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Li RZ, Han CZ, Glass CK. TIANA: transcription factors cooperativity inference analysis with neural attention. BMC Bioinformatics 2024; 25:274. [PMID: 39174927 PMCID: PMC11342676 DOI: 10.1186/s12859-024-05852-0] [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: 10/11/2023] [Accepted: 07/01/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Growing evidence suggests that distal regulatory elements are essential for cellular function and states. The sequences within these distal elements, especially motifs for transcription factor binding, provide critical information about the underlying regulatory programs. However, cooperativities between transcription factors that recognize these motifs are nonlinear and multiplexed, rendering traditional modeling methods insufficient to capture the underlying mechanisms. Recent development of attention mechanism, which exhibit superior performance in capturing dependencies across input sequences, makes them well-suited to uncover and decipher intricate dependencies between regulatory elements. RESULT We present Transcription factors cooperativity Inference Analysis with Neural Attention (TIANA), a deep learning framework that focuses on interpretability. In this study, we demonstrated that TIANA could discover biologically relevant insights into co-occurring pairs of transcription factor motifs. Compared with existing tools, TIANA showed superior interpretability and robust performance in identifying putative transcription factor cooperativities from co-occurring motifs. CONCLUSION Our results suggest that TIANA can be an effective tool to decipher transcription factor cooperativities from distal sequence data. TIANA can be accessed through: https://github.com/rzzli/TIANA .
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Affiliation(s)
- Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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2
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Patrick R, Naval-Sanchez M, Deshpande N, Huang Y, Zhang J, Chen X, Yang Y, Tiwari K, Esmaeili M, Tran M, Mohamed AR, Wang B, Xia D, Ma J, Bayliss J, Wong K, Hun ML, Sun X, Cao B, Cottle DL, Catterall T, Barzilai-Tutsch H, Troskie RL, Chen Z, Wise AF, Saini S, Soe YM, Kumari S, Sweet MJ, Thomas HE, Smyth IM, Fletcher AL, Knoblich K, Watt MJ, Alhomrani M, Alsanie W, Quinn KM, Merson TD, Chidgey AP, Ricardo SD, Yu D, Jardé T, Cheetham SW, Marcelle C, Nilsson SK, Nguyen Q, White MD, Nefzger CM. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metab 2024; 36:1858-1881.e23. [PMID: 38959897 DOI: 10.1016/j.cmet.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
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Affiliation(s)
- Ralph Patrick
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yifei Huang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ying Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Kanupriya Tiwari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammadhossein Esmaeili
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Amin R Mohamed
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Binxu Wang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jun Ma
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kahlia Wong
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael L Hun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tara Catterall
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Hila Barzilai-Tutsch
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Robin-Lee Troskie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhian Chen
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Andrea F Wise
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sheetal Saini
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ye Mon Soe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Snehlata Kumari
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Konstantin Knoblich
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Tobias D Merson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann P Chidgey
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Surgery, Cabrini Monash University, Malvern, VIC 3144, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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3
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Buono L, Annona G, Magri MS, Negueruela S, Sepe RM, Caccavale F, Maeso I, Arnone MI, D’Aniello S. Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation. Cells 2024; 13:1121. [PMID: 38994973 PMCID: PMC11240583 DOI: 10.3390/cells13131121] [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: 05/15/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Throughout embryonic development, the shaping of the functional and morphological characteristics of embryos is orchestrated by an intricate interaction between transcription factors and cis-regulatory elements. In this study, we conducted a comprehensive analysis of deuterostome cis-regulatory landscapes during gastrulation, focusing on four paradigmatic species: the echinoderm Strongylocentrotus purpuratus, the cephalochordate Branchiostoma lanceolatum, the urochordate Ciona intestinalis, and the vertebrate Danio rerio. Our approach involved comparative computational analysis of ATAC-seq datasets to explore the genome-wide blueprint of conserved transcription factor binding motifs underlying gastrulation. We identified a core set of conserved DNA binding motifs associated with 62 known transcription factors, indicating the remarkable conservation of the gastrulation regulatory landscape across deuterostomes. Our findings offer valuable insights into the evolutionary molecular dynamics of embryonic development, shedding light on conserved regulatory subprograms and providing a comprehensive perspective on the conservation and divergence of gene regulation underlying the gastrulation process.
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Affiliation(s)
- Lorena Buono
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Research Infrastructure for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarollo (CABD), Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | | | - Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 80133 Naples, Italy
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
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4
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Chen J, Wen Y, Lin L, Cui Y, Chen Z, Gao J, Zhuang Y, Chen Q. Fosl2 Deficiency Predisposes Mice to Osteopetrosis, Leading to Bone Marrow Failure. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1081-1093. [PMID: 38380993 DOI: 10.4049/jimmunol.2300592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Arthritis causes Fos-like 2 (Fosl2) inactivation, and various immune cells contribute to its pathogenesis. However, little is known about the role of Fosl2 in hematopoiesis and the possible pathological role of Fosl2 inactivation in the hematopoietic system in arthritis. In this study, we show that Fosl2 maintains hematopoietic stem cell (HSC) quiescence and differentiation while controlling the inflammatory response via macrophages. Fosl2-specific deletion in the hematopoietic system caused the expansion of HSCs and myeloid cell growth while affecting erythroid and B cell differentiation. Fosl2 inactivation enhanced macrophage M1 polarization and stimulated proinflammatory cytokines and myeloid growth factors, skewing HSCs toward myeloid cell differentiation, similar to hematopoietic alterations in arthritic mice. Loss of Fosl2 mediated by Vav-iCre also displays an unexpected deletion in embryonic erythro-myeloid progenitor-derived osteoclasts, leading to osteopetrosis and anemia. The reduced bone marrow cellularity in Vav-iCreFosl2f/f mice is a consequence of the reduced bone marrow space in osteopetrotic mice rather than a direct role of Fosl2 in hematopoiesis. Thus, Fosl2 is indispensable for erythro-myeloid progenitor-derived osteoclasts to maintain the medullary cavity to ensure normal hematopoiesis. These findings improve our understanding of the pathogenesis of bone-destructive diseases and provide important implications for developing therapeutic approaches for these diseases.
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Affiliation(s)
- Jinfeng Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Yi Wen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lili Lin
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Yuchen Cui
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Zhenyu Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Jing Gao
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Yifang Zhuang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, China
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5
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Dochnal SA, Whitford AL, Francois AK, Krakowiak PA, Cuddy S, Cliffe AR. c-Jun signaling during initial HSV-1 infection modulates latency to enhance later reactivation in addition to directly promoting the progression to full reactivation. J Virol 2024; 98:e0176423. [PMID: 38193709 PMCID: PMC10878265 DOI: 10.1128/jvi.01764-23] [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: 11/10/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
Herpes simplex virus-1 (HSV-1) establishes a latent infection in peripheral neurons and periodically reactivates to permit transmission, which can result in clinical manifestations. Viral transactivators required for lytic infection are largely absent during latent infection, and therefore, HSV-1 relies on the co-option of neuronal host signaling pathways to initiate its gene expression. The activation of the neuronal c-Jun N-terminal kinase (JNK) cell stress pathway is central to initiating biphasic reactivation in response to multiple stimuli. However, how host factors work with JNK to stimulate the initial wave of gene expression (known as Phase I) or the progression to full Phase II reactivation remains unclear. Here, we found that c-Jun, the primary target downstream of neuronal JNK cell stress signaling, functions during reactivation but not during the JNK-mediated initiation of Phase I gene expression. Instead, c-Jun was required to transition from Phase I to full HSV-1 reactivation and was detected in viral replication compartments of reactivating neurons. Interestingly, we also identified a role for both c-Jun and enhanced neuronal stress during initial neuronal infection in promoting a more reactivation-competent form of HSV-1 latency. Therefore, c-Jun functions at multiple stages during the HSV latent infection of neurons to promote reactivation but not during the initial JNK-dependent Phase I. Importantly, by demonstrating that initial infection conditions can contribute to later reactivation abilities, this study highlights the potential for latently infected neurons to maintain a molecular scar of previous exposure to neuronal stressors.IMPORTANCEThe molecular mechanisms that regulate the reactivation of herpes simplex virus-1 (HSV-1) from latent infection are unknown. The host transcription and pioneer factor c-Jun is the main target of the JNK cell stress pathway that is known to be important in exit of HSV from latency. Surprisingly, we found that c-Jun does not act with JNK during exit from latency but instead promotes the transition to full reactivation. Moreover, c-Jun and enhanced neuronal stress during initial neuronal infection promoted a more reactivation-competent form of HSV-1 latency. c-Jun, therefore, functions at multiple stages during HSV-1 latent infection of neurons to promote reactivation. Importantly, this study contributes to a growing body of evidence that de novo HSV-1 infection conditions can modulate latent infection and impact future reactivation events, raising important questions on the clinical impact of stress during initial HSV-1 acquisition on future reactivation events and consequences.
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Affiliation(s)
- Sara A. Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Abigail L. Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Alison K. Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Patryk A. Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Sean Cuddy
- Neuroscience Graduate Program, University of Virginia, Charlottesville, Virginia, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. Affinity-optimizing enhancer variants disrupt development. Nature 2024; 626:151-159. [PMID: 38233525 PMCID: PMC10830414 DOI: 10.1038/s41586-023-06922-8] [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: 01/11/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Enhancers control the location and timing of gene expression and contain the majority of variants associated with disease1-3. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the expression of Shh in the developing limb4. Thirty-one human single-nucleotide variants (SNVs) within the ZRS are associated with polydactyly4-6. However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.
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Affiliation(s)
- Fabian Lim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Joe J Solvason
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Genevieve E Ryan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sophia H Le
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Granton A Jindal
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Paige Steffen
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Simran K Jandu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emma K Farley
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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7
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Cosgrove BD, Bounds LR, Taylor CK, Su AL, Rizzo AJ, Barrera A, Crawford GE, Hoffman BD, Gersbach CA. Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574997. [PMID: 38260455 PMCID: PMC10802421 DOI: 10.1101/2024.01.10.574997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Epigenetic control of cellular transcription and phenotype is influenced by changes in the cellular microenvironment, yet how mechanical cues from these microenvironments precisely influence epigenetic state to regulate transcription remains largely unmapped. Here, we combine genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq CRISPR screening to identify a new class of genomic enhancers that responds to the mechanical microenvironment. These 'mechanoenhancers' could be active on either soft or stiff extracellular matrix contexts, and regulated transcription to influence critical cell functions including apoptosis, mechanotransduction, proliferation, and migration. Epigenetic editing of mechanoenhancers on rigid materials tuned gene expression to levels observed on softer materials, thereby reprogramming the cellular response to the mechanical microenvironment. These editing approaches may enable the precise alteration of mechanically-driven disease states.
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Affiliation(s)
- Brian D. Cosgrove
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Lexi R. Bounds
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Carson Key Taylor
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Alan L. Su
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Anthony J. Rizzo
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E. Crawford
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Pediatrics, Duke University Medical Center; Durham, NC 27708, USA
| | - Brenton D. Hoffman
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Department of Cell Biology, Duke University; Durham, NC 27708, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University; Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University; Durham, NC 27708, USA
- Department of Cell Biology, Duke University; Durham, NC 27708, USA
- Department of Surgery, Duke University Medical Center; Durham, NC 27708, USA
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8
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Coxon M, Dennis MA, Dananberg A, Collins C, Wilson H, Meekma J, Savenkova M, Ng D, Osbron C, Mertz T, Goodman A, Duttke S, Maciejowski J, Roberts S. An impaired ubiquitin-proteasome system increases APOBEC3A abundance. NAR Cancer 2023; 5:zcad058. [PMID: 38155930 PMCID: PMC10753533 DOI: 10.1093/narcan/zcad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023] Open
Abstract
Apolipoprotein B messenger RNA (mRNA) editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases cause genetic instability during cancer development. Elevated APOBEC3A (A3A) levels result in APOBEC signature mutations; however, mechanisms regulating A3A abundance in breast cancer are unknown. Here, we show that dysregulating the ubiquitin-proteasome system with proteasome inhibitors, including Food and Drug Administration-approved anticancer drugs, increased A3A abundance in breast cancer and multiple myeloma cell lines. Unexpectedly, elevated A3A occurs via an ∼100-fold increase in A3A mRNA levels, indicating that proteasome inhibition triggers a transcriptional response as opposed to or in addition to blocking A3A degradation. This transcriptional regulation is mediated in part through FBXO22, a protein that functions in SKP1-cullin-F-box ubiquitin ligase complexes and becomes dysregulated during carcinogenesis. Proteasome inhibitors increased cellular cytidine deaminase activity, decreased cellular proliferation and increased genomic DNA damage in an A3A-dependent manner. Our findings suggest that proteasome dysfunction, either acquired during cancer development or induced therapeutically, could increase A3A-induced genetic heterogeneity and thereby influence therapeutic responses in patients.
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Affiliation(s)
- Margo Coxon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Madeline A Dennis
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Collins
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Jordyn Meekma
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Daniel Ng
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Chelsea A Osbron
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Tony M Mertz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
| | - Alan G Goodman
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
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9
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Dochnal SA, Whitford AL, Francois AK, Krakowiak PA, Cuddy S, Cliffe AR. c-Jun Signaling During Initial HSV-1 Infection Modulates Latency to Enhance Later Reactivation in addition to Directly Promoting the Progression to Full Reactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566462. [PMID: 37986840 PMCID: PMC10659354 DOI: 10.1101/2023.11.10.566462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Herpes simplex virus-1 (HSV-1) establishes a latent infection in peripheral neurons and can periodically reactivate to permit transmission and clinical manifestations. Viral transactivators required for lytic infection are largely absent during latent infection and therefore HSV-1 relies on the co-option of neuronal host signaling pathways to initiate its gene expression. Activation of the neuronal c-Jun N-terminal kinase (JNK) cell stress pathway is central to initiating biphasic reactivation in response to multiple stimuli. However, how host factors work with JNK to stimulate the initial wave of gene expression (known as Phase I) or the progression to full, Phase II reactivation remains unclear. Here, we found that c-Jun, the primary target downstream of neuronal JNK cell stress signaling, functions during reactivation but not during the JNK-mediated initiation of Phase I gene expression. Instead, c-Jun was required for the transition from Phase I to full HSV-1 reactivation and was detected in viral replication compartments of reactivating neurons. Interestingly, we also identified a role for both c-Jun and enhanced neuronal stress during initial neuronal infection in promoting a more reactivation-competent form of HSV-1 latency. Therefore, c-Jun functions at multiple stages during HSV latent infection of neurons to promote reactivation. Importantly, by demonstrating that initial infection conditions can contribute to later reactivation abilities, this study highlights the potential for latently infected neurons to maintain a molecular scar of previous exposure to neuronal stressors.
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Affiliation(s)
- Sara A. Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Abigail L. Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Alison K. Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Patryk A. Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Sean Cuddy
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, 22908
| | - Anna R. Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
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10
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Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol 2023; 25:1600-1615. [PMID: 37857833 PMCID: PMC11005034 DOI: 10.1038/s41556-023-01248-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of Legionnaires' disease, secretes a subset of protein effectors into host cells that inhibit translation elongation. Mechanistic insights into how the bacterium targets translation elongation remain poorly defined. We report here that the Legionella effector SidI functions in an unprecedented way as a transfer-RNA mimic that directly binds to and glycosylates the ribosome. The 3.1 Å cryo-electron microscopy structure of SidI reveals an N-terminal domain with an 'inverted L' shape and surface-charge distribution characteristic of tRNA mimicry, and a C-terminal domain that adopts a glycosyl transferase fold that licenses SidI to utilize GDP-mannose as a sugar precursor. This coupling of tRNA mimicry and enzymatic action endows SidI with the ability to block protein synthesis with a potency comparable to ricin, one of the most powerful toxins known. In Legionella-infected cells, the translational pausing activated by SidI elicits a stress response signature mimicking the ribotoxic stress response, which is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus and orchestrates the transcription of stress-inducible genes that promote cell death, revealing a major role for ATF3 in the response to collided ribosome stress. Together, our findings elucidate a novel mechanism by which a pathogenic bacterium employs tRNA mimicry to hijack a ribosome-to-nuclear signalling pathway that regulates cell fate.
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Affiliation(s)
- Advait Subramanian
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Lan Wang
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Tom Moss
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Smriti Sangwan
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Ernst H Pulido
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
| | - Samentha Kwok
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, CA, USA
| | - Robert J Chalkley
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Kathy H Li
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Alma L Burlingame
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA.
- Bay Area Institute of Science, Altos Labs, Redwood City, CA, USA.
| | - Shaeri Mukherjee
- G.W. Hooper Foundation, University of California at San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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11
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Abe Y, Kofman ER, Almeida M, Ouyang Z, Ponte F, Mueller JR, Cruz-Becerra G, Sakai M, Prohaska TA, Spann NJ, Resende-Coelho A, Seidman JS, Stender JD, Taylor H, Fan W, Link VM, Cobo I, Schlachetzki JCM, Hamakubo T, Jepsen K, Sakai J, Downes M, Evans RM, Yeo GW, Kadonaga JT, Manolagas SC, Rosenfeld MG, Glass CK. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Mol Cell 2023; 83:3421-3437.e11. [PMID: 37751740 PMCID: PMC10591845 DOI: 10.1016/j.molcel.2023.08.029] [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: 04/03/2023] [Revised: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the NCoR/HDAC3 co-repressor complex to a co-activator of AP-1 and NF-κB target genes that are required for mouse osteoclast differentiation. Accordingly, the dominant function of NCoR/HDAC3 complexes in response to RANK signaling is to activate, rather than repress, gene expression. Mechanistically, RANK signaling promotes RNA-dependent interaction of the transcriptional co-activator PGC1β with the NCoR/HDAC3 complex, resulting in the activation of PGC1β and inhibition of HDAC3 activity for acetylated histone H3. Non-coding RNAs Dancr and Rnu12, which are associated with altered human bone homeostasis, promote NCoR/HDAC3 complex assembly and are necessary for RANKL-induced osteoclast differentiation in vitro. These findings may be prototypic for signal-dependent functions of NCoR in other biological contexts.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Almeida
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Filipa Ponte
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biochemistry and Molecular Biology, Nippon Medical School Hospital, Tokyo 113-8602, Japan
| | - Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Resende-Coelho
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stavros C Manolagas
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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12
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Gallegos DA, Minto M, Liu F, Hazlett MF, Aryana Yousefzadeh S, Bartelt LC, West AE. Cell-type specific transcriptional adaptations of nucleus accumbens interneurons to amphetamine. Mol Psychiatry 2023; 28:3414-3428. [PMID: 35173267 PMCID: PMC9378812 DOI: 10.1038/s41380-022-01466-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Parvalbumin-expressing (PV+) interneurons of the nucleus accumbens (NAc) play an essential role in the addictive-like behaviors induced by psychostimulant exposure. To identify molecular mechanisms of PV+ neuron plasticity, we isolated interneuron nuclei from the NAc of male and female mice following acute or repeated exposure to amphetamine (AMPH) and sequenced for cell type-specific RNA expression and chromatin accessibility. AMPH regulated the transcription of hundreds of genes in PV+ interneurons, and this program was largely distinct from that regulated in other NAc GABAergic neurons. Chromatin accessibility at enhancers predicted cell-type specific gene regulation, identifying transcriptional mechanisms of differential AMPH responses. Finally, we assessed expression of PV-enriched, AMPH-regulated genes in an Mecp2 mutant mouse strain that shows heightened behavioral sensitivity to psychostimulants to explore the functional importance of this transcriptional program. Together these data provide novel insight into the cell-type specific programs of transcriptional plasticity in NAc neurons that underlie addictive-like behaviors.
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Affiliation(s)
- David A Gallegos
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Melyssa Minto
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Fang Liu
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Mariah F Hazlett
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | | | - Luke C Bartelt
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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13
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Bejjani F, Evanno E, Mahfoud S, Tolza C, Zibara K, Piechaczyk M, Jariel-Encontre I. Multiple Fra-1-bound enhancers showing different molecular and functional features can cooperate to repress gene transcription. Cell Biosci 2023; 13:129. [PMID: 37464380 DOI: 10.1186/s13578-023-01077-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND How transcription factors (TFs) down-regulate gene expression remains ill-understood, especially when they bind to multiple enhancers contacting the same gene promoter. In particular, it is not known whether they exert similar or significantly different molecular effects at these enhancers. RESULTS To address this issue, we used a particularly well-suited study model consisting of the down-regulation of the TGFB2 gene by the TF Fra-1 in Fra-1-overexpressing cancer cells, as Fra-1 binds to multiple enhancers interacting with the TGFB2 promoter. We show that Fra-1 does not repress TGFB2 transcription via reducing RNA Pol II recruitment at the gene promoter but by decreasing the formation of its transcription-initiating form. This is associated with complex long-range chromatin interactions implicating multiple molecularly and functionally heterogeneous Fra-1-bound transcriptional enhancers distal to the TGFB2 transcriptional start site. In particular, the latter display differential requirements upon the presence and the activity of the lysine acetyltransferase p300/CBP. Furthermore, the final transcriptional output of the TGFB2 gene seems to depend on a balance between the positive and negative effects of Fra-1 at these enhancers. CONCLUSION Our work unveils complex molecular mechanisms underlying the repressive actions of Fra-1 on TGFB2 gene expression. This has consequences for our general understanding of the functioning of the ubiquitous transcriptional complex AP-1, of which Fra-1 is the most documented component for prooncogenic activities. In addition, it raises the general question of the heterogeneity of the molecular functions of TFs binding to different enhancers regulating the same gene.
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Affiliation(s)
- Fabienne Bejjani
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- DSST, ER045, PRASE, Lebanese University, Beirut, Lebanon
| | | | - Samantha Mahfoud
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- DSST, ER045, PRASE, Lebanese University, Beirut, Lebanon
| | - Claire Tolza
- IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Kazem Zibara
- DSST, ER045, PRASE, Lebanese University, Beirut, Lebanon
- Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | | | - Isabelle Jariel-Encontre
- IGMM, Univ Montpellier, CNRS, Montpellier, France.
- Institut de Recherche en Cancérologie de Montpellier, IRCM, INSERM U1194, ICM, Université de Montpellier, Montpellier, France.
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14
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Nguyen HT, Martin LJ. Regulation of Cdh2 by the AP-1 family transcription factor Junb in TM4 Sertoli cells. Biochem Biophys Res Commun 2023; 663:32-40. [PMID: 37119763 DOI: 10.1016/j.bbrc.2023.04.078] [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: 04/12/2023] [Revised: 04/15/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cadherins are transmembrane proteins that mediate cell-to-cell adhesion and various cellular processes. In Sertoli cells of the testis, Cdh2 contributes to the development of the testis and the formation of the blood-testis barrier, being essential for germ cells' protection. Analyses of chromatin accessibility and epigenetic marks in adult mouse testis have shown that the region from -800 to +900 bp respective to Cdh2 transcription start site (TSS) is likely the active regulatory region of this gene. In addition, the JASPAR 2022 matrix has predicted an AP-1 binding element at about -600 bp. Transcription factors of the activator protein 1 (AP-1) family have been implicated in the regulation of the expression of genes encoding cell-to-cell interaction proteins such as Gja1, Nectin2 and Cdh3. To test the potential regulation of Cdh2 by members of the AP-1 family, siRNAs were transfected into TM4 Sertoli cells. The knockdown of Junb led to a decrease in Cdh2 expression. ChIP-qPCR and luciferase reporter assays with site-directed mutagenesis confirmed the recruitment of Junb to several AP-1 regulatory elements in the proximal region of the Cdh2 promoter in TM4 cells. Further investigation with luciferase reporter assays showed that other AP-1 members can also activate the Cdh2 promoter albeit to a lesser extent than Junb. Taken together, these data suggest that in TM4 Sertoli cells, Junb is responsible for the regulation of Cdh2 expression which requires its recruitment to the proximal region of the Cdh2 promoter.
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Affiliation(s)
- Ha Tuyen Nguyen
- Biology Department, Université de Moncton, Moncton, New Brunswick, E1A 3E9, Canada
| | - Luc J Martin
- Biology Department, Université de Moncton, Moncton, New Brunswick, E1A 3E9, Canada.
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15
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Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell 2023; 83:373-392. [PMID: 36693380 PMCID: PMC9898153 DOI: 10.1016/j.molcel.2022.12.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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Affiliation(s)
- Seungsoo Kim
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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16
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Nguyen HT, Martin LJ. The transcription factors Junb and Fosl2 cooperate to regulate Cdh3 expression in 15P-1 Sertoli cells. Mol Reprod Dev 2023; 90:27-41. [PMID: 36468795 DOI: 10.1002/mrd.23656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/31/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
In Sertoli cells of the testis, cadherins (Cdh) are important cell-to-cell interaction proteins and contribute to the formation of the blood-testis barrier being essential for germ cells' protection. P-cadherin or Cdh3 is only expressed in Sertoli cells from embryonic to prepubertal development. Interestingly, the expression profile of Cdh3 correlates with that of activating protein-1 (AP-1) transcription factors during Sertoli cells development. To assess their potential implications in the regulation of Cdh3, different AP-1 transcription factors were overexpressed in 15P-1 Sertoli cells. We found that the overexpressions of Junb and Fosl2 activated Cdh3 promoter. ChIP-qPCR assay and luciferase reporter assay with 5' promoter deletions and site-directed mutagenesis confirmed the recruitment of Junb and Fosl2 to an AP-1 regulatory element at -47 bp in the proximal region of Cdh3 promoter in 15P-1 cells. These findings were further supported by histone modification markers and chromatin accessibility surrounding Cdh3 promoter in mouse testis. Moreover, the knockdowns of Junb and/or Fosl2 by siRNA decreased Cdh3 protein levels. Taken together, these data suggest that in 15P-1 Sertoli cells, the AP-1 family members Junb and Fosl2 are responsible for the regulation of Cdh3 expression, which requires the recruitment of both factors to the proximal region of the Cdh3 promoter.
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Affiliation(s)
- Ha T Nguyen
- Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Luc J Martin
- Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
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17
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Osman A, Lindén M, Österlund T, Vannas C, Andersson L, Escobar M, Ståhlberg A, Åman P. Identification of genomic binding sites and direct target genes for the transcription factor DDIT3/CHOP. Exp Cell Res 2023; 422:113418. [PMID: 36402425 DOI: 10.1016/j.yexcr.2022.113418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene in several types of cancer. DDIT3 was originally believed to act as a dominant-negative inhibitor by forming heterodimers with other bZIP transcription factors, preventing their DNA binding and transactivating functions. DDIT3 has, however, been reported to bind DNA and regulate target genes. Here, we employed ChIP sequencing combined with microarray-based expression analysis to identify direct binding motifs and target genes of DDIT3. The results reveal DDIT3 binding to motifs similar to other bZIP transcription factors, known to form heterodimers with DDIT3. Binding to a class III satellite DNA repeat sequence was also detected. DDIT3 acted as a DNA-binding transcription factor and bound mainly to the promotor region of regulated genes. ChIP sequencing analysis of histone H3K27 methylation and acetylation showed a strong overlap between H3K27-acetylated marks and DDIT3 binding. These results support a role for DDIT3 as a transcriptional regulator of H3K27ac-marked genes in transcriptionally active chromatin.
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Affiliation(s)
- Ayman Osman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Malin Lindén
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Christoffer Vannas
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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18
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Kijima Y, Wantong W, Igarashi Y, Yoshitake K, Asakawa S, Suzuki Y, Watabe S, Kinoshita S. Age-Associated Different Transcriptome Profiling in Zebrafish and Rats: an Insight into the Diversity of Vertebrate Aging. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:895-910. [PMID: 36063238 DOI: 10.1007/s10126-022-10153-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish can be attractive models to study senescence because of their unique aging characteristics. The lifespan of fish varies widely, and several species can live for over 200 years. Moreover, some fish show anti-aging features and indeterminate growth throughout their life. Therefore, exploring the aging mechanism in fish could provide new insights into vertebrate aging. To this end, we conducted RNA sequencing (RNA-seq) assays for various organs and growth stages of zebrafish and compared the data with previously published RNA-seq data of rats. Age-associated differentially expressed genes (DEGs) for all zebrafish tissue samples reveal the upregulation of circadian genes and downregulation of hmgb3a. On one hand, a comparative analysis of DEG profiles associated with aging between zebrafish and rats identifies upregulation of circadian genes and downregulation of collagen genes as conserved transcriptome changes. On the other hand, in zebrafish, upregulation of autophagy-related genes in muscles and AP-1 transcription factor genes in various tissues is observed, which may imply fish-specific anti-aging characteristics. Consistent with our knowledge of mammalian aging, DEG profiles related to tissue senescence are observed in rats. We also detect age-associated downregulation of muscle homeostasis and differentiation-related genes in zebrafish gills, indicating a fish-specific senescence phenotype. Our results indicate both common and different aging profiles between fish and mammals, which could be used for future translational research.
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Affiliation(s)
- Yusuke Kijima
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Wang Wantong
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
- Graduate School of Bioresources, Mie University, Mie, 514-8507, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, 272-8562, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan.
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19
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Kumar P, Soory A, Mustfa SA, Sarmah DT, Devvanshi H, Chatterjee S, Bossis G, Ratnaparkhi GS, Srikanth CV. Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signalling during Salmonella infection. J Cell Sci 2022; 135:276158. [PMID: 35904007 DOI: 10.1242/jcs.260096] [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: 04/06/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Post-translational modifications (PTMs), such as SUMOylation, are known to modulate fundamental processes of a cell. Infectious agents such as Salmonella Typhimurium (STm) that causes gastroenteritis, utilizes PTM mechanism SUMOylation to highjack host cell. STm suppresses host SUMO-pathway genes Ubc9 and PIAS1 to perturb SUMOylation for an efficient infection. In the present study, the regulation of SUMO-pathway genes during STm infection was investigated. A direct binding of c-Fos, a component of AP-1 (Activator Protein-1), to promoters of both UBC9 and PIAS1 was observed. Experimental perturbation of c-Fos led to changes in expression of both Ubc9 and PIAS1. STm infection of fibroblasts with SUMOylation deficient c-Fos (c-FOS-KOSUMO-def-FOS) resulted in uncontrolled activation of target genes, resulting in massive immune activation. Infection of c-FOS-KOSUMO-def-FOS cells favored STm replication, indicating misdirected immune mechanisms. Finally, chromatin Immuno-precipitation assays confirmed a context dependent differential binding and release of AP-1 to/from target genes due to its Phosphorylation and SUMOylation respectively. Overall, our data point towards existence of a bidirectional cross-talk between c-Fos and the SUMO pathway and highlighting its importance in AP-1 function relevant to STm infection and beyond.
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Affiliation(s)
- Pharvendra Kumar
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India.,Kalinga Institute of Industrial Technology, Bhubaneshwar, India
| | | | | | - Dipanka Tanu Sarmah
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Himadri Devvanshi
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Samrat Chatterjee
- Translational Health Science and Technology Institute, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), Univ Montpellier, CNRS, Montpellier, France
| | | | - C V Srikanth
- Regional Centre for Biotechnology, 3rd milestone Gurgaon Faridabad Expressway, Faridabad, India
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20
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Postmitotic differentiation of human monocytes requires cohesin-structured chromatin. Nat Commun 2022; 13:4301. [PMID: 35879286 PMCID: PMC9314343 DOI: 10.1038/s41467-022-31892-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Cohesin is a major structural component of mammalian genomes and is required to maintain loop structures. While acute depletion in short-term culture models suggests a limited importance of cohesin for steady-state transcriptional circuits, long-term studies are hampered by essential functions of cohesin during replication. Here, we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profile and compare epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome and detect numerous architectural changes, ranging from higher level compartments down to chromatin loops. Changes in loop structures correlate with cohesin-binding, as well as epigenetic and transcriptional changes during differentiation. Functional studies show that the siRNA-mediated depletion of cohesin (and to a lesser extent also CTCF) markedly disturbs loop structures and dysregulates genes and enhancers that are primarily regulated during normal MO differentiation. In addition, gene activation programs in cohesin-depleted MO-derived macrophages are disturbed. Our findings implicate an essential function of cohesin in controlling long-term, differentiation- and activation-associated gene expression programs. How chromatin structure and gene accessibility changes during monocyte differentiation is not clearly defined. Here the authors characterize the chromatin changes during macrophage or dendritic cell maturation from monocytes and the dependence of this upon cohesin and CTCF.
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21
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Tian GG, Hou C, Li J, Wu J. Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development. Clin Transl Med 2022; 12:e927. [PMID: 35730671 PMCID: PMC9214757 DOI: 10.1002/ctm2.927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND During meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three-dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood. METHODS The high-throughput chromosome conformation capture technique was used to probe the 3D structure of chromatin in mouse germ cells at each stage of FGSC development. RESULTS The global 3D genome was dramatically reorganized during FGSC development. In topologically associating domains, the chromatin structure was weakened in germinal vesicle stage oocytes and still present in meiosis I stage oocytes but had vanished in meiosis II oocytes. This switch between topologically associating domains was related to the biological process of FGSC development. Moreover, we constructed a landscape of chromosome X organization, which showed that the X chromosome occupied a smaller proportion of the active (A) compartment than the autosome during FGSC development. By comparing the high-order chromatin structure between female and male germline development, we found that 3D genome organization was remodelled by two different potential mechanisms during gamete development, in which interchromosomal interactions, compartments, and topologically associating domain were decreased during FGSC development but reorganized and recovered during spermatogenesis. Finally, we identified conserved chromatin structures between FGSC development and early embryonic development. CONCLUSIONS These results provide a valuable resource to characterize chromatin organization and for further studies of FGSC development.
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Affiliation(s)
- Geng G. Tian
- Renji HospitalKey Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education)Bio‐X InstitutesSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Changliang Hou
- Renji HospitalKey Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education)Bio‐X InstitutesSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Jing Li
- Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ji Wu
- Renji HospitalKey Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education)Bio‐X InstitutesSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of EducationNingxia Medical UniversityYinchuanChina
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22
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Feoktistov AV, Georgieva SG, Soshnikova NV. Role of the SWI/SNF Chromatin Remodeling Complex in Regulation of Inflammation Gene Expression. Mol Biol 2022. [DOI: 10.1134/s0026893322020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Blair L, Pattison MJ, Chakravarty P, Papoutsopoulou S, Bakiri L, Wagner EF, Smale S, Ley SC. TPL-2 Inhibits IFN-β Expression via an ERK1/2-TCF-FOS Axis in TLR4-Stimulated Macrophages. THE JOURNAL OF IMMUNOLOGY 2022; 208:941-954. [PMID: 35082159 PMCID: PMC9012084 DOI: 10.4049/jimmunol.2100213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 10/20/2021] [Indexed: 12/29/2022]
Abstract
TPL-2 activation of ERK1/2 regulates gene expression in TLR-stimulated macrophages. TPL-2 regulates transcription via ERK1/2 phosphorylation of ternary complex factors. TPL-2 inhibits Ifnb1 transcription via ternary complex factor–induced Fos mRNA expression.
TPL-2 kinase plays an important role in innate immunity, activating ERK1/2 MAPKs in myeloid cells following TLR stimulation. We investigated how TPL-2 controls transcription in TLR4-stimulated mouse macrophages. TPL-2 activation of ERK1/2 regulated expression of genes encoding transcription factors, cytokines, chemokines, and signaling regulators. Bioinformatics analysis of gene clusters most rapidly induced by TPL-2 suggested that their transcription was mediated by the ternary complex factor (TCF) and FOS transcription factor families. Consistently, TPL-2 induced ERK1/2 phosphorylation of the ELK1 TCF and the expression of TCF target genes. Furthermore, transcriptomic analysis of TCF-deficient macrophages demonstrated that TCFs mediate approximately half of the transcriptional output of TPL-2 signaling, partially via induced expression of secondary transcription factors. TPL-2 signaling and TCFs were required for maximal TLR4-induced FOS expression. Comparative analysis of the transcriptome of TLR4-stimulated Fos−/− macrophages indicated that TPL-2 regulated a significant fraction of genes by controlling FOS expression levels. A key function of this ERK1/2-TCF-FOS pathway was to mediate TPL-2 suppression of type I IFN signaling, which is essential for host resistance against intracellular bacterial infection.
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Affiliation(s)
- Louise Blair
- Immune Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael J Pattison
- Immune Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Probir Chakravarty
- Bioinformatics and Biostatistics Technology Platform, The Francis Crick Institute, London, United Kingdom
| | | | - Latifa Bakiri
- Laboratory of Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Erwin F Wagner
- Laboratory of Genes and Disease, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Laboratory of Genes and Disease, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Stephen Smale
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA; and
| | - Steven C Ley
- Immune Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
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24
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Shen Z, Li RZ, Prohaska TA, Hoeksema MA, Spann NJ, Tao J, Fonseca GJ, Le T, Stolze LK, Sakai M, Romanoski CE, Glass CK. Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs. eLife 2022; 11:e70878. [PMID: 35049498 PMCID: PMC8809895 DOI: 10.7554/elife.70878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 73 TFs in human K562 cells as determined by ChIP-seq (chromatin immunoprecipitation sequencing). We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 45 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. These analyses suggested that spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. To experimentally validate this prediction, we introduced synthetic spacing alterations between PU.1 and C/EBPβ binding sites at six endogenous genomic loci in a macrophage cell line. Remarkably, collaborative binding of PU.1 and C/EBPβ at these locations tolerated changes in spacing ranging from 5 bp increase to >30 bp decrease. Collectively, these findings have implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.
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Affiliation(s)
- Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, United States
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
| | - Thomas A Prohaska
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, United States
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Infection and Immunity, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Nathan J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
- Department of Medicine, McGill University, Montreal, Canada
| | - Thomas Le
- Division of Biological Sciences, University of California San Diego, La Jolla, United States
| | - Lindsey K Stolze
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, United States
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, United States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, United States
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, United States
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25
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Dichtl S, Sanin DE, Koss CK, Willenborg S, Petzold A, Tanzer MC, Dahl A, Kabat AM, Lindenthal L, Zeitler L, Satzinger S, Strasser A, Mann M, Roers A, Eming SA, El Kasmi KC, Pearce EJ, Murray PJ. Gene-selective transcription promotes the inhibition of tissue reparative macrophages by TNF. Life Sci Alliance 2022; 5:5/4/e202101315. [PMID: 35027468 PMCID: PMC8761491 DOI: 10.26508/lsa.202101315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/24/2022] Open
Abstract
Pro-inflammatory TNF is a highly gene-selective inhibitor of the gene expression program of tissue repair and wound healing macrophages. Anti-TNF therapies are a core anti-inflammatory approach for chronic diseases such as rheumatoid arthritis and Crohn’s Disease. Previously, we and others found that TNF blocks the emergence and function of alternative-activated or M2 macrophages involved in wound healing and tissue-reparative functions. Conceivably, anti-TNF drugs could mediate their protective effects in part by an altered balance of macrophage activity. To understand the mechanistic basis of how TNF regulates tissue-reparative macrophages, we used RNAseq, scRNAseq, ATACseq, time-resolved phospho-proteomics, gene-specific approaches, metabolic analysis, and signaling pathway deconvolution. We found that TNF controls tissue-reparative macrophage gene expression in a highly gene-specific way, dependent on JNK signaling via the type 1 TNF receptor on specific populations of alternative-activated macrophages. We further determined that JNK signaling has a profound and broad effect on activated macrophage gene expression. Our findings suggest that TNF’s anti-M2 effects evolved to specifically modulate components of tissue and reparative M2 macrophages and TNF is therefore a context-specific modulator of M2 macrophages rather than a pan-M2 inhibitor.
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Affiliation(s)
| | - David E Sanin
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Carolin K Koss
- Boehringer Ingelheim Pharma GmbH and Co KG, Biberach, Germany
| | | | - Andreas Petzold
- Deep Sequencing Group, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Maria C Tanzer
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Dahl
- Deep Sequencing Group, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Agnieszka M Kabat
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | | | - Leonie Zeitler
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Matthias Mann
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sabine A Eming
- Department of Dermatology, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | | | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,The Bloomberg∼Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Peter J Murray
- Max Planck Institute of Biochemistry, Martinsried, Germany
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26
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Nguyen HCB, Chao TN, Cohen NA, Mirza N. Persistent Inflammation and Nitric Oxide Dysregulation Are Transcriptomic Blueprints of Subglottic Stenosis. Front Immunol 2021; 12:748533. [PMID: 34987502 PMCID: PMC8720859 DOI: 10.3389/fimmu.2021.748533] [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: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
Subglottic stenosis (SGS) is a recurrent, obstructive, fibroinflammatory disease of the upper airway resulting in severe dyspnea, dysphonia, as well as other potentially fatal complications. Although aberrant inflammation and wound-healing are commonly associated with pathogenesis, the mechanism through which such processes occur and recur in affected patients remains poorly studied. Here we report that transcriptomic profiling of laryngotracheal regions from minimally-invasive mucosal swabs of SGS patients reveals a distinctively pro-inflammatory gene signature. Surprisingly, comparative genomics between SGS patients and mice with direct laryngotracheal injury suggest that SGS patients bear more resemblance to the acute than chronic phase of injury. Furthermore, functional and regulatory network analyses identify neutrophilic involvement through hyper-activation of NF-κB and its downstream inflammasome as a potential master regulator. Interestingly, nitric oxide synthesis was found to be downregulated in SGS patients compared to healthy controls. Thus, SGS represents a state of immunodeficiency whereby defective immune clearance triggers recurrent, long-lasting production of pro-inflammatory cytokines.
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Affiliation(s)
- Hoang C. B. Nguyen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Tiffany N. Chao
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA, United States
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA, United States
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA, United States
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA, United States
| | - Natasha Mirza
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA, United States
- Division of Otolaryngology, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA, United States
- *Correspondence: Natasha Mirza,
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27
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Li R, Li L, Xu Y, Yang J. Machine learning meets omics: applications and perspectives. Brief Bioinform 2021; 23:6425809. [PMID: 34791021 DOI: 10.1093/bib/bbab460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 02/07/2023] Open
Abstract
The innovation of biotechnologies has allowed the accumulation of omics data at an alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge from various omics data remains a daunting problem in bioinformatics. Better solutions often need some kind of more innovative methods for efficient handlings and effective results. Recent advancements in integrated analysis and computational modeling of multi-omics data helped address such needs in an increasingly harmonious manner. The development and application of machine learning have largely advanced our insights into biology and biomedicine and greatly promoted the development of therapeutic strategies, especially for precision medicine. Here, we propose a comprehensive survey and discussion on what happened, is happening and will happen when machine learning meets omics. Specifically, we describe how artificial intelligence can be applied to omics studies and review recent advancements at the interface between machine learning and the ever-widest range of omics including genomics, transcriptomics, proteomics, metabolomics, radiomics, as well as those at the single-cell resolution. We also discuss and provide a synthesis of ideas, new insights, current challenges and perspectives of machine learning in omics.
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Affiliation(s)
- Rufeng Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China
| | - Lixin Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China
| | - Yungang Xu
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an 710061, P. R. China
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28
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Adlanmerini M, Krusen BM, Nguyen HCB, Teng CW, Woodie LN, Tackenberg MC, Geisler CE, Gaisinsky J, Peed LC, Carpenter BJ, Hayes MR, Lazar MA. REV-ERB nuclear receptors in the suprachiasmatic nucleus control circadian period and restrict diet-induced obesity. SCIENCE ADVANCES 2021; 7:eabh2007. [PMID: 34705514 PMCID: PMC8550249 DOI: 10.1126/sciadv.abh2007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/07/2021] [Indexed: 05/28/2023]
Abstract
Circadian disruption, as occurs in shift work, is associated with metabolic diseases often attributed to a discordance between internal clocks and environmental timekeepers. REV-ERB nuclear receptors are key components of the molecular clock, but their specific role in the SCN master clock is unknown. We report here that mice lacking circadian REV-ERB nuclear receptors in the SCN maintain free-running locomotor and metabolic rhythms, but these rhythms are notably shortened by 3 hours. When housed under a 24-hour light:dark cycle and fed an obesogenic diet, these mice gained excess weight and accrued more liver fat than controls. These metabolic disturbances were corrected by matching environmental lighting to the shortened endogenous 21-hour clock period, which decreased food consumption. Thus, SCN REV-ERBs are not required for rhythmicity but determine the free-running period length. Moreover, these results support the concept that dissonance between environmental conditions and endogenous time periods causes metabolic disruption.
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Affiliation(s)
- Marine Adlanmerini
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brianna M. Krusen
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hoang C. B. Nguyen
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Clare W. Teng
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lauren N. Woodie
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael C. Tackenberg
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Caroline E. Geisler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jane Gaisinsky
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lindsey C. Peed
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bryce J. Carpenter
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew R. Hayes
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A. Lazar
- Institute for Diabetes, Obesity, and Metabolism and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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29
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Troutman TD, Kofman E, Glass CK. Exploiting dynamic enhancer landscapes to decode macrophage and microglia phenotypes in health and disease. Mol Cell 2021; 81:3888-3903. [PMID: 34464593 PMCID: PMC8500948 DOI: 10.1016/j.molcel.2021.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/19/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022]
Abstract
The development and functional potential of metazoan cells is dependent on combinatorial roles of transcriptional enhancers and promoters. Macrophages provide exceptionally powerful model systems for investigation of mechanisms underlying the activation of cell-specific enhancers that drive transitions in cell fate and cell state. Here, we review recent advances that have expanded appreciation of the diversity of macrophage phenotypes in health and disease, emphasizing studies of liver, adipose tissue, and brain macrophages as paradigms for other tissue macrophages and cell types. Studies of normal tissue-resident macrophages and macrophages associated with cirrhosis, obese adipose tissue, and neurodegenerative disease illustrate the major roles of tissue environment in remodeling enhancer landscapes to specify the development and functions of distinct macrophage phenotypes. We discuss the utility of quantitative analysis of environment-dependent changes in enhancer activity states as an approach to discovery of regulatory transcription factors and upstream signaling pathways.
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Affiliation(s)
- Ty D Troutman
- Department of Medicine, University of California, San Diego, San Diego, CA, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Christopher K Glass
- Department of Medicine, University of California, San Diego, San Diego, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA.
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30
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Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS OMEGA 2021; 6:24834-24847. [PMID: 34604665 PMCID: PMC8482465 DOI: 10.1021/acsomega.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among the latter, FOSL1 and FOSL2 modulate the effector functions of Th17 cells. However, the molecular mechanisms underlying these effects are unclear, owing to the poorly characterized protein interaction networks of FOSL factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a significant fraction of these interactors to be associated with RNA-binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17 fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL proteins that potentially govern Th17 cell differentiation and associated pathologies.
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Affiliation(s)
- Ankitha Shetty
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Santosh D. Bhosale
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- Protein
Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Subhash Kumar Tripathi
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
| | - Tanja Buchacher
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Rahul Biradar
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Riitta Lahesmaa
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
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31
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Dahlet T, Truss M, Frede U, Al Adhami H, Bardet AF, Dumas M, Vallet J, Chicher J, Hammann P, Kottnik S, Hansen P, Luz U, Alvarez G, Auclair G, Hecht J, Robinson PN, Hagemeier C, Weber M. E2F6 initiates stable epigenetic silencing of germline genes during embryonic development. Nat Commun 2021; 12:3582. [PMID: 34117224 PMCID: PMC8195999 DOI: 10.1038/s41467-021-23596-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development. DNA methylation targets CpG island promoters of germline genes to repress their expression in mouse somatic cells. Here the authors show that a transcription factor E2F6 is required to target CpG island DNA methylation and epigenetic silencing to germline genes during early mouse development.
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Affiliation(s)
- Thomas Dahlet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Matthias Truss
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ute Frede
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Anaïs F Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Sarah Kottnik
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Hansen
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Uschi Luz
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gonzalo Alvarez
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ghislain Auclair
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Jochen Hecht
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Centre for Genomic Regulation, Barcelona, Spain
| | - Peter N Robinson
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christian Hagemeier
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France.
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32
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Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. Circ Res 2021; 129:240-258. [PMID: 34024118 PMCID: PMC8260472 DOI: 10.1161/circresaha.121.318971] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Genome-wide association studies have identified hundreds of loci associated with coronary artery disease (CAD). Many of these loci are enriched in cisregulatory elements but not linked to cardiometabolic risk factors nor to candidate causal genes, complicating their functional interpretation.
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Affiliation(s)
- Tiit Örd
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Kadri Õunap
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Lindsey K. Stolze
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona, Tucson, AZ (L.K.S., C.E.R.)
| | - Redouane Aherrahrou
- Center for Public Health Genomics (R.A., M.C.), University of Virginia, Charlottesville
| | - Valtteri Nurminen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Anu Toropainen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Ilakya Selvarajan
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Finland (T.L.)
| | - Einari Aavik
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
| | - Mete Civelek
- Center for Public Health Genomics (R.A., M.C.), University of Virginia, Charlottesville
- Department of Biomedical Engineering (M.C.), University of Virginia, Charlottesville
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, The College of Medicine, The University of Arizona, Tucson, AZ (L.K.S., C.E.R.)
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio (T.Ö., K.Õ., V.N., A.T., I.S., E.A., S.Y.-H., M.U.K.)
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33
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Zong D, Huang B, Li Y, Lu Y, Xiang N, Guo C, Liu Q, Sha Q, Du P, Yu Q, Zhang W, Cai P, Sun Y, Tao J, Li X, Cai S, Qu K. Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis. BMC Biol 2021; 19:79. [PMID: 33863328 PMCID: PMC8050920 DOI: 10.1186/s12915-021-01011-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/24/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease that involves a variety of cell types. However, how the epigenetic dysregulations of peripheral immune cells contribute to the pathogenesis of RA still remains largely unclear. RESULTS Here, we analysed the genome-wide active DNA regulatory elements of four major immune cells, namely monocytes, B cells, CD4+ T cells and CD8+ T cells, in peripheral blood of RA patients, osteoarthritis (OA) patients and healthy donors using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq). We found a strong RA-associated chromatin dysregulation signature in monocytes, but no other examined cell types. Moreover, we found that serum C-reactive protein (CRP) can induce the RA-associated chromatin dysregulation in monocytes via in vitro experiments. And the extent of this dysregulation was regulated through the transcription factor FRA2. CONCLUSIONS Together, our study revealed a CRP-induced pathogenic chromatin dysregulation signature in monocytes from RA patients and predicted the responsible signalling pathway as potential therapeutic targets for the disease.
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Affiliation(s)
- Dandan Zong
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Beibei Huang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Young Li
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China.
| | - Yichen Lu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Nan Xiang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Chuang Guo
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Qian Liu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Qing Sha
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengcheng Du
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Qiaoni Yu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Wen Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengfei Cai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Yanping Sun
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Jinhui Tao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Xiaomei Li
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China.
| | - Shanbao Cai
- Department of Orthopaedics and Bone Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230021, China.
| | - Kun Qu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China. .,CAS Center for Excellence in Molecular Cell Sciences, the CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, 230027, Anhui, China. .,School of Data Science, University of Science and Technology of China, Hefei, 230027, China.
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34
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Shen Z, Hoeksema MA, Ouyang Z, Benner C, Glass CK. MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. Bioinformatics 2021; 36:i84-i92. [PMID: 32657363 PMCID: PMC7355228 DOI: 10.1093/bioinformatics/btaa476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which motifs are prone to impact transcriptional regulation if mutated. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. RESULTS We present MAGGIE (Motif Alteration Genome-wide to Globally Investigate Elements), a novel method for identifying motifs mediating TF binding and function. By leveraging measurements from diverse genotypes, MAGGIE uses a statistical approach to link mutations of a motif to changes of an epigenomic feature without assuming a linear relationship. We benchmark MAGGIE across various applications using both simulated and biological datasets and demonstrate its improvement in sensitivity and specificity compared with the state-of-the-art motif analysis approaches. We use MAGGIE to gain novel insights into the divergent functions of distinct NF-κB factors in pro-inflammatory macrophages, revealing the association of p65-p50 co-binding with transcriptional activation and the association of p50 binding lacking p65 with transcriptional repression. AVAILABILITY AND IMPLEMENTATION The Python package for MAGGIE is freely available at https://github.com/zeyang-shen/maggie. The accession number for the NF-κB ChIP-seq data generated for this study is Gene Expression Omnibus: GSE144070. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine.,Department of Bioengineering, Jacobs School of Engineering
| | | | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, School of Medicine
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine.,Department of Medicine, School of Medicine, University of California, San Diego, CA 92093, USA
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35
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Seo J, Koçak DD, Bartelt LC, Williams CA, Barrera A, Gersbach CA, Reddy TE. AP-1 subunits converge promiscuously at enhancers to potentiate transcription. Genome Res 2021; 31:538-550. [PMID: 33674350 PMCID: PMC8015846 DOI: 10.1101/gr.267898.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022]
Abstract
The AP-1 transcription factor (TF) dimer contributes to many biological processes and environmental responses. AP-1 can be composed of many interchangeable subunits. Unambiguously determining the binding locations of these subunits in the human genome is challenging because of variable antibody specificity and affinity. Here, we definitively establish the genome-wide binding patterns of five AP-1 subunits by using CRISPR to introduce a common antibody tag on each subunit. We find limited evidence for strong dimerization preferences between subunits at steady state and find that, under a stimulus, dimerization patterns reflect changes in the transcriptome. Further, our analysis suggests that canonical AP-1 motifs indiscriminately recruit all AP-1 subunits to genomic sites, which we term AP-1 hotspots. We find that AP-1 hotspots are predictive of cell type–specific gene expression and of genomic responses to glucocorticoid signaling (more so than super-enhancers) and are significantly enriched in disease-associated genetic variants. Together, these results support a model where promiscuous binding of many AP-1 subunits to the same genomic location play a key role in regulating cell type–specific gene expression and environmental responses.
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Affiliation(s)
- Jungkyun Seo
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - D Dewran Koçak
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Courtney A Williams
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Alejandro Barrera
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
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36
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Kozyrev N, Albers S, Yang J, Prado VF, Prado MAM, Fonseca GJ, Rylett RJ, Dekaban GA. Infiltrating Hematogenous Macrophages Aggregate Around β-Amyloid Plaques in an Age- and Sex-Dependent Manner in a Mouse Model of Alzheimer Disease. J Neuropathol Exp Neurol 2021; 79:1147-1162. [PMID: 33011810 DOI: 10.1093/jnen/nlaa093] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
β-Amyloid (Aβ) plaques can trigger chronic inflammation in the cellular environment that recruits infiltrating macrophages during the course of Alzheimer disease (AD). Activated macrophages release pro-inflammatory cytokines that increase neurotoxicity associated with AD. A major impediment to investigating neuroinflammation involving macrophage activity is the inability to discriminate resident microglial macrophages (mMϕ) from hematogenous macrophages (hMϕ), as they are morphologically and phenotypically similar when activated. To distinguish between mMϕ and hMϕ and to determine their respective roles in chronic inflammation associated with the progression of amyloidosis, we used lys-EGFP-ki transgenic mice that express enhanced green fluorescent protein in hMϕ, but not in mMϕ. These mice were crossed with 5XFAD mice. The offspring demonstrated robust AD pathology and enabled visual discrimination of mMϕ from hMϕ. Mutant mice demonstrated robust increases in Aβ1-42, area of Aβ plaques, gliosis and deficits in spatial learning by age 5 months. The time-course of Aβ accumulation, paralleled by the accumulation of hMϕ around Aβ plaques, was more robust in female compared with male mice and preceded behavioral changes. Thus, the accumulation of infiltrating hMϕ around Aβ plaques was age- and sex-dependent and preceded cognitive impairment.
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Affiliation(s)
- Natalie Kozyrev
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario
| | - Shawn Albers
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario.,Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
| | - Jennifer Yang
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Vania F Prado
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario.,Department of Physiology and Pharmacology, Western University, London, Ontario, Canada.,Department of Anatomy & Cell Biology (VFP, MAMP), Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Marco A M Prado
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario.,Department of Physiology and Pharmacology, Western University, London, Ontario, Canada.,Department of Anatomy & Cell Biology (VFP, MAMP), Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Gregory J Fonseca
- Division of Experimental Medicine, Department of Medicine, McGill University, Canada
| | - R Jane Rylett
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario.,Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
| | - Gregory A Dekaban
- Molecular Medicine Research Laboratories, Robarts Research Institute, Western University, London, Ontario.,Department of Microbiology and Immunology, Western University, London, Ontario, Canada
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37
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MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen. PLoS Genet 2021; 17:e1008540. [PMID: 33513133 PMCID: PMC7875385 DOI: 10.1371/journal.pgen.1008540] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/10/2021] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Androgen deprivation therapy (ADT) is a mainstay of prostate cancer treatment, given the dependence of prostate cells on androgen and the androgen receptor (AR). However, tumors become ADT-resistant, and there is a need to understand the mechanism. One possible mechanism is the upregulation of AR co-regulators, although only a handful have been definitively linked to disease. We previously identified the Mediator subunit MED19 as an AR co-regulator, and reported that MED19 depletion inhibits AR transcriptional activity and growth of androgen-insensitive LNCaP-abl cells. Therefore, we proposed that MED19 upregulation would promote AR activity and drive androgen-independent growth. Here, we show that stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation. To delineate the mechanism, we determined the MED19 and AR transcriptomes and cistromes in control and MED19-overexpressing LNCaP cells. We also examined genome-wide H3K27 acetylation. MED19 overexpression selectively alters AR occupancy, H3K27 acetylation, and gene expression. Under conditions of androgen deprivation, genes regulated by MED19 correspond to genes regulated by ELK1, a transcription factor that binds the AR N-terminus to induce select AR target gene expression and proliferation, and genomic sites occupied by MED19 and AR are enriched for motifs associated with ELK1. Strikingly, MED19 upregulates expression of monoamine oxidase A (MAOA), a factor that promotes prostate cancer growth. MAOA depletion reduces androgen-independent growth. MED19 and AR occupy the MAOA promoter, with MED19 overexpression enhancing AR occupancy and H3K27 acetylation. Furthermore, MED19 overexpression increases ELK1 occupancy at the MAOA promoter, and ELK1 depletion reduces MAOA expression and androgen-independent growth. This suggests that MED19 cooperates with ELK1 to regulate AR occupancy and H3K27 acetylation at MAOA, upregulating its expression and driving androgen independence in prostate cancer cells. This study provides important insight into the mechanisms of prostate cancer cell growth under low androgen, and underscores the importance of the MED19-MAOA axis in this process.
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38
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The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages. Mol Cell 2021; 81:953-968.e9. [PMID: 33503407 DOI: 10.1016/j.molcel.2020.12.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/20/2020] [Accepted: 12/24/2020] [Indexed: 01/08/2023]
Abstract
While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the involvement of corepressors is not. Using inflammatory macrophage activation as a model, we investigate here a corepressor complex containing GPS2 and SMRT both genome-wide and at the Ccl2 locus, encoding the chemokine CCL2 (MCP-1). We report that corepressors co-occupy candidate enhancers along with the coactivators CBP (H3K27 acetylase) and MED1 (mediator) but act antagonistically by repressing eRNA transcription-coupled H3K27 acetylation. Genome editing, transcriptional interference, and cistrome analysis reveals that apparently related enhancer and silencer elements control Ccl2 transcription in opposite ways. 4C-seq indicates that corepressor depletion or inflammatory signaling functions mechanistically similarly to trigger enhancer activation. In ob/ob mice, adipose tissue macrophage-selective depletion of the Ccl2 enhancer-transcribed eRNA reduces metaflammation. Thus, the identified corepressor-eRNA-chemokine pathway operates in vivo and suggests therapeutic opportunities by targeting eRNAs in immuno-metabolic diseases.
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39
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Trizzino M, Zucco A, Deliard S, Wang F, Barbieri E, Veglia F, Gabrilovich D, Gardini A. EGR1 is a gatekeeper of inflammatory enhancers in human macrophages. SCIENCE ADVANCES 2021; 7:7/3/eaaz8836. [PMID: 33523892 PMCID: PMC7806227 DOI: 10.1126/sciadv.aaz8836] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/20/2020] [Indexed: 05/20/2023]
Abstract
Monocytes and monocyte-derived macrophages originate through a multistep differentiation process. First, hematopoietic stem cells generate lineage-restricted progenitors that eventually develop into peripheral, postmitotic monocytes. Second, blood-circulating monocytes undergo differentiation into macrophages, which are specialized phagocytic cells capable of tissue infiltration. While monocytes mediate some level of inflammation and cell toxicity, macrophages boast the widest set of defense mechanisms against pathogens and elicit robust inflammatory responses. Here, we analyze the molecular determinants of monocytic and macrophagic commitment by profiling the EGR1 transcription factor. EGR1 is essential for monopoiesis and binds enhancers that regulate monocytic developmental genes such as CSF1R However, differentiating macrophages present a very different EGR1 binding pattern. We identify novel binding sites of EGR1 at a large set of inflammatory enhancers, even in the absence of its binding motif. We show that EGR1 repressive activity results in suppression of inflammatory genes and is mediated by the NuRD corepressor complex.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Avery Zucco
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Fang Wang
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Filippo Veglia
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
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40
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Dichotomous engagement of HDAC3 activity governs inflammatory responses. Nature 2020; 584:286-290. [PMID: 32760002 PMCID: PMC7725280 DOI: 10.1038/s41586-020-2576-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
Abstract
The histone deacetylases (HDACs) are a superfamily of chromatin-modifying enzymes that silence transcription through the modification of histones. Among them, HDAC3 is unique in that interaction with nuclear receptor corepressors 1 and 2 (NCoR1/2) is required to engage its catalytic activity1-3. However, global loss of HDAC3 also results in the repression of transcription, the mechanism of which is currently unclear4-8. Here we report that, during the activation of macrophages by lipopolysaccharides, HDAC3 is recruited to activating transcription factor 2 (ATF2)-bound sites without NCoR1/2 and activates the expression of inflammatory genes through a non-canonical mechanism. By contrast, the deacetylase activity of HDAC3 is selectively engaged at ATF3-bound sites that suppress Toll-like receptor signalling. Loss of HDAC3 in macrophages safeguards mice from lethal exposure to lipopolysaccharides, but this protection is not conferred upon genetic or pharmacological abolition of the catalytic activity of HDAC3. Our findings show that HDAC3 is a dichotomous transcriptional activator and repressor, with a non-canonical deacetylase-independent function that is vital for the innate immune system.
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41
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Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas. Nat Commun 2020; 11:1019. [PMID: 32094355 PMCID: PMC7040020 DOI: 10.1038/s41467-020-14701-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
Uterine leiomyomas (fibroids) are a major source of gynecologic morbidity in reproductive age women and are characterized by the excessive deposition of a disorganized extracellular matrix, resulting in rigid benign tumors. Although down regulation of the transcription factor AP-1 is highly prevalent in leiomyomas, the functional consequence of AP-1 loss on gene transcription in uterine fibroids remains poorly understood. Using high-resolution ChIP-sequencing, promoter capture Hi-C, and RNA-sequencing of matched normal and leiomyoma tissues, here we show that modified enhancer architecture is a major driver of transcriptional dysregulation in MED12 mutant uterine leiomyomas. Furthermore, modifications in enhancer architecture are driven by the depletion of AP-1 occupancy on chromatin. Silencing of AP-1 subunits in primary myometrium cells leads to transcriptional dysregulation of extracellular matrix associated genes and partly recapitulates transcriptional and epigenetic changes observed in leiomyomas. These findings establish AP-1 driven aberrant enhancer regulation as an important mechanism of leiomyoma disease pathogenesis.
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42
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Gatchalian J, Liao J, Maxwell MB, Hargreaves DC. Control of Stimulus-Dependent Responses in Macrophages by SWI/SNF Chromatin Remodeling Complexes. Trends Immunol 2020; 41:126-140. [PMID: 31928914 PMCID: PMC6995420 DOI: 10.1016/j.it.2019.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic regulation plays an important role in controlling the activation, timing, and resolution of innate immune responses in macrophages. Previously, SWI/SNF chromatin remodeling was found to define the kinetics and selectivity of gene activation in response to microbial ligands; however, these studies do not reflect a comprehensive understanding of SWI/SNF complex regulation. In 2018, a new variant of the SWI/SNF complex was identified with unknown function in inflammatory gene regulation. Here, we summarize the biochemical and genomic properties of SWI/SNF complex variants and the potential for increased regulatory control of innate immune transcriptional programs in light of such biochemical diversity. Finally, we review the development of SWI/SNF complex chemical inhibitors and degraders that could be used to modulate immune responses.
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Affiliation(s)
- Jovylyn Gatchalian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingwen Liao
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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43
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Czimmerer Z, Halasz L, Nagy L. Unorthodox Transcriptional Mechanisms of Lipid-Sensing Nuclear Receptors in Macrophages: Are We Opening a New Chapter? Front Endocrinol (Lausanne) 2020; 11:609099. [PMID: 33362723 PMCID: PMC7758493 DOI: 10.3389/fendo.2020.609099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022] Open
Abstract
Work over the past 30 years has shown that lipid-activated nuclear receptors form a bridge between metabolism and immunity integrating metabolic and inflammatory signaling in innate immune cells. Ligand-induced direct transcriptional activation and protein-protein interaction-based transrepression were identified as the most common mechanisms of liganded-nuclear receptor-mediated transcriptional regulation. However, the integration of different next-generation sequencing-based methodologies including chromatin immunoprecipitation followed by sequencing and global run-on sequencing allowed to investigate the DNA binding and ligand responsiveness of nuclear receptors at the whole-genome level. Surprisingly, these studies have raised the notion that a major portion of lipid-sensing nuclear receptor cistromes are not necessarily responsive to ligand activation. Although the biological role of the ligand insensitive portion of nuclear receptor cistromes is largely unknown, recent findings indicate that they may play roles in the organization of chromatin structure, in the regulation of transcriptional memory, and the epigenomic modification of responsiveness to other microenvironmental signals in macrophages. In this review, we will provide an overview and discuss recent advances of our understanding of lipid-activated nuclear receptor-mediated non-classical or unorthodox actions in macrophages.
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Affiliation(s)
- Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laszlo Halasz
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Departments of Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, United States
- *Correspondence: Laszlo Nagy,
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