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Kim J, Martinez E, Qiu J, Zhouli Ni J, Kwan KY. Chromatin remodeling protein CHD4 regulates axon guidance of spiral ganglion neurons in developing cochlea. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578202. [PMID: 38352369 PMCID: PMC10862897 DOI: 10.1101/2024.01.31.578202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The chromodomain helicase binding protein 4 (CHD4) is an ATP-dependent chromatin remodeler. De-novo pathogenic variants of CHD4 cause Sifrim-Hitz-Weiss syndrome (SIHIWES). Patients with SIHIWES show delayed development, intellectual disability, facial dysmorphism, and hearing loss. Many cochlear cell types, including spiral ganglion neurons (SGNs), express CHD4. SGNs are the primary afferent neurons that convey sound information from the cochlea, but the function of CHD4 in SGNs is unknown. We employed the Neurog1(Ngn1) CreERT2 Chd4 conditional knockout animals to delete Chd4 in SGNs. SGNs are classified as type I and type II neurons. SGNs lacking CHD4 showed abnormal fasciculation of type I neurons along with improper pathfinding of type II fibers. CHD4 binding to chromatin from immortalized multipotent otic progenitor-derived neurons was used to identify candidate target genes in SGNs. Gene ontology analysis of CHD4 target genes revealed cellular processes involved in axon guidance, axonal fasciculation, and ephrin receptor signaling pathway. We validated increased Epha4 transcripts in SGNs from Chd4 conditional knockout cochleae. The results suggest that CHD4 attenuates the transcription of axon guidance genes to form the stereotypic pattern of SGN peripheral projections. The results implicate epigenetic changes in circuit wiring by modulating axon guidance molecule expression and provide insights into neurodevelopmental diseases.
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Affiliation(s)
- Jihyun Kim
- Keck Center for Collaborative Neuroscience and Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Edward Martinez
- Keck Center for Collaborative Neuroscience and Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Jingyun Qiu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Kelvin Y. Kwan
- Keck Center for Collaborative Neuroscience and Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
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Larrigan S, Joshi SV, Mattar P. Divergent phenotypes in constitutive versus conditional mutant mouse models of Sifrim-Hitz-Weiss syndrome. Hum Mol Genet 2023; 32:3361-3373. [PMID: 37738575 PMCID: PMC10695680 DOI: 10.1093/hmg/ddad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
Chromatin remodellers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), however, their functions during brain development are not fully understood. Here, we focused on Sifrim-Hitz-Weiss Syndrome (SIHIWES)-an intellectual disability disorder caused by mutations in the CHD4 chromodomain helicase gene. We utilized mouse genetics to excise the Chd4 ATPase/helicase domain-either constitutively, or conditionally in the developing telencephalon. Conditional heterozygotes exhibited no change in cortical size and cellular composition, and had only subtle behavioral phenotypes. Telencephalon-specific conditional knockouts had marked reductions in cortical growth, reduced numbers of upper-layer neurons, and exhibited alterations in anxiety and repetitive behaviors. Despite the fact that whole-body heterozygotes exhibited comparable growth defects, they were unaffected in these behaviors, but instead exhibited female-specific alterations in learning and memory. These data reveal unexpected phenotypic divergence arising from differences in the spatiotemporal deployment of loss-of-function manipulations, underscoring the importance of context in chromatin remodeller function during neurodevelopment.
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Affiliation(s)
- Sarah Larrigan
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shrilaxmi V Joshi
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pierre Mattar
- Ottawa Hospital Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell 2023; 186:5269-5289.e22. [PMID: 37995656 PMCID: PMC10895928 DOI: 10.1016/j.cell.2023.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.
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Affiliation(s)
- Yeguang Hu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Daniela Salgado Figueroa
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Bioinformatics and Systems Biology Program, La Jolla, CA, USA
| | - Zhihong Zhang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Margaret Veselits
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Sourya Bhattacharyya
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Mariko Kashiwagi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marcus R Clark
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Bruce A Morgan
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ferhat Ay
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Bioinformatics and Systems Biology Program, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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Laureano A, Kim J, Martinez E, Kwan KY. Chromodomain helicase DNA binding protein 4 in cell fate decisions. Hear Res 2023; 436:108813. [PMID: 37329862 PMCID: PMC10463912 DOI: 10.1016/j.heares.2023.108813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
Loss of spiral ganglion neurons (SGNs) in the cochlea causes hearing loss. Understanding the mechanisms of cell fate transition accelerates efforts that employ directed differentiation and lineage conversion to repopulate lost SGNs. Proposed strategies to regenerate SGNs rely on altering cell fate by activating transcriptional regulatory networks, but repressing networks for alternative cell lineages is also essential. Epigenomic changes during cell fate transitions suggest that CHD4 represses gene expression by altering the chromatin status. Despite limited direct investigations, human genetic studies implicate CHD4 function in the inner ear. The possibility of CHD4 in suppressing alternative cell fates to promote inner ear regeneration is discussed.
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Affiliation(s)
- Alejandra Laureano
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jihyun Kim
- Department of Cell Biology & Neuroscience, Rutgers University, Nelson Labs D250 604 Allison Rd., Piscataway, NJ 08854, USA; Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Edward Martinez
- Department of Cell Biology & Neuroscience, Rutgers University, Nelson Labs D250 604 Allison Rd., Piscataway, NJ 08854, USA; Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Kelvin Y Kwan
- Department of Cell Biology & Neuroscience, Rutgers University, Nelson Labs D250 604 Allison Rd., Piscataway, NJ 08854, USA; Stem Cell Research Center and Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854, USA.
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Shi W, Scialdone AP, Emerson JI, Mei L, Wasson LK, Davies HA, Seidman CE, Seidman JG, Cook JG, Conlon FL. Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1. Circ Res 2023; 133:48-67. [PMID: 37254794 PMCID: PMC10284140 DOI: 10.1161/circresaha.122.322223] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is a prevalent cardiomyopathy associated with excessive trabeculation and thin compact myocardium. Patients with LVNC are vulnerable to cardiac dysfunction and at high risk of sudden death. Although sporadic and inherited mutations in cardiac genes are implicated in LVNC, understanding of the mechanisms responsible for human LVNC is limited. METHODS We screened the complete exome sequence database of the Pediatrics Cardiac Genomics Consortium and identified a cohort with a de novo CHD4 (chromodomain helicase DNA-binding protein 4) proband, CHD4M202I, with congenital heart defects. We engineered a humanized mouse model of CHD4M202I (mouse CHD4M195I). Histological analysis, immunohistochemistry, flow cytometry, transmission electron microscopy, and echocardiography were used to analyze cardiac anatomy and function. Ex vivo culture, immunopurification coupled with mass spectrometry, transcriptional profiling, and chromatin immunoprecipitation were performed to deduce the mechanism of CHD4M195I-mediated ventricular wall defects. RESULTS CHD4M195I/M195I mice developed biventricular hypertrabeculation and noncompaction and died at birth. Proliferation of cardiomyocytes was significantly increased in CHD4M195I hearts, and the excessive trabeculation was associated with accumulation of ECM (extracellular matrix) proteins and a reduction of ADAMTS1 (ADAM metallopeptidase with thrombospondin type 1 motif 1), an ECM protease. We rescued the hyperproliferation and hypertrabeculation defects in CHD4M195I hearts by administration of ADAMTS1. Mechanistically, the CHD4M195I protein showed augmented affinity to endocardial BRG1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4). This enhanced affinity resulted in the failure of derepression of Adamts1 transcription such that ADAMTS1-mediated trabeculation termination was impaired. CONCLUSIONS Our study reveals how a single mutation in the chromatin remodeler CHD4, in mice or humans, modulates ventricular chamber maturation and that cardiac defects associated with the missense mutation CHD4M195I can be attenuated by the administration of ADAMTS1.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Angel P. Scialdone
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - James I. Emerson
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Liu Mei
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
| | - Haley A. Davies
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Jonathan G. Seidman
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
| | - Jeanette G. Cook
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
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Wang J, Zhong F, Li J, Yue H, Li W, Lu X. The epigenetic factor CHD4 contributes to metastasis by regulating the EZH2/β-catenin axis and acts as a therapeutic target in ovarian cancer. J Transl Med 2023; 21:38. [PMID: 36681835 PMCID: PMC9862813 DOI: 10.1186/s12967-022-03854-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/26/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The overall survival rate of patients with advanced ovarian cancer (OC) has remained static for several decades. Advanced ovarian cancer is known for its poor prognosis due to extensive metastasis. Epigenetic alterations contribute to tumour progression and therefore are of interest for potential therapeutic strategies. METHODS Following our previous study, we identified that CHD4, a chromatin remodelling factor, plays a strong role in ovarian cancer cell metastasis. We investigated the clinical significance of CHD4 through TCGA and GEO database analyses and explored the effect of CHD4 expression modulation and romidepsin treatment on the biological behaviour of ovarian cancer through CCK-8 and transwell assays. Bioluminescence imaging of tumours in xenografted mice was applied to determine the therapeutic effect of romidepsin. GSEA and western blotting were used to screen the regulatory mechanism of CHD4. RESULTS In ovarian cancer patient specimens, high CHD4 expression was associated with a poor prognosis. Loss of function of CHD4 in ovarian cancer cells induced suppression of migration and invasion. Mechanistically, CHD4 knockdown suppressed the expression of EZH2 and the nuclear accumulation of β-catenin. CHD4 also suppressed the metastasis of ovarian cancer cells and prevented disease progression in a mouse model. To inhibit the functions of CHD4 that are mediated by histone deacetylase, we evaluated the effect of the HDAC1/2 selective inhibitor romidepsin. Our findings indicated that treatment with romidepsin suppressed the progression of metastases in vitro and in vivo. CONCLUSIONS Collectively, our results uncovered an oncogenic function of CHD4 in ovarian cancer and provide a rationale for clinical trials of romidepsin in ovarian cancer patients.
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Affiliation(s)
- Jieyu Wang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China
| | - Fangfang Zhong
- Department of Pathology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Jun Li
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Huiran Yue
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Wenzhi Li
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China
| | - Xin Lu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China.
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Jia M, Zou X, Yin S, Tian W, Zhao Y, Wang H, Xu G, Cai W, Shao Q. CHD4 orchestrates the symphony of T and B lymphocytes development and a good mediator in preventing from autoimmune disease. Immun Inflamm Dis 2022; 10:e644. [PMID: 35759243 PMCID: PMC9168550 DOI: 10.1002/iid3.644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/02/2022] Open
Abstract
Chromodomain helicase DNA binding protein 4 (CHD4) is an ATPase subunit of the nucleosome remodeling and deacetylation complex. It has been implicated in gene transcription, DNA damage repair, maintenance of genome stability, and chromatin assembly. Meanwhile, it is highly related to cell cycle progression and the proceeding of malignancy. Most of the previous studies were focused on the function of CHD4 with tumor cells, cancer stem cells, and cancer cells multidrug resistance. Recently, some researchers have explored the CHD4 functions on the development and differentiation of adaptive immune cells, such as T and B lymphocytes. In this review, we will discuss details of CHD4 in lymphocyte differentiation and development, as well as the critical role of CHD4 in the pathogenesis of the autoimmune disease.
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Affiliation(s)
- Miaomiao Jia
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Xueqin Zou
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Shuying Yin
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Weihong Tian
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Yangjing Zhao
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Hui Wang
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Guoying Xu
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
| | - Weili Cai
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
| | - Qixiang Shao
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
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Tu Z, Zheng Y. Role of ATP-dependent chromatin remodelers in hematopoietic stem and progenitor cell maintenance. Curr Opin Hematol 2022; 29:174-180. [PMID: 35787545 PMCID: PMC9257093 DOI: 10.1097/moh.0000000000000710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW ATP-dependent chromatin remodeling factors utilize energy from ATP hydrolysis to modulate DNA-histone structures and regulate gene transcription. They are essential during hematopoiesis and for hematopoietic stem and progenitor cell (HSPC) function. This review discusses the recently unveiled roles of these chromatin remodelers in HSPC regulation, with an emphasis on the mechanism of chromodomain helicase DNA-binding (CHD) family members. RECENT FINDINGS Recent studies of ATP-dependent chromatin remodelers have revealed that individual CHD family members engage in distinct mechanisms in regulating HSPC cell fate. For example, CHD8 is required for HSPC survival by restricting both P53 transcriptional activity and protein stability in steady state hematopoiesis while the related CHD7 physically interacts with RUNX family transcription factor 1 (RUNX1) and suppresses RUNX1-induced expansion of HSPCs during blood development. Moreover, other CHD subfamily members such as CHD1/CHD2 and CHD3/CHD4, as well as the switch/sucrose non-fermentable, imitation SWI, and SWI2/SNF2 related (SWR) families of chromatin modulators, have also been found important for HSPC maintenance by distinct mechanisms. SUMMARY The expanding knowledge of ATP-dependent chromatin remodelers in hematopoiesis illustrates their respective critical roles in HSPC maintenance including the regulation of HSPC differentiation, survival, and self-renewal. Further studies are warranted to elucidate how different chromatin remodeling complexes are integrated in various HSPC cell fate decisions during steady-state and stress hematopoiesis.
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Affiliation(s)
- Zhaowei Tu
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, Hepperla AJ, Akerberg BN, Pu WT, Cristea IM, Davis IJ, Conlon FL. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev 2022; 36:468-482. [PMID: 35450884 PMCID: PMC9067406 DOI: 10.1101/gad.349154.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.
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Affiliation(s)
- Zachary L Robbe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei Shi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lauren K Wasson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Angel P Scialdone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Frank L Conlon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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10
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Ito Y, Yamamoto Y, Suzuki Y, Noda K, Nakajima A. Clinical and Serological Features and Pregnancy Outcomes in Women with Polymyositis/Dermatomyositis: A Case-based Review. Intern Med 2022; 61:143-149. [PMID: 34334572 PMCID: PMC8851185 DOI: 10.2169/internalmedicine.7924-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We encountered a 30-year-old woman who developed dermatomyositis during pregnancy and was positive for anti-Mi-2 antibodies. She was successfully treated with prednisolone and tacrolimus and delivered a healthy child. We reviewed the cases of idiopathic inflammatory myositis (IIM) that developed during pregnancy that were published after the year 2000 to elucidate the profile of myositis-specific antibodies (MSAs) in them and to evaluate their obstetric outcomes. In cases with IIM that developed during pregnancy, anti-Mi-2, anti-TIF1-g, anti-Jo-1, and anti-EJ antibodies was detected in one case each. The obstetric outcomes of the IIM-complicated pregnancies were poor, especially when complicated with active maternal myositis. Further studies focusing on the possible causal relationships between MSAs and cases with IIM that developed during pregnancy are needed. For better obstetric outcomes, appropriate suppression of the maternal disease activity using immunosuppressants and vigilance regarding the patient's requirement of Caesarean section is important.
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Affiliation(s)
- Yuhei Ito
- Center for Rheumatic Diseases, Mie University Hospital, Japan
| | | | - Yasuo Suzuki
- Center for Rheumatic Diseases, Mie University Hospital, Japan
| | - Kentaro Noda
- Center for Rheumatic Diseases, Mie University Hospital, Japan
| | - Ayako Nakajima
- Center for Rheumatic Diseases, Mie University Hospital, Japan
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11
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Hagman JR, Arends T, Laborda C, Knapp JR, Harmacek L, O'Connor BP. Chromodomain helicase DNA-binding 4 (CHD4) regulates early B cell identity and V(D)J recombination. Immunol Rev 2021; 305:29-42. [PMID: 34927255 DOI: 10.1111/imr.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022]
Abstract
B lymphocytes develop from uncommitted precursors into immunoglobulin (antibody)-producing B cells, a major arm of adaptive immunity. Progression of early progenitors to antibody-expressing cells in the bone marrow is orchestrated by the temporal regulation of different gene programs at discrete developmental stages. A major question concerns how B cells control the accessibility of these genes to transcription factors. Research has implicated nucleosome remodeling ATPases as mediators of chromatin accessibility. Here, we describe studies of chromodomain helicase DNA-binding 4 (CHD4; also known as Mi-2β) in early B cell development. CHD4 comprises multiple domains that function in nucleosome mobilization and histone binding. CHD4 is a key component of Nucleosome Remodeling and Deacetylase, or NuRD (Mi-2) complexes, which assemble with other proteins that mediate transcriptional repression. We review data demonstrating that CHD4 is necessary for B lineage identity: early B lineage progression, proliferation in response to interleukin-7, responses to DNA damage, and cell survival in vivo. CHD4-NuRD is also required for the Ig heavy-chain repertoire by promoting utilization of distal variable (VH ) gene segments in V(D)J recombination. In conclusion, the regulation of chromatin accessibility by CHD4 is essential for production of antibodies by B cells, which in turn mediate humoral immune responses to pathogens and disease.
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Affiliation(s)
- James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Tessa Arends
- Program in Molecular Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Curtis Laborda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Jennifer R Knapp
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
| | - Brian P O'Connor
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, USA
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12
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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13
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Tu Z, Wang C, Davis AK, Hu M, Zhao C, Xin M, Lu QR, Zheng Y. The chromatin remodeler CHD8 governs hematopoietic stem/progenitor survival by regulating ATM-mediated P53 protein stability. Blood 2021; 138:221-233. [PMID: 34292326 PMCID: PMC8310427 DOI: 10.1182/blood.2020009997] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/06/2021] [Indexed: 01/15/2023] Open
Abstract
The Chd8 gene encodes a member of the chromodomain helicase DNA-binding (CHD) family of SNF2H-like adenosine triphosphate (ATP)-dependent chromatin remodeler, the mutations of which define a subtype of autism spectrum disorders. Increasing evidence from recent studies indicates that ATP-dependent chromatin-remodeling genes are involved in the control of crucial gene-expression programs in hematopoietic stem/progenitor cell (HSPC) regulation. In this study, we identified CHD8 as a specific and essential regulator of normal hematopoiesis. Loss of Chd8 leads to severe anemia, pancytopenia, bone marrow failure, and engraftment failure related to a drastic depletion of HSPCs. CHD8 forms a complex with ATM and its deficiency increases chromatin accessibility and drives genomic instability in HSPCs causing an activation of ATM kinase that further stabilizes P53 protein by phosphorylation and leads to increased HSPC apoptosis. Deletion of P53 rescues the apoptotic defects of HSPCs and restores overall hematopoiesis in Chd8-/- mice. Our findings demonstrate that chromatin organization by CHD8 is uniquely necessary for the maintenance of hematopoiesis by integrating the ATM-P53-mediated survival of HSPCs.
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Affiliation(s)
| | | | | | | | | | | | | | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH
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14
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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15
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Read KA, Jones DM, Freud AG, Oestreich KJ. Established and emergent roles for Ikaros transcription factors in lymphoid cell development and function. Immunol Rev 2020; 300:82-99. [PMID: 33331000 DOI: 10.1111/imr.12936] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Ikaros zinc finger transcription factors are important regulators of the gene programs underlying the development of hematopoietic cell lineages. The family consists of five members: Ikaros, Helios, Aiolos, Eos, and Pegasus, which engage in both homo- and heterotypic intrafamilial interactions to exert diverse functional effects. Pioneering studies focused on the role of these factors in early lymphoid development, as their absence resulted in severe defects in lymphocyte populations. More recent work has now begun to define nuanced, stage-specific roles for Ikaros family members in the differentiation and function of mature T, B, and innate lymphoid cell populations including natural killer (NK) cells. The precise transcriptional mechanisms by which these factors function, both independently and collaboratively, is an area of active investigation. However, several key themes appear to be emerging regarding the pathways influenced by Ikaros family members, including the end-to-end regulation of cytokine signaling. Here, we review roles for Ikaros factors in lymphoid cell development, differentiation, and function, including a discussion of the current understanding of the transcriptional mechanisms they employ and considerations for the future study of this important transcription factor family.
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Affiliation(s)
- Kaitlin A Read
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Biomedical Sciences Graduate Program, Columbus, OH, USA
| | - Devin M Jones
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Biomedical Sciences Graduate Program, Columbus, OH, USA
| | - Aharon G Freud
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA.,Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
| | - Kenneth J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
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16
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Shibata S, Kashiwagi M, Morgan BA, Georgopoulos K. Functional interactions between Mi-2β and AP1 complexes control response and recovery from skin barrier disruption. J Exp Med 2020; 217:132751. [PMID: 31834931 PMCID: PMC7062528 DOI: 10.1084/jem.20182402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 07/29/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022] Open
Abstract
Keratinocytes respond to environmental signals by eliciting induction of genes that preserve skin's integrity. Here we show that the transcriptional response to stress signaling is supported by short-lived epigenetic changes. Comparison of chromatin accessibility and transcriptional changes induced by barrier disruption or by loss of the nucleosome remodeler Mi-2β identified their striking convergence in mouse and human keratinocytes. Mi-2β directly repressed genes induced by barrier disruption by restricting AP1-enriched promoter-distal sites, occupied by Mi-2β and JUNB at steady state and by c-JUN after Mi-2β depletion or stress signaling. Barrier disruption led to a modest reduction in Mi-2β expression and a further selective reduction of Mi-2β localization at stress response genes, possibly through competition with activated c-JUN. Consistent with a repressive role at stress response genes, genetic ablation of Mi-2β did not prevent reestablishment of barrier integrity but was required for return to homeostasis. Thus, a competition between Mi-2β-repressive and activating AP1 complexes may permit rapid transcriptional response to and resolution from stress signaling.
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Affiliation(s)
- Sayaka Shibata
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Mariko Kashiwagi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Bruce A Morgan
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
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17
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Tomofuji Y, Takaba H, Suzuki HI, Benlaribi R, Martinez CDP, Abe Y, Morishita Y, Okamura T, Taguchi A, Kodama T, Takayanagi H. Chd4 choreographs self-antigen expression for central immune tolerance. Nat Immunol 2020; 21:892-901. [PMID: 32601470 DOI: 10.1038/s41590-020-0717-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
Autoreactive T cells are eliminated in the thymus to prevent autoimmunity by promiscuous expression of tissue-restricted self-antigens in medullary thymic epithelial cells. This expression is dependent on the transcription factor Fezf2, as well as the transcriptional regulator Aire, but the entire picture of the transcriptional program has been obscure. Here, we found that the chromatin remodeler Chd4, also called Mi-2β, plays a key role in the self-antigen expression in medullary thymic epithelial cells. To maximize the diversity of self-antigen expression, Fezf2 and Aire utilized completely distinct transcriptional mechanisms, both of which were under the control of Chd4. Chd4 organized the promoter regions of Fezf2-dependent genes, while contributing to the Aire-mediated induction of self-antigens via super-enhancers. Mice deficient in Chd4 specifically in thymic epithelial cells exhibited autoimmune phenotypes, including T cell infiltration. Thus, Chd4 plays a critical role in integrating Fezf2- and Aire-mediated gene induction to establish central immune tolerance.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takaba
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi I Suzuki
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rayene Benlaribi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Cristian David Peña Martinez
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Abe
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Morishita
- Department of Molecular Pathology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Section of Animal Models, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akashi Taguchi
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Kodama
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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18
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Goodman JV, Yamada T, Yang Y, Kong L, Wu DY, Zhao G, Gabel HW, Bonni A. The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain. Nat Commun 2020; 11:3419. [PMID: 32647123 PMCID: PMC7347877 DOI: 10.1038/s41467-020-17065-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
The development and function of the brain require tight control of gene expression. Genome architecture is thought to play a critical regulatory role in gene expression, but the mechanisms governing genome architecture in the brain in vivo remain poorly understood. Here, we report that conditional knockout of the chromatin remodeling enzyme Chd4 in granule neurons of the mouse cerebellum increases accessibility of gene regulatory sites genome-wide in vivo. Conditional knockout of Chd4 promotes recruitment of the architectural protein complex cohesin preferentially to gene enhancers in granule neurons in vivo. Importantly, in vivo profiling of genome architecture reveals that conditional knockout of Chd4 strengthens interactions among developmentally repressed contact domains as well as genomic loops in a manner that tightly correlates with increased accessibility, enhancer activity, and cohesin occupancy at these sites. Collectively, our findings define a role for chromatin remodeling in the control of genome architecture organization in the mammalian brain.
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Affiliation(s)
- Jared V Goodman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Yue Yang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Lingchun Kong
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.
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19
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Leighton G, Williams DC. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex. J Mol Biol 2019:S0022-2836(19)30599-6. [PMID: 31626804 DOI: 10.1016/j.jmb.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex uniquely combines both deacetylase and remodeling enzymatic activities in a single macromolecular complex. The methyl-CpG-binding domain 2 and 3 (MBD2 and MBD3) proteins provide a critical structural link between the deacetylase and remodeling components, while MBD2 endows the complex with the ability to selectively recognize methylated DNA. Hence, NuRD combines three major arms of epigenetic gene regulation. Research over the past few decades has revealed much of the structural basis driving formation of this complex and started to uncover the functional roles of NuRD in epigenetic gene regulation. However, we have yet to fully understand the molecular and biophysical basis for methylation-dependent chromatin remodeling and transcription regulation by NuRD. In this review, we discuss the structural information currently available for the complex, the role MBD2 and MBD3 play in forming and recruiting the complex to methylated DNA, and the biological functions of NuRD.
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Affiliation(s)
- Gage Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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