteins on Nascent DNA, we provide time-resolved binding kinetics for thousands of proteins behind replisomes within euchromatin and heterochromatin in human cells. This shows that most proteins regain access within minutes to newly replicated DNA. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function or nuclear abundance. Instead, chromatin organization and G1 phase entry affect their reassociation. Finally, DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory.
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Affiliation(s)
- Vanesa Alvarez
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Susanne Bandau
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Diana Rios-Szwed
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Hukelmann
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Elisa Garcia-Wilson
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola Wiechens
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Eva Griesser
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara Ten Have
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Constance Alabert
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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33
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Kariti H, Feld T, Kaplan N. Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments. Nucleic Acids Res 2023; 51:1103-1119. [PMID: 36629266 PMCID: PMC9943678 DOI: 10.1093/nar/gkac1258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
The Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challenge. Genomic compartments are a checkered Hi-C interaction pattern suggested to represent the partitioning of the genome into two self-interacting states associated with active and inactive chromatin. Based on a few elementary mechanistic assumptions, we derive a generative probabilistic model of genomic compartments, called deGeco. Testing our model, we find it can explain observed Hi-C interaction maps in a highly robust manner, allowing accurate inference of interaction probability maps from extremely sparse data without any training of parameters. Taking advantage of the interpretability of the model parameters, we then test hypotheses regarding the nature of genomic compartments. We find clear evidence of multiple states, and that these states self-interact with different affinities. We also find that the interaction rules of chromatin states differ considerably within and between chromosomes. Inspecting the molecular underpinnings of a four-state model, we show that a simple classifier can use histone marks to predict the underlying states with 87% accuracy. Finally, we observe instances of mixed-state loci and analyze these loci in single-cell Hi-C maps, finding that mixing of states occurs mainly at the cell level.
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Affiliation(s)
- Hagai Kariti
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Tal Feld
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel,Viterbi Faculty of Electrical & Computer Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Noam Kaplan
- To whom correspondence should be addressed. Tel: +972 4 8295293;
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34
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Spracklin G, Yang L, Pradhan S, Dekker J. Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq. Methods Mol Biol 2023; 2611:53-61. [PMID: 36807063 DOI: 10.1007/978-1-0716-2899-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Chromatin accessibility has been an immensely powerful metric for identifying and understanding regulatory elements in the genome. Many important regulatory elements, such as enhancers and transcriptional start sites, are characterized by "open" or nucleosome-free regions. Understanding the areas of the genome that are not considered open chromatin has been more difficult. Protect-seq is a genomics technique that aims to identify inaccessible chromatin associated with the nuclear periphery. These regions are enriched for histone modifications associated with transcriptional repression and correlate with loci identified by other techniques measuring heterochromatin and peripheral localization. Here, we discuss the protocol and best practices to perform Protect-seq.
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Affiliation(s)
- George Spracklin
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Liyan Yang
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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35
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The influence of high-order chromatin state in the regulation of stem cell fate. Biochem Soc Trans 2022; 50:1809-1822. [DOI: 10.1042/bst20220763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, genomic DNA is hierarchically compacted by histones into chromatin, which is initially assembled by the nucleosome and further folded into orderly and flexible structures that include chromatin fiber, chromatin looping, topologically associated domains (TADs), chromosome compartments, and chromosome territories. These distinct structures and motifs build the three-dimensional (3D) genome architecture, which precisely controls spatial and temporal gene expression in the nucleus. Given that each type of cell is characterized by its own unique gene expression profile, the state of high-order chromatin plays an essential role in the cell fate decision. Accumulating evidence suggests that the plasticity of high-order chromatin is closely associated with stem cell fate. In this review, we summarize the biological roles of the state of high-order chromatin in embryogenesis, stem cell differentiation, the maintenance of stem cell identity, and somatic cell reprogramming. In addition, we highlight the roles of epigenetic factors and pioneer transcription factors (TFs) involved in regulating the state of high-order chromatin during the determination of stem cell fate and discuss how H3K9me3-heterochromatin restricts stem cell fate. In summary, we review the most recent progress in research on the regulatory functions of high-order chromatin dynamics in the determination and maintenance of stem cell fate.
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36
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Levinsky AJ, McEdwards G, Sethna N, Currie MA. Targets of histone H3 lysine 9 methyltransferases. Front Cell Dev Biol 2022; 10:1026406. [PMID: 36568972 PMCID: PMC9768651 DOI: 10.3389/fcell.2022.1026406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone H3 lysine 9 di- and trimethylation are well-established marks of constitutively silenced heterochromatin domains found at repetitive DNA elements including pericentromeres, telomeres, and transposons. Loss of heterochromatin at these sites causes genomic instability in the form of aberrant DNA repair, chromosome segregation defects, replication stress, and transposition. H3K9 di- and trimethylation also regulate cell type-specific gene expression during development and form a barrier to cellular reprogramming. However, the role of H3K9 methyltransferases extends beyond histone methylation. There is a growing list of non-histone targets of H3K9 methyltransferases including transcription factors, steroid hormone receptors, histone modifying enzymes, and other chromatin regulatory proteins. Additionally, two classes of H3K9 methyltransferases modulate their own function through automethylation. Here we summarize the structure and function of mammalian H3K9 methyltransferases, their roles in genome regulation and constitutive heterochromatin, as well as the current repertoire of non-histone methylation targets including cases of automethylation.
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Affiliation(s)
- Aidan J. Levinsky
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasha Sethna
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Mark A. Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada,*Correspondence: Mark A. Currie,
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37
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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38
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Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech 2022; 33:3fc1f5fe.7910785e. [PMID: 36910579 PMCID: PMC10001930 DOI: 10.7171/3fc1f5fe.7910785e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels. Results In this study, we evaluated the performance of 4 ChIP-Seq library preparation protocols (New England Biolabs [NEB] NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo [now PerkinElmer] NEXTflex) on 3 target proteins, chosen to represent the 3 typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. Conclusions Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice, as it performed well for each of the 3 targets we tested across a wide array of input DNA levels.
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Affiliation(s)
- M S Simper
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - L Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - S Gaddis
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - K Lin
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - C D Mikulec
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - True Takata
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - M W Tomida
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - D Zhang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: College of Biology Hunan University Changsha410082 China
| | - D G Tang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: Department of Pharmacology and Therapeutics Roswell Park Cancer Institute BuffaloNew York14263 USA
| | - M R Estecio
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - J Shen
- Department of Epigenetics and Molecular Carcinogenesis.,Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Program in Genetics and Epigenetics MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences The University of Texas MD Anderson Cancer Center SmithvilleTexas78957 USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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40
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Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery. Nat Commun 2022; 13:4199. [PMID: 35859152 PMCID: PMC9300685 DOI: 10.1038/s41467-022-31857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/06/2022] [Indexed: 11/08/2022] Open
Abstract
The genome can be divided into two spatially segregated compartments, A and B, which partition active and inactive chromatin states. While constitutive heterochromatin is predominantly located within the B compartment near the nuclear lamina, facultative heterochromatin marked by H3K27me3 spans both compartments. How epigenetic modifications, compartmentalization, and lamina association collectively maintain heterochromatin architecture remains unclear. Here we develop Lamina-Inducible Methylation and Hi-C (LIMe-Hi-C) to jointly measure chromosome conformation, DNA methylation, and lamina positioning. Through LIMe-Hi-C, we identify topologically distinct sub-compartments with high levels of H3K27me3 and differing degrees of lamina association. Inhibition of Polycomb repressive complex 2 (PRC2) reveals that H3K27me3 is essential for sub-compartment segregation. Unexpectedly, PRC2 inhibition promotes lamina association and constitutive heterochromatin spreading into H3K27me3-marked B sub-compartment regions. Consistent with this repositioning, genes originally marked with H3K27me3 in the B compartment, but not the A compartment, remain largely repressed, suggesting that constitutive heterochromatin spreading can compensate for H3K27me3 loss at a transcriptional level. These findings demonstrate that Polycomb sub-compartments and their antagonism with lamina association are fundamental features of genome structure. More broadly, by jointly measuring nuclear position and Hi-C contacts, our study demonstrates how compartmentalization and lamina association represent distinct but interdependent modes of heterochromatin regulation.
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41
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Berger F. Which field of research would Gregor Mendel choose in the 21st century? THE PLANT CELL 2022; 34:2462-2465. [PMID: 35238371 PMCID: PMC9252487 DOI: 10.1093/plcell/koac072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/17/2022] [Indexed: 05/13/2023]
Abstract
Gregor Mendel's work on segregation of traits in plants established the basic methodology and rules of genetics. The interruption of Mendel's research activities in 1870 impeded the immediate recognition of the value of his work until the dawn of the 20th century. Only then were his founding laws of genetics validated, propelling the development of biological research toward the birth of molecular biology in the second half of the 20th century. While molecular plant genetics can be viewed as the spiritual heir of Mendel's research, one might wonder whether in the 21st century Gregor Mendel would prefer to practice scientific approaches other than molecular genetics such as population genetics, comparative genomics, or the emerging field of evo-chromo. In this perspective, I review aspects of these fields that might have attracted or perplexed a 21st century Mendel.
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42
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Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE. 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. Cell 2022; 185:2690-2707. [PMID: 35868274 DOI: 10.1016/j.cell.2022.06.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/16/2022]
Abstract
Nearly half of the human genome is comprised of diverse repetitive sequences ranging from satellite repeats to retrotransposable elements. Such sequences are susceptible to stepwise expansions, duplications, inversions, and recombination events which can compromise genome function. In this review, we discuss the higher-order folding mechanisms of compartmentalization and loop extrusion and how they shape, and are shaped by, heterochromatin. Using primarily mammalian model systems, we contrast mechanisms governing H3K9me3-mediated heterochromatinization of the repetitive genome and highlight emerging links between repetitive elements and chromatin folding.
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Affiliation(s)
- Spencer A Haws
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Simandi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Jordan Barnett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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43
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Lacerda JT, Gomes PRL, Zanetti G, Mezzalira N, Lima OG, de Assis LVM, Guler A, Castrucci AM, Moraes MN. Lack of TRPV1 Channel Modulates Mouse Gene Expression and Liver Proteome with Glucose Metabolism Changes. Int J Mol Sci 2022; 23:ijms23137014. [PMID: 35806020 PMCID: PMC9266899 DOI: 10.3390/ijms23137014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
To investigate the role of the transient receptor potential channel vanilloid type 1 (TRPV1) in hepatic glucose metabolism, we analyzed genes related to the clock system and glucose/lipid metabolism and performed glycogen measurements at ZT8 and ZT20 in the liver of C57Bl/6J (WT) and Trpv1 KO mice. To identify molecular clues associated with metabolic changes, we performed proteomics analysis at ZT8. Liver from Trpv1 KO mice exhibited reduced Per1 expression and increased Pparα, Pparγ, Glut2, G6pc1 (G6pase), Pck1 (Pepck), Akt, and Gsk3b expression at ZT8. Liver from Trpv1 KO mice also showed reduced glycogen storage at ZT8 but not at ZT20 and significant proteomics changes consistent with enhanced glycogenolysis, as well as increased gluconeogenesis and inflammatory features. The network propagation approach evidenced that the TRPV1 channel is an intrinsic component of the glucagon signaling pathway, and its loss seems to be associated with increased gluconeogenesis through PKA signaling. In this sense, the differentially identified kinases and phosphatases in WT and Trpv1 KO liver proteomes show that the PP2A phosphatase complex and PKA may be major players in glycogenolysis in Trpv1 KO mice.
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Affiliation(s)
- José Thalles Lacerda
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
| | - Patrícia R. L. Gomes
- Laboratory of Neurobiology, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Giovanna Zanetti
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
| | - Nathana Mezzalira
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
| | - Otoniel G. Lima
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
| | - Leonardo V. M. de Assis
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
- Institute of Neurobiology, University of Lübeck, 23562 Lübeck, Germany
| | - Ali Guler
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA;
| | - Ana Maria Castrucci
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA;
| | - Maria Nathália Moraes
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil; (J.T.L.); (G.Z.); (N.M.); (O.G.L.); (L.V.M.d.A.); (A.M.C.)
- Laboratory of Neurobiology, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil;
- Correspondence:
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44
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Zuo F, Jiang J, Fu H, Yan K, Liefke R, Zhang J, Hong Y, Chang Z, Liu N, Wang Z, Xi Q. A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells. Cell Stem Cell 2022; 29:948-961.e6. [DOI: 10.1016/j.stem.2022.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 03/22/2022] [Accepted: 05/09/2022] [Indexed: 12/22/2022]
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45
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Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics 2022; 22:e2100206. [PMID: 35633285 DOI: 10.1002/pmic.202100206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
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46
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Zhao L, Polavarapu VK, Yadav RP, Xing P, Chen X. A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples. Bio Protoc 2022; 12:e4418. [PMID: 35865114 PMCID: PMC9257839 DOI: 10.21769/bioprotoc.4418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/31/2022] [Indexed: 12/29/2022] Open
Abstract
The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. Nevertheless, it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissue of interest are limited. Here, we present F FPE tissue with a ntibody-guided c hromatin t agmentation with sequencing (FACT-seq), highly sensitive method to efficiently profile histone modifications in FFPE tissue by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We showed a very small piece of FFPE tissue section containing ~4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. In archived FFPE human colorectal and human glioblastoma cancer tissue, H3K27ac FACT-seq revealed disease specific super enhancers. In summary, FACT-seq allows researchers to decode histone modifications like H3K27ac and H3K27me3 in archival FFPE tissues with high sensitivity, thus allowing us to understand epigenetic regulation. Graphical abstract: ( i ) FFPE tissue section; ( ii ) Isolated nuclei; ( iii ) Primary antibody, secondary antibody and T7-pA-Tn5 bind to targets; ( iv ) DNA purification; ( v ) In vitro transcription and sequencing library preparation; ( vi ) Sequencing.
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Affiliation(s)
- Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Ram Prakash Yadav
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden;
,
*For correspondence:
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 133] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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48
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Zhou K, Gebala M, Woods D, Sundararajan K, Edwards G, Krzizike D, Wereszczynski J, Straight AF, Luger K. CENP-N promotes the compaction of centromeric chromatin. Nat Struct Mol Biol 2022; 29:403-413. [PMID: 35422519 PMCID: PMC9010303 DOI: 10.1038/s41594-022-00758-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022]
Abstract
The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Dustin Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | | | - Garrett Edwards
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Dan Krzizike
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA.
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Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains. Nat Commun 2022; 13:1483. [PMID: 35304483 PMCID: PMC8933459 DOI: 10.1038/s41467-022-29146-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.
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50
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Rawal CC, Butova NL, Mitra A, Chiolo I. An Expanding Toolkit for Heterochromatin Repair Studies. Genes (Basel) 2022; 13:genes13030529. [PMID: 35328082 PMCID: PMC8955653 DOI: 10.3390/genes13030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/04/2022] Open
Abstract
Pericentromeric heterochromatin is mostly composed of repetitive DNA sequences prone to aberrant recombination. Cells have developed highly specialized mechanisms to enable ‘safe’ homologous recombination (HR) repair while preventing aberrant recombination in this domain. Understanding heterochromatin repair responses is essential to understanding the critical mechanisms responsible for genome integrity and tumor suppression. Here, we review the tools, approaches, and methods currently available to investigate double-strand break (DSB) repair in pericentromeric regions, and also suggest how technologies recently developed for euchromatin repair studies can be adapted to characterize responses in heterochromatin. With this ever-growing toolkit, we are witnessing exciting progress in our understanding of how the ‘dark matter’ of the genome is repaired, greatly improving our understanding of genome stability mechanisms.
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