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Aoki K, Hyuga M, Tarumoto Y, Nishibuchi G, Ueda A, Ochi Y, Sugino S, Mikami T, Kobushi H, Kato I, Akahane K, Inukai T, Takaori-Kondo A, Takita J, Ogawa S, Yusa K. Canonical BAF complex regulates the oncogenic program in human T-cell acute lymphoblastic leukemia. Blood 2024; 143:604-618. [PMID: 37922452 DOI: 10.1182/blood.2023020857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Acute leukemia cells require bone marrow microenvironments, known as niches, which provide leukemic cells with niche factors that are essential for leukemic cell survival and/or proliferation. However, it remains unclear how the dynamics of the leukemic cell-niche interaction are regulated. Using a genome-wide CRISPR screen, we discovered that canonical BRG1/BRM-associated factor (cBAF), a variant of the switch/sucrose nonfermenting chromatin remodeling complex, regulates the migratory response of human T-cell acute lymphoblastic leukemia (T-ALL) cells to a niche factor CXCL12. Mechanistically, cBAF maintains chromatin accessibility and allows RUNX1 to bind to CXCR4 enhancer regions. cBAF inhibition evicts RUNX1 from the genome, resulting in CXCR4 downregulation and impaired migration activity. In addition, cBAF maintains chromatin accessibility preferentially at RUNX1 binding sites, ensuring RUNX1 binding at these sites, and is required for expression of RUNX1-regulated genes, such as CDK6; therefore, cBAF inhibition negatively impacts cell proliferation and profoundly induces apoptosis. This anticancer effect was also confirmed using T-ALL xenograft models, suggesting cBAF as a promising therapeutic target. Thus, we provide novel evidence that cBAF regulates the RUNX1-driven leukemic program and governs migration activity toward CXCL12 and cell-autonomous growth in human T-ALL.
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Affiliation(s)
- Kazunari Aoki
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mizuki Hyuga
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Tarumoto
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Gohei Nishibuchi
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Atsushi Ueda
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Seiichi Sugino
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirokazu Kobushi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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Kuroda Y, Iwata-Otsubo A, Dias KR, Temple SEL, Nagao K, De Hayr L, Zhu Y, Isobe SY, Nishibuchi G, Fiordaliso SK, Fujita Y, Rippert AL, Baker SW, Leung ML, Koboldt DC, Harman A, Keena BA, Kazama I, Subramanian GM, Manickam K, Schmalz B, Latsko M, Zackai EH, Edwards M, Evans CA, Dulik MC, Buckley MF, Yamashita T, O'Brien WT, Harvey RJ, Obuse C, Roscioli T, Izumi K. Dominant-negative variants in CBX1 cause a neurodevelopmental disorder. Genet Med 2023:100861. [PMID: 37087635 DOI: 10.1016/j.gim.2023.100861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023] Open
Abstract
PURPOSE This study aimed to establish variants in CBX1, encoding heterochromatin protein 1β (HP1β), as a cause of a novel syndromic neurodevelopmental disorder. METHODS Patients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays, neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. RESULTS In three unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1β, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1β binding to heterochromatin, while HP1β interactome analysis demonstrated that the majority of HP1β-interacting proteins remained unchanged between the wild-type and mutant HP1β. CONCLUSION These collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1β chromatin binding during neurocognitive development. As HP1β forms homodimers and heterodimers, mutant HP1β likely sequesters wild-type HP1β and other HP1 proteins, exerting dominant-negative effects.
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Affiliation(s)
- Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Aiko Iwata-Otsubo
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Kerith-Rae Dias
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, Australia
| | - Suzanna E L Temple
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, Australia
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Lachlan De Hayr
- School of Health, University of the Sunshine Coast, Maroochydore, Australia; Sunshine Coast Health Institute, Birtinya, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia
| | - Shin-Ya Isobe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Gohei Nishibuchi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Sarah K Fiordaliso
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, USA; Department of Pathology, The Ohio State University College of Medicine, Columbus, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, USA
| | - Adele Harman
- Transgenic core, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Beth A Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Izumi Kazama
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | | | - Kandamurugu Manickam
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, USA; Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, USA
| | - Betsy Schmalz
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, USA
| | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Matt Edwards
- Hunter Genetics, Newcastle, New South Wales, Australia; University of Western Sydney School of Medicine, New South Wales. Australia
| | - Carey-Anne Evans
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, Australia
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Michael F Buckley
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - W Timothy O'Brien
- Institute for Translational Medicine and Therapeutics. Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Robert J Harvey
- School of Health, University of the Sunshine Coast, Maroochydore, Australia; Sunshine Coast Health Institute, Birtinya, Australia
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tony Roscioli
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, Australia
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA; Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, USA; Laboratory of Rare Disease Research, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan; Current affiliation: Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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Oya E, Nakagawa R, Yoshimura Y, Tanaka M, Nishibuchi G, Machida S, Shirai A, Ekwall K, Kurumizaka H, Tagami H, Nakayama JI. H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly. EMBO Rep 2019; 20:e48111. [PMID: 31468675 DOI: 10.15252/embr.201948111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022] Open
Abstract
The methylation of histone H3 at lysine 9 (H3K9me), performed by the methyltransferase Clr4/SUV39H, is a key event in heterochromatin assembly. In fission yeast, Clr4, together with the ubiquitin E3 ligase Cul4, forms the Clr4 methyltransferase complex (CLRC), whose physiological targets and biological role are currently unclear. Here, we show that CLRC-dependent H3 ubiquitylation regulates Clr4's methyltransferase activity. Affinity-purified CLRC ubiquitylates histone H3, and mass spectrometric and mutation analyses reveal that H3 lysine 14 (H3K14) is the preferred target of the complex. Chromatin immunoprecipitation analysis shows that H3K14 ubiquitylation (H3K14ub) is closely associated with H3K9me-enriched chromatin. Notably, the CLRC-mediated H3 ubiquitylation promotes H3K9me by Clr4, suggesting that H3 ubiquitylation is intimately linked to the establishment and/or maintenance of H3K9me. These findings demonstrate a cross-talk mechanism between histone ubiquitylation and methylation that is involved in heterochromatin assembly.
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Affiliation(s)
- Eriko Oya
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
| | - Mayo Tanaka
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
| | - Gohei Nishibuchi
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | | | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan.,Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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Nishibuchi G, Machida S, Nakagawa R, Yoshimura Y, Hiragami-Hamada K, Abe Y, Kurumizaka H, Tagami H, Nakayama JI. Mitotic phosphorylation of HP1α regulates its cell cycle-dependent chromatin binding. J Biochem 2018; 165:433-446. [DOI: 10.1093/jb/mvy117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/14/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gohei Nishibuchi
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Reiko Nakagawa
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
| | - Kyoko Hiragami-Hamada
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Nishigonaka 38, Myodaiji, Okazaki, Japan
| | - Yusuke Abe
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research, Koto-ku, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Japan
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Nishigonaka 38, Myodaiji, Okazaki, Japan
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5
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Nishibuchi G, Déjardin J. The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals. Chromosome Res 2017; 25:77-87. [PMID: 28078514 DOI: 10.1007/s10577-016-9547-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
Abstract
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes. Genetic and biochemical studies have revealed that histone methylation at H3K9 and its recognition by heterochromatin protein 1 represent the fundamental mechanism by which heterochromatin forms. Although this molecular mechanism is highly conserved from yeast to human cells, its detailed epigenetic regulation is more complex and dynamic for each distinct constitutive heterochromatin structure in higher eukaryotes. It can also vary according to the developmental stage. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis is a powerful tool to investigate the epigenetic regulation of eukaryote genomes, but non-unique reads are usually discarded during standard ChIP-seq data alignment to reference genome databases. Therefore, specific methods to obtain global epigenetic information concerning repetitive elements are needed. In this review, we focus on such approaches and we summarize the latest molecular models for distinct constitutive heterochromatin types in mammals.
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Affiliation(s)
- Gohei Nishibuchi
- Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France
| | - Jérôme Déjardin
- Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France.
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Nishibuchi G, Machida S, Osakabe A, Murakoshi H, Hiragami-Hamada K, Nakagawa R, Fischle W, Nishimura Y, Kurumizaka H, Tagami H, Nakayama JI. N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity. Nucleic Acids Res 2014; 42:12498-511. [PMID: 25332400 PMCID: PMC4227797 DOI: 10.1093/nar/gku995] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/09/2014] [Accepted: 10/06/2014] [Indexed: 01/08/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved chromosomal protein that binds to lysine 9-methylated histone H3 (H3K9me), a hallmark of heterochromatin. Although HP1 phosphorylation has been described in several organisms, the biological implications of this modification remain largely elusive. Here we show that HP1's phosphorylation has a critical effect on its nucleosome binding properties. By in vitro phosphorylation assays and conventional chromatography, we demonstrated that casein kinase II (CK2) is the kinase primarily responsible for phosphorylating the N-terminus of human HP1α. Pull-down assays using in vitro-reconstituted nucleosomes showed that unmodified HP1α bound H3K9-methylated and H3K9-unmethylated nucleosomes with comparable affinity, whereas CK2-phosphorylated HP1α showed a high specificity for H3K9me3-modified nucleosomes. Electrophoretic mobility shift assays showed that CK2-mediated phosphorylation diminished HP1α's intrinsic DNA binding, which contributed to its H3K9me-independent nucleosome binding. CK2-mediated phosphorylation had a similar effect on the nucleosome-binding specificity of fly HP1a and S. pombe Swi6. These results suggested that HP1 phosphorylation has an evolutionarily conserved role in HP1's recognition of H3K9me-marked nucleosomes.
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Affiliation(s)
- Gohei Nishibuchi
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiromu Murakoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Reiko Nakagawa
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
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7
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Nishibuchi G, Shibata Y, Hayakawa T, Hayakawa N, Ohtani Y, Sinmyozu K, Tagami H, Nakayama JI. Physical and functional interactions between the histone H3K4 demethylase KDM5A and the nucleosome remodeling and deacetylase (NuRD) complex. J Biol Chem 2014; 289:28956-70. [PMID: 25190814 DOI: 10.1074/jbc.m114.573725] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Histone H3K4 methylation has been linked to transcriptional activation. KDM5A (also known as RBP2 or JARID1A), a member of the KDM5 protein family, is an H3K4 demethylase, previously implicated in the regulation of transcription and differentiation. Here, we show that KDM5A is physically and functionally associated with two histone deacetylase complexes. Immunoaffinity purification of KDM5A confirmed a previously described association with the SIN3B-containing histone deacetylase complex and revealed an association with the nucleosome remodeling and deacetylase (NuRD) complex. Sucrose density gradient and sequential immunoprecipitation analyses further confirmed the stable association of KDM5A with these two histone deacetylase complexes. KDM5A depletion led to changes in the expression of hundreds of genes, two-thirds of which were also controlled by CHD4, the NuRD catalytic subunit. Gene ontology analysis confirmed that the genes commonly regulated by both KDM5A and CHD4 were categorized as developmentally regulated genes. ChIP analyses suggested that CHD4 modulates H3K4 methylation levels at the promoter and coding regions of target genes. We further demonstrated that the Caenorhabditis elegans homologues of KDM5 and CHD4 function in the same pathway during vulva development. These results suggest that KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes.
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Affiliation(s)
- Gohei Nishibuchi
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501
| | - Yukimasa Shibata
- the Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo 669-1337, and
| | | | | | | | - Kaori Sinmyozu
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Hideaki Tagami
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501
| | - Jun-ichi Nakayama
- From the Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, the Laboratory for Chromatin Dynamics and
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8
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Nishibuchi G, Nakayama JI. Biochemical and structural properties of heterochromatin protein 1: understanding its role in chromatin assembly. J Biochem 2014; 156:11-20. [DOI: 10.1093/jb/mvu032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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