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Ding M, Jiang J, Yang F, Zheng F, Fang J, Wang Q, Wang J, Yao W, Liu X, Gao X, Mullen M, He P, Rono C, Ding X, Hong J, Fu C, Liu X, Yao X. Holliday junction recognition protein interacts with and specifies the centromeric assembly of CENP-T. J Biol Chem 2018; 294:968-980. [PMID: 30459232 DOI: 10.1074/jbc.ra118.004688] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/19/2018] [Indexed: 02/02/2023] Open
Abstract
The centromere is an evolutionarily conserved eukaryotic protein machinery essential for precision segregation of the parental genome into two daughter cells during mitosis. Centromere protein A (CENP-A) organizes the functional centromere via a constitutive centromere-associated network composing the CENP-T complex. However, how CENP-T assembles onto the centromere remains elusive. Here we show that CENP-T binds directly to Holliday junction recognition protein (HJURP), an evolutionarily conserved chaperone involved in loading CENP-A. The binding interface of HJURP was mapped to the C terminus of CENP-T. Depletion of HJURP by CRISPR-elicited knockout minimized recruitment of CENP-T to the centromere, indicating the importance of HJURP in CEPN-T loading. Our immunofluorescence analyses indicate that HJURP recruits CENP-T to the centromere in S/G2 phase during the cell division cycle. Significantly, the HJURP binding-deficient mutant CENP-T6L failed to locate to the centromere. Importantly, CENP-T insufficiency resulted in chromosome misalignment, in particular chromosomes 15 and 18. Taken together, these data define a novel molecular mechanism underlying the assembly of CENP-T onto the centromere by a temporally regulated HJURP-CENP-T interaction.
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Affiliation(s)
- Mingrui Ding
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China.,the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Jiying Jiang
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Fengrui Yang
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Fan Zheng
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Jingwen Fang
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Qian Wang
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Jianyu Wang
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China.,the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - William Yao
- the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Xu Liu
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China.,the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Xinjiao Gao
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - McKay Mullen
- the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Ping He
- the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Cathy Rono
- the Keck Center for Cellular Dynamics and Organoid Plasticity, Morehouse School of Medicine, Atlanta, Georgia 30310, and
| | - Xia Ding
- the Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jingjun Hong
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Chuanhai Fu
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China
| | - Xing Liu
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China,
| | - Xuebiao Yao
- From the Anhui Key Laboratory of Cellular Dynamics and Chemical Biology, Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of the China School of Life Sciences, Chinese Academy of Sciences Center of Excellence on Cell Sciences, Hefei 230027, China,
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Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes Dev 2017; 31:1958-1972. [PMID: 29074736 PMCID: PMC5710141 DOI: 10.1101/gad.304782.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/05/2017] [Indexed: 12/16/2022]
Abstract
Histone CENP-A-containing nucleosomes play an important role in nucleating kinetochores at centromeres for chromosome segregation. However, the molecular mechanisms by which CENP-A nucleosomes engage with kinetochore proteins are not well understood. Here, we report the finding of a new function for the budding yeast Cse4/CENP-A histone-fold domain interacting with inner kinetochore protein Mif2/CENP-C. Strikingly, we also discovered that AT-rich centromere DNA has an important role for Mif2 recruitment. Mif2 contacts one side of the nucleosome dyad, engaging with both Cse4 residues and AT-rich nucleosomal DNA. Both interactions are directed by a contiguous DNA- and histone-binding domain (DHBD) harboring the conserved CENP-C motif, an AT hook, and RK clusters (clusters enriched for arginine-lysine residues). Human CENP-C has two related DHBDs that bind preferentially to DNA sequences of higher AT content. Our findings suggest that a DNA composition-based mechanism together with residues characteristic for the CENP-A histone variant contribute to the specification of centromere identity.
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Affiliation(s)
- Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Peter C FitzGerald
- Genome Analysis Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yingzi Huang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Shipeng Li
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Dechassa ML, Wyns K, Luger K. Scm3 deposits a (Cse4-H4)2 tetramer onto DNA through a Cse4-H4 dimer intermediate. Nucleic Acids Res 2014; 42:5532-42. [PMID: 24623811 PMCID: PMC4027189 DOI: 10.1093/nar/gku205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The assembly of centromeric nucleosomes is mediated by histone variant-specific chaperones. In budding yeast, the centromere-specific histone H3 variant is Cse4, and the histone chaperone Scm3 functions as a Cse4-specific nucleosome assembly factor. Here, we show that Scm3 exhibits specificity for Cse4-H4, but also interacts with major-type H3-H4 and H2A-H2B. Previously published structures of the Scm3 histone complex demonstrate that Scm3 binds only one copy of Cse4-H4. Consistent with this, we show that Scm3 deposits Cse4-H4 through a dimer intermediate onto deoxyribonucleic acid (DNA) to form a (Cse4-H4)2-DNA complex (tetrasome). Scm3-bound Cse4-H4 does not form a tetramer in the absence of DNA. Moreover, we demonstrate that Cse4 and H3 are structurally compatible to be incorporated in the same nucleosome to form heterotypic particles. Our data shed light on the mechanism of Scm3-mediated nucleosome assembly at the centromere.
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Affiliation(s)
- Mekonnen Lemma Dechassa
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
| | - Katharina Wyns
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
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D'Arcy S, Martin KW, Panchenko T, Chen X, Bergeron S, Stargell LA, Black BE, Luger K. Chaperone Nap1 shields histone surfaces used in a nucleosome and can put H2A-H2B in an unconventional tetrameric form. Mol Cell 2013; 51:662-77. [PMID: 23973327 DOI: 10.1016/j.molcel.2013.07.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/06/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Abstract
The histone H2A-H2B heterodimer is an integral component of the nucleosome. The cellular localization and deposition of H2A-H2B into chromatin is regulated by numerous factors, including histone chaperones such as nucleosome assembly protein 1 (Nap1). We use hydrogen-deuterium exchange coupled to mass spectrometry to characterize H2A-H2B and Nap1. Unexpectedly, we find that at low ionic strength, the α helices in H2A-H2B are frequently sampling partially disordered conformations and that binding to Nap1 reduces this conformational sampling. We identify the interaction surface between H2A-H2B and Nap1 and confirm its relevance both in vitro and in vivo. We show that two copies of H2A-H2B bound to a Nap1 homodimer form a tetramer with contacts between H2B chains similar to those in the four-helix bundle structural motif. The organization of the complex reveals that Nap1 competes with histone-DNA and interhistone interactions observed in the nucleosome, thereby regulating the availability of histones for chromatin assembly.
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Affiliation(s)
- Sheena D'Arcy
- Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523, USA.
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Abstract
Most histones are assembled into nucleosomes during replication to package genomic DNA. However, several variant histones are deposited independently of replication at particular regions of chromosomes. Such histone variants include cenH3, which forms the nucleosomal foundation for the centromere, and H3.3, which replaces histones that are lost during dynamic processes that disrupt nucleosomes. Furthermore, various H2A variants participate in DNA repair, gene regulation and other processes that are, as yet, not fully understood. Here, we review recent studies that have implicated histone variants in maintaining pluripotency and as causal factors in cancer and other diseases.
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Affiliation(s)
- Peter J Skene
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Quinlan RA, Ellis RJ. Chaperones: needed for both the good times and the bad times. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130091. [PMID: 23530265 DOI: 10.1098/rstb.2013.0091] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this issue, we explore the assembly roles of protein chaperones, mainly through the portal of their associated human diseases (e.g. cardiomyopathy, cataract, neurodegeneration, cancer and neuropathy). There is a diversity to chaperone function that goes beyond the current emphasis in the scientific literature on their undoubted roles in protein folding and refolding. The focus on chaperone-mediated protein folding needs to be broadened by the original Laskey discovery that a chaperone assists the assembly of an oligomeric structure, the nucleosome, and the subsequent suggestion by Ellis that other chaperones may function in assembly processes, as well as in folding. There have been a number of recent discoveries that extend this relatively neglected aspect of chaperone biology to include proteostasis, maintenance of the cellular redox potential, genome stability, transcriptional regulation and cytoskeletal dynamics. So central are these processes that we propose that chaperones stand at the crossroads of life and death because they mediate essential functions, not only during the bad times, but also in the good times. We suggest that chaperones facilitate the success of a species, and hence the evolution of individuals within populations, because of their contributions to so many key cellular processes, of which protein folding is only one.
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Affiliation(s)
- Roy A Quinlan
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK.
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