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Iwase S, Brookes E, Agarwal S, Badeaux AI, Ito H, Vallianatos CN, Tomassy GS, Kasza T, Lin G, Thompson A, Gu L, Kwan KY, Chen C, Sartor MA, Egan B, Xu J, Shi Y. A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation. Cell Rep 2016; 14:1000-1009. [PMID: 26804915 DOI: 10.1016/j.celrep.2015.12.091] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/17/2015] [Accepted: 12/20/2015] [Indexed: 11/26/2022] Open
Abstract
Mutations in a number of chromatin modifiers are associated with human neurological disorders. KDM5C, a histone H3 lysine 4 di- and tri-methyl (H3K4me2/3)-specific demethylase, is frequently mutated in X-linked intellectual disability (XLID) patients. Here, we report that disruption of the mouse Kdm5c gene recapitulates adaptive and cognitive abnormalities observed in XLID, including impaired social behavior, memory deficits, and aggression. Kdm5c-knockout brains exhibit abnormal dendritic arborization, spine anomalies, and altered transcriptomes. In neurons, Kdm5c is recruited to promoters that harbor CpG islands decorated with high levels of H3K4me3, where it fine-tunes H3K4me3 levels. Kdm5c predominantly represses these genes, which include members of key pathways that regulate the development and function of neuronal circuitries. In summary, our mouse behavioral data strongly suggest that KDM5C mutations are causal to XLID. Furthermore, our findings suggest that loss of KDM5C function may impact gene expression in multiple regulatory pathways relevant to the clinical phenotypes.
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Affiliation(s)
- Shigeki Iwase
- Division of Newborn Medicine, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.
| | - Emily Brookes
- Division of Newborn Medicine, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Saurabh Agarwal
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Aimee I Badeaux
- Division of Newborn Medicine, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Hikaru Ito
- Department of Integrative Physiology and Neuroscience, Washington State University, 1815 Ferdinand's Lane, Pullman, WA 99164, USA
| | - Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Giulio Srubek Tomassy
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Tomas Kasza
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Grace Lin
- Molecular & Behavioral Neuroscience Institute and Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew Thompson
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Lei Gu
- Division of Newborn Medicine, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Kenneth Y Kwan
- Molecular & Behavioral Neuroscience Institute and Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chinfei Chen
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Brian Egan
- Active Motif Inc., Carlsbad, CA 92008, USA
| | - Jun Xu
- Department of Integrative Physiology and Neuroscience, Washington State University, 1815 Ferdinand's Lane, Pullman, WA 99164, USA.
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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2
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Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature 2016; 528:218-24. [PMID: 26659182 PMCID: PMC4866648 DOI: 10.1038/nature15749] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022]
Abstract
Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNAi screens targeting chromatin factors during transcription factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPSCs). Remarkably, subunits of the chromatin assembly factor-1 (CAF-1) complex emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPSC formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 as a novel regulator of somatic cell identity during transcription factor-induced cell fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.
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Affiliation(s)
- Sihem Cheloufi
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Barbara Hopfgartner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Aimee I Badeaux
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Cheen Euong Ang
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Danielle Tenen
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Daniel J Wesche
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nadezhda Abazova
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Max Hogue
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nilgun Tasdemir
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Justin Brumbaugh
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Andres Blanco
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Daniel Wenzel
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Marietta Zinner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Simon E Vidal
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Scott W Lowe
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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3
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Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizábal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y. A histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Rep 2014; 7:113-26. [PMID: 24685137 DOI: 10.1016/j.celrep.2014.02.044] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/30/2014] [Accepted: 02/27/2014] [Indexed: 01/03/2023] Open
Abstract
How epigenetic information is transmitted from generation to generation remains largely unknown. Deletion of the C. elegans histone H3 lysine 4 dimethyl (H3K4me2) demethylase spr-5 leads to inherited accumulation of the euchromatic H3K4me2 mark and progressive decline in fertility. Here, we identified multiple chromatin-modifying factors, including H3K4me1/me2 and H3K9me3 methyltransferases, an H3K9me3 demethylase, and an H3K9me reader, which either suppress or accelerate the progressive transgenerational phenotypes of spr-5 mutant worms. Our findings uncover a network of chromatin regulators that control the transgenerational flow of epigenetic information and suggest that the balance between euchromatic H3K4 and heterochromatic H3K9 methylation regulates transgenerational effects on fertility.
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Affiliation(s)
- Eric L Greer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Sara E Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Ruggero Spadafora
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Yun Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Scott B Rothbart
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - David Aristizábal-Corrales
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Shuzhen Chen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Aimee I Badeaux
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Qiuye Jin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA.
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5
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Badeaux AI, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, Li W, Bedford MT. Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF. J Biol Chem 2011; 287:429-437. [PMID: 22072714 DOI: 10.1074/jbc.m111.271163] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In epigenetic signaling pathways, histone tails are heavily modified, resulting in the recruitment of effector molecules that can influence transcription. One such molecule, plant homeodomain finger protein 20 (PHF20), uses a Tudor domain to read dimethyl lysine residues and is a known component of the MOF (male absent on the first) histone acetyltransferase protein complex, suggesting it plays a role in the cross-talk between lysine methylation and histone acetylation. We sought to investigate the biological role of PHF20 by generating a knockout mouse. Without PHF20, mice die shortly after birth and display a wide variety of phenotypes within the skeletal and hematopoietic systems. Mechanistically, PHF20 is not required for maintaining the global H4K16 acetylation levels or locus specific histone acetylation but instead works downstream in transcriptional regulation of MOF target genes.
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Affiliation(s)
- Aimee I Badeaux
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Yanzhong Yang
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Kim Cardenas
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Vidyasiri Vemulapalli
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Kaifu Chen
- Division of Biostatistics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Donna Kusewitt
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Ellen Richie
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957
| | - Wei Li
- Division of Biostatistics, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957.
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