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Gopinathan Nair A, Rabas N, Lejon S, Homiski C, Osborne MJ, Cyr N, Sverzhinsky A, Melendy T, Pascal JM, Laue ED, Borden KLB, Omichinski JG, Verreault A. Unorthodox PCNA Binding by Chromatin Assembly Factor 1. Int J Mol Sci 2022; 23:ijms231911099. [PMID: 36232396 PMCID: PMC9570017 DOI: 10.3390/ijms231911099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
The eukaryotic DNA replication fork is a hub of enzymes that continuously act to synthesize DNA, propagate DNA methylation and other epigenetic marks, perform quality control, repair nascent DNA, and package this DNA into chromatin. Many of the enzymes involved in these spatiotemporally correlated processes perform their functions by binding to proliferating cell nuclear antigen (PCNA). A long-standing question has been how the plethora of PCNA-binding enzymes exert their activities without interfering with each other. As a first step towards deciphering this complex regulation, we studied how Chromatin Assembly Factor 1 (CAF-1) binds to PCNA. We demonstrate that CAF-1 binds to PCNA in a heretofore uncharacterized manner that depends upon a cation-pi (π) interaction. An arginine residue, conserved among CAF-1 homologs but absent from other PCNA-binding proteins, inserts into the hydrophobic pocket normally occupied by proteins that contain canonical PCNA interaction peptides (PIPs). Mutation of this arginine disrupts the ability of CAF-1 to bind PCNA and to assemble chromatin. The PIP of the CAF-1 p150 subunit resides at the extreme C-terminus of an apparent long α-helix (119 amino acids) that has been reported to bind DNA. The length of that helix and the presence of a PIP at the C-terminus are evolutionarily conserved among numerous species, ranging from yeast to humans. This arrangement of a very long DNA-binding coiled-coil that terminates in PIPs may serve to coordinate DNA and PCNA binding by CAF-1.
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Affiliation(s)
- Amogh Gopinathan Nair
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Molecular Biology Program, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
| | - Nick Rabas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sara Lejon
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Caleb Homiski
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - Michael J. Osborne
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Normand Cyr
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Thomas Melendy
- Departments of Biochemistry and Microbiology & Immunology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, 955 Main Street, Buffalo, NY 14210, USA
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katherine L. B. Borden
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - James G. Omichinski
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC H3T 1J4, Canada
- Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3T 1J4, Canada
- Correspondence: (A.G.N.); (A.V.)
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Wang D, Wang X, Zhang C, Yang K, Wang X, Cui J, Liu D, You C. Genome-wide Identification, Expression, and Functional Analysis of MdMSI Genes in Apples (Malus domestica Borkh.). Front Genet 2022; 13:846321. [PMID: 35309144 PMCID: PMC8927680 DOI: 10.3389/fgene.2022.846321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/04/2022] [Indexed: 11/25/2022] Open
Abstract
The multicopy suppressor of IRA (MSI) is a subfamily of WD40 repeat proteins, which is widely involved in plant growth and development. In order to explore the function of MdMSI members in abiotic stress, we identified eight MSI gene family members from the Malus × domestica reference genome. They were distributed on six chromosomes, and they had similar secondary and tertiary structures. We found a variety of regulatory elements in response to hormones and abiotic stress in MdMSI promoters. Through qRT-PCR analysis, it was revealed that MdMSIs were expressed in all tissues, especially in roots. The analysis results also revealed that the expression of MdMSIs was induced in varying degrees under salt, drought stress, and ABA treatments. Furthermore, we obtained the overexpression of MdMSI1-1 transgenic apple calli and Arabidopsis. The overexpression of MdMSI1-1 in calli and Arabidopsis played a negative regulatory role in salt stress response. Our work laid a foundation for further verifying the function of MSI genes under abiotic stress in apples.
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Affiliation(s)
- Daru Wang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Xun Wang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Chunling Zhang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Kuo Yang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Xinjie Wang
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Jianying Cui
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
| | - Dandan Liu
- College of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Dandan Liu, ; Chunxiang You,
| | - Chunxiang You
- National Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, China
- *Correspondence: Dandan Liu, ; Chunxiang You,
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Popova LV, Nagarajan P, Lovejoy CM, Sunkel B, Gardner M, Wang M, Freitas M, Stanton B, Parthun M. Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones. Nucleic Acids Res 2021; 49:12136-12151. [PMID: 34788845 PMCID: PMC8643632 DOI: 10.1093/nar/gkab1044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/20/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
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Affiliation(s)
- Liudmila V Popova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Callie M Lovejoy
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin D Sunkel
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Miranda L Gardner
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Meng Wang
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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Insights into the roles of histone chaperones in nucleosome assembly and disassembly in virus infection. Virus Res 2021; 297:198395. [PMID: 33737155 DOI: 10.1016/j.virusres.2021.198395] [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: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/23/2022]
Abstract
Nucleosomes are assembled or disassembled with the aid of histone chaperones in a cell. Viruses can exist either as minichromosomes/episomes or can integrate into the host genome and in both the cases the viral proteins interact and manipulate the cellular nucleosome assembly machinery to ensure their survival and propagation. Recent studies have provided insight into the mechanism and role of histone chaperones in nucleosome assembly and disassembly on the virus genome. Further, the interactions between viral proteins and histone chaperones have been implicated in the integration of the virus genome into the host genome. This review highlights the recent progress and future challenges in understanding the role of histone chaperones in viruses with DNA or RNA genome and their role in governing viral pathogenesis.
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The Amazing Acrobat: Yeast's Histone H3K56 Juggles Several Important Roles While Maintaining Perfect Balance. Genes (Basel) 2021; 12:genes12030342. [PMID: 33668997 PMCID: PMC7996553 DOI: 10.3390/genes12030342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 01/16/2023] Open
Abstract
Acetylation on lysine 56 of histone H3 of the yeast Saccharomyces cerevisiae has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.
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Young TJ, Cui Y, Pfeffer C, Hobbs E, Liu W, Irudayaraj J, Kirchmaier AL. CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac, preventing ectopic silencing. PLoS Genet 2020; 16:e1009226. [PMID: 33284793 PMCID: PMC7746308 DOI: 10.1371/journal.pgen.1009226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/17/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022] Open
Abstract
Replication-coupled chromatin assembly is achieved by a network of alternate pathways containing different chromatin assembly factors and histone-modifying enzymes that coordinate deposition of nucleosomes at the replication fork. Here we describe the organization of a CAF-1-dependent pathway in Saccharomyces cerevisiae that regulates acetylation of histone H4 K16. We demonstrate factors that function in this CAF-1-dependent pathway are important for preventing establishment of silenced states at inappropriate genomic sites using a crippled HMR locus as a model, while factors specific to other assembly pathways do not. This CAF-1-dependent pathway required the cullin Rtt101p, but was functionally distinct from an alternate pathway involving Rtt101p-dependent ubiquitination of histone H3 and the chromatin assembly factor Rtt106p. A major implication from this work is that cells have the inherent ability to create different chromatin modification patterns during DNA replication via differential processing and deposition of histones by distinct chromatin assembly pathways within the network.
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Affiliation(s)
- Tiffany J. Young
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
| | - Yi Cui
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Claire Pfeffer
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Emilie Hobbs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Wenjie Liu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Joseph Irudayaraj
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Ann L. Kirchmaier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America
- Purdue University Center for Cancer Research, West Lafayette, Indiana, United States of America
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States of America
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Hewawasam GS, Dhatchinamoorthy K, Mattingly M, Seidel C, Gerton JL. Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast. Nucleic Acids Res 2019. [PMID: 29522205 PMCID: PMC5961020 DOI: 10.1093/nar/gky169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could affect chromosome segregation, DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into non-centromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone with subunits shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. yCAF-1 interacts with Cse4 and can assemble Cse4 nucleosomes in vitro. Loss of yCAF-1 dramatically reduces the amount of Cse4 deposited into chromatin genome-wide when Cse4 is overexpressed. The incorporation of Cse4 genome-wide may have multifactorial effects on growth and gene expression. Loss of yCAF-1 can rescue growth defects and some changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin.
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Affiliation(s)
| | | | - Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chris Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.,University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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Modulation of Gene Silencing by Cdc7p via H4 K16 Acetylation and Phosphorylation of Chromatin Assembly Factor CAF-1 in Saccharomyces cerevisiae. Genetics 2019; 211:1219-1237. [PMID: 30728156 DOI: 10.1534/genetics.118.301858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/29/2019] [Indexed: 11/18/2022] Open
Abstract
CAF-1 is an evolutionarily conserved H3/H4 histone chaperone that plays a key role in replication-coupled chromatin assembly and is targeted to the replication fork via interactions with PCNA, which, if disrupted, leads to epigenetic defects. In Saccharomyces cerevisiae, when the silent mating-type locus HMR contains point mutations within the E silencer, Sir protein association and silencing is lost. However, mutation of CDC7, encoding an S-phase-specific kinase, or subunits of the H4 K16-specific acetyltransferase complex SAS-I, restore silencing to this crippled HMR, HMR a e** Here, we observed that loss of Cac1p, the largest subunit of CAF-1, also restores silencing at HMR a e**, and silencing in both cac1Δ and cdc7 mutants is suppressed by overexpression of SAS2 We demonstrate Cdc7p and Cac1p interact in vivo in S phase, but not in G1, consistent with observed cell cycle-dependent phosphorylation of Cac1p, and hypoacetylation of chromatin at H4 K16 in both cdc7 and cac1Δ mutants. Moreover, silencing at HMR a e** is restored in cells expressing cac1p mutants lacking Cdc7p phosphorylation sites. We also discovered that cac1Δ and cdc7-90 synthetically interact negatively in the presence of DNA damage, but that Cdc7p phosphorylation sites on Cac1p are not required for responses to DNA damage. Combined, our results support a model in which Cdc7p regulates replication-coupled histone modification via a CAC1-dependent mechanism involving H4 K16ac deposition, and thereby silencing, while CAF-1-dependent replication- and repair-coupled chromatin assembly per se are functional in the absence of phosphorylation of Cdc7p consensus sites on CAF-1.
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ASF1a inhibition induces p53-dependent growth arrest and senescence of cancer cells. Cell Death Dis 2019; 10:76. [PMID: 30692519 PMCID: PMC6349940 DOI: 10.1038/s41419-019-1357-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 12/13/2022]
Abstract
Anti-silencing function 1a (ASF1a) is a histone H3-H4 chaperone isoform involved in chromatin assembling and transcription regulation. Recently, ASF1a has been shown to be up-regulated in certain human malignancies and required for the expression of telomerase reverse transcriptase (TERT), a factor essential for the immortal phenotype of cancer cells; however, its role in oncogenesis remains poorly defined. In the present study, we determine whether ASF1a is required for the unlimited proliferation of cancer cells, a key cancer hallmark. Elevated ASF1a mRNA expression was observed in hepatocellular carcinoma (HCC) tumors. The overexpression of ASF1a was similarly found in 20 cancer types contained in TCGA and GTEx datasets. ASF1a knockdown led to growth arrest and senescence of wild-type (wt) p53-carrying HCC and prostate cancer cells. Cellular senescence mediated by ASF1a inhibition resulted from the robust up-regulation of p53 and p21cip1 expression, but without detectable changes in TERT expression. p53 inhibition attenuated p21cip1 induction caused by ASF1a depletion. Mechanistically, ASF1a-knocked down cells displayed widespread DNA damage. The TCGA dataset analysis revealed a negative correlation between ASF1a and p21cip1 expression in multiple types of primary tumors, including HCC, prostate, gastric, and breast cancer. Higher ASF1a and lower p21cip1 expression predicted a poor outcome in patients with HCC. Our results reveal that ASF1a overexpression is widespread in human malignancies and is required for the infinite proliferation of cancer cells, whereas its inhibition induces DNA damage and subsequent up-regulation of p53-p21cip1 expression, thereby triggering cellular senescence. Thus, ASF1a may serve as a potential target in cancer therapy.
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Transcriptional Profiling of Patient Isolates Identifies a Novel TOR/Starvation Regulatory Pathway in Cryptococcal Virulence. mBio 2018; 9:mBio.02353-18. [PMID: 30563896 PMCID: PMC6299223 DOI: 10.1128/mbio.02353-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human infection with Cryptococcus causes up to a quarter of a million AIDS-related deaths annually and is the most common cause of nonviral meningitis in the United States. As an opportunistic fungal pathogen, Cryptococcus neoformans is distinguished by its ability to adapt to diverse host environments, including plants, amoebae, and mammals. In the present study, comparative transcriptomics of the fungus within human cerebrospinal fluid identified expression profiles representative of low-nutrient adaptive responses. Transcriptomics of fungal isolates from a cohort of HIV/AIDS patients identified high expression levels of an alternative carbon nutrient transporter gene, STL1, to be associated with poor early fungicidal activity, an important clinical prognostic marker. Mouse modeling and pathway analysis demonstrated a role for STL1 in mammalian pathogenesis and revealed that STL1 expression is regulated by a novel multigene regulatory mechanism involving the CAC2 subunit of the chromatin assembly complex 1, CAF-1. In this pathway, the global regulator of virulence gene VAD1 was found to transcriptionally regulate a cryptococcal homolog of a cytosolic protein, Ecm15, in turn required for nuclear transport of the Cac2 protein. Derepression of STL1 by the CAC2-containing CAF-1 complex was mediated by Cac2 and modulated binding and suppression of the STL1 enhancer element. Derepression of STL1 resulted in enhanced survival and growth of the fungus in the presence of low-nutrient, alternative carbon sources, facilitating virulence in mice. This study underscores the utility of ex vivo expression profiling of fungal clinical isolates and provides fundamental genetic understanding of saprophyte adaption to the human host.IMPORTANCE Cryptococcus is a fungal pathogen that kills an estimated quarter of a million individuals yearly and is the most common cause of nonviral meningitis in the United States. The fungus is carried in about 10% of the adult population and, after reactivation, causes disease in a wide variety of immunosuppressed individuals, including the HIV infected and patients receiving transplant conditioning, cancer therapy, or corticosteroid therapy for autoimmune diseases. The fungus is widely carried in the soil but can also cause infections in plants and mammals. However, the mechanisms for this widespread ability to infect a variety of hosts are poorly understood. The present study identified adaptation to low nutrients as a key property that allows the fungus to inhabit these diverse environments. Further studies identified a nutrient transporter gene, STL1, to be upregulated under low nutrients and to be associated with early fungicidal activity, a marker of poor clinical outcome in a cohort of HIV/AIDS patients. Understanding molecular mechanisms involved in adaptation to the human host may help to design better methods of control and treatment of widely dispersed fungal pathogens such as Cryptococcus.
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Zasadzińska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Dev Cell 2018; 47:348-362.e7. [PMID: 30293838 PMCID: PMC6219920 DOI: 10.1016/j.devcel.2018.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/26/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Abstract
Centromeric chromatin defines the site of kinetochore formation and ensures faithful chromosome segregation. Centromeric identity is epigenetically specified by the incorporation of CENP-A nucleosomes. DNA replication presents a challenge for inheritance of centromeric identity because nucleosomes are removed to allow for replication fork progression. Despite this challenge, CENP-A nucleosomes are stably retained through S phase. We used BioID to identify proteins transiently associated with CENP-A during DNA replication. We found that during S phase, HJURP transiently associates with centromeres and binds to pre-existing CENP-A, suggesting a distinct role for HJURP in CENP-A retention. We demonstrate that HJURP is required for centromeric nucleosome inheritance during S phase. HJURP co-purifies with the MCM2-7 helicase complex and, together with the MCM2 subunit, binds CENP-A simultaneously. Therefore, pre-existing CENP-A nucleosomes require an S phase function of the HJURP chaperone and interaction with MCM2 to ensure faithful inheritance of centromere identity through DNA replication.
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Affiliation(s)
- Ewelina Zasadzińska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jiehuan Huang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Lucie Y Guo
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy S Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Shashank Srivastava
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kelvin A Wong
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bradley T French
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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12
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Sauer PV, Gu Y, Liu WH, Mattiroli F, Panne D, Luger K, Churchill MEA. Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1. Nucleic Acids Res 2018; 46:9907-9917. [PMID: 30239791 PMCID: PMC6212844 DOI: 10.1093/nar/gky823] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/15/2018] [Indexed: 02/03/2023] Open
Abstract
Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3-H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3-H4 onto substrate DNA. The CAF-1 trimer binds to a single H3-H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.
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Affiliation(s)
- Paul V Sauer
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | - Yajie Gu
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Wallace H Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Daniel Panne
- European Molecular Biology Laboratory, 38042 Grenoble, France,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Mair EA Churchill
- Department of Pharmacology and Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA,To whom correspondence should be addressed. Tel: +1 303 724 3670;
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Li M, Xu X, Chang CW, Zheng L, Shen B, Liu Y. SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts. Nat Commun 2018; 9:2706. [PMID: 30006506 PMCID: PMC6045570 DOI: 10.1038/s41467-018-05236-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
During DNA synthesis, DNA replication and transcription machinery can collide, and the replication fork may temporarily dislodge RNA polymerase II (RNAPII) to resolve the transcription-replication conflict (TRC), a major source of endogenous DNA double-strand breaks (DSBs) and common fragile site (CFS) instability. However, the mechanism of TRC resolution remains unclear. Here, we show that conjugation of SUMO2, but not SUMO1 or SUMO3, to the essential replication factor PCNA is induced on transcribed chromatin by the RNAPII-bound helicase RECQ5. Proteomic analysis reveals that SUMO2-PCNA enriches histone chaperones CAF1 and FACT in the replication complex via interactions with their SUMO-interacting motifs. SUMO2-PCNA enhances CAF1-dependent histone deposition, which correlates with increased histone H3.1 at CFSs and repressive histone marks in the chromatin to reduce chromatin accessibility. Hence, SUMO2-PCNA dislodges RNAPII at CFSs, and overexpressing either SUMO2-PCNA or CAF1 reduces the incidence of DSBs in TRC-prone RECQ5-deficient cells.
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Affiliation(s)
- Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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14
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Muñoz-Viana R, Wildhaber T, Trejo-Arellano MS, Mozgová I, Hennig L. Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:363-374. [PMID: 28786541 DOI: 10.1111/tpj.13658] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 07/21/2017] [Accepted: 08/01/2017] [Indexed: 05/23/2023]
Abstract
Chromatin Assembly Factor 1 (CAF-1) is a major nucleosome assembly complex which functions particularly during DNA replication and repair. Here we studied how the nucleosome landscape changes in a CAF-1 mutant in the model plant Arabidopsis thaliana. Globally, most nucleosomes were not affected by loss of CAF-1, indicating the presence of efficient alternative nucleosome assemblers. Nucleosomes that we found depleted in the CAF-1 mutant were enriched in non-transcribed regions, consistent with the notion that CAF-1-independent nucleosome assembly can compensate for loss of CAF-1 mainly in transcribed regions. Depleted nucleosomes were particularly enriched in proximal promoters, suggesting that CAF-1-independent nucleosome assembly mechanisms are often not efficient upstream of transcription start sites. Genes related to plant defense were particularly prone to lose nucleosomes in their promoters upon CAF-1 depletion. Reduced nucleosome occupancy at promoters of many defense-related genes is associated with a primed gene expression state that may considerably increase plant fitness by facilitating plant defense. Together, our results establish that the nucleosome landscape in Arabidopsis is surprisingly robust even in the absence of the dedicated nucleosome assembly machinery CAF-1 and that CAF-1-independent nucleosome assembly mechanisms are less efficient in particular genome regions.
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Affiliation(s)
- Rafael Muñoz-Viana
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Thomas Wildhaber
- Department of Biology, ETH Zürich, Universitätsstrasse 2, CH-8092, Zürich, Switzerland
| | - Minerva S Trejo-Arellano
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Iva Mozgová
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
- Institute of Microbiology, Centre Algatech, Opatovický mlýn, 37981, Třeboň, Czech Republic
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
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15
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Agudelo Garcia PA, Hoover ME, Zhang P, Nagarajan P, Freitas MA, Parthun MR. Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly. Nucleic Acids Res 2017; 45:9319-9335. [PMID: 28666361 PMCID: PMC5766187 DOI: 10.1093/nar/gkx545] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
Histone acetyltransferase 1 (Hat1) catalyzes the acetylation of newly synthesized histone H4 at lysines 5 and 12 that accompanies replication-coupled chromatin assembly. The acetylation of newly synthesized H4 occurs in the cytoplasm and the function of this acetylation is typically ascribed to roles in either histone nuclear import or deposition. Using cell lines from Hat1+/+ and Hat1−/− mouse embryos, we demonstrate that Hat1 is not required for either histone nuclear import or deposition. We employed quantitative proteomics to characterize Hat1-dependent changes in the composition of nascent chromatin structure. Among the proteins depleted from nascent chromatin isolated from Hat1−/− cells are several bromodomain-containing proteins, including Brg1, Baz1A and Brd3. Analysis of the binding specificity of their bromodomains suggests that Hat1-dependent acetylation of H4 is directly involved in their recruitment. Hat1−/− nascent chromatin is enriched for topoisomerase 2α and 2β. The enrichment of topoisomerase 2 is functionally relevant as Hat1−/− cells are hyper-sensitive to topoisomerase 2 inhibition suggesting that Hat1 is required for proper chromatin topology. In addition, our results indicate that Hat1 is transiently recruited to sites of chromatin assembly, dissociating prior to the maturation of chromatin structure.
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Affiliation(s)
- Paula A Agudelo Garcia
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael E Hoover
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Pei Zhang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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16
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Lee KY, Im JS, Shibata E, Dutta A. ASF1a Promotes Non-homologous End Joining Repair by Facilitating Phosphorylation of MDC1 by ATM at Double-Strand Breaks. Mol Cell 2017; 68:61-75.e5. [PMID: 28943310 PMCID: PMC5743198 DOI: 10.1016/j.molcel.2017.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/17/2017] [Accepted: 08/22/2017] [Indexed: 11/15/2022]
Abstract
Double-strand breaks (DSBs) of DNA in eukaryotic cells are predominantly repaired by non-homologous end joining (NHEJ). The histone chaperone anti-silencing factor 1a (ASF1a) interacts with MDC1 and is recruited to sites of DSBs to facilitate the interaction of phospho-ATM with MDC1 and phosphorylation of MDC1, which are required for the recruitment of RNF8/RNF168 histone ubiquitin ligases. Thus, ASF1a deficiency reduces histone ubiquitination at DSBs, decreasing the recruitment of 53BP1, and decreases NHEJ, rendering cells more sensitive to DSBs. This role of ASF1a in DSB repair cannot be provided by the closely related ASF1b and does not require its histone chaperone activity. Homozygous deletion of ASF1A is seen in 10%-15% of certain cancers, suggesting that loss of NHEJ may be selected in some malignancies and that the deletion can be used as a molecular biomarker for cancers susceptible to radiotherapy or to DSB-inducing chemotherapy.
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Affiliation(s)
- Kyung Yong Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Jun-Sub Im
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.
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17
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The Effects of Replication Stress on S Phase Histone Management and Epigenetic Memory. J Mol Biol 2017; 429:2011-2029. [DOI: 10.1016/j.jmb.2016.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022]
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18
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Abstract
The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation.
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19
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Sauer PV, Timm J, Liu D, Sitbon D, Boeri-Erba E, Velours C, Mücke N, Langowski J, Ochsenbein F, Almouzni G, Panne D. Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1. eLife 2017; 6:e23474. [PMID: 28315525 PMCID: PMC5404918 DOI: 10.7554/elife.23474] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/09/2017] [Indexed: 12/16/2022] Open
Abstract
How the very first step in nucleosome assembly, deposition of histone H3-H4 as tetramers or dimers on DNA, is accomplished remains largely unclear. Here, we report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution. We identify a new DNA-binding domain in the large Cac1 subunit of CAF1, which is required for high-affinity DNA binding by the CAF1 three-subunit complex, and which is distinct from the previously described C-terminal winged-helix domain. CAF1 binds preferentially to DNA molecules longer than 40 bp, and two CAF1-H3-H4 complexes concertedly associate with DNA molecules of this size, resulting in deposition of H3-H4 tetramers. While DNA binding is not essential for H3-H4 tetrasome deposition in vitro, it is required for efficient DNA synthesis-coupled nucleosome assembly. Mutant histones with impaired H3-H4 tetramerization interactions fail to release from CAF1, indicating that DNA deposition of H3-H4 tetramers by CAF1 requires a hierarchical cooperation between DNA binding, H3-H4 deposition and histone tetramerization.
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Affiliation(s)
| | - Jennifer Timm
- European Molecular Biology Laboratory, Grenoble, France
| | - Danni Liu
- CEA, DRF, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - David Sitbon
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Elisabetta Boeri-Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Norbert Mücke
- Abteilung Biophysik der Makromoleküle, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jörg Langowski
- Abteilung Biophysik der Makromoleküle, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Françoise Ochsenbein
- CEA, DRF, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France
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20
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Xie J, Wooten M, Tran V, Chen X. Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells. Trends Cell Biol 2017; 27:527-540. [PMID: 28268050 DOI: 10.1016/j.tcb.2017.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 01/17/2023]
Abstract
Asymmetric cell division (ACD) gives rise to two daughter cells with distinct fates. ACD is widely used during development and by many types of adult stem cells during tissue homeostasis and regeneration. ACD can be regulated by extrinsic cues, such as signaling molecules, as well as by intrinsic factors, such as organelles and cortex proteins. The recent discovery of asymmetric histone inheritance during stem cell ACD has revealed another intrinsic mechanism by which ACD produces two distinct daughters. In this review we discuss these findings in the context of cell-cycle regulation, as well as other studies of ACD, to begin understanding the underlying mechanisms and biological relevance of this phenomenon.
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Affiliation(s)
- Jing Xie
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vuong Tran
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Current address: Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North Seattle, Seattle, WA 98109, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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21
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Chang HW, Studitsky VM. Chromatin replication: TRANSmitting the histone code. JOURNAL OF NATURE AND SCIENCE 2017; 3:e322. [PMID: 28393112 PMCID: PMC5384335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Efficient overcoming of the nucleosomal barrier and accurate maintenance of associated histone marks during chromatin replication are essential for normal functioning of the cell. Recent studies revealed new protein factors and histone modifications contributing to overcoming the nucleosomal barrier, and suggested an important role for DNA looping in survival of the original histones during replication. These studies suggest new possible mechanisms for transmitting the histone code to next generations of cells.
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Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Vasily M. Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Biology Faculty, Lomonosov Moscow State University; Moscow, Russia
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22
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Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 2017; 18:141-158. [PMID: 28053344 DOI: 10.1038/nrm.2016.159] [Citation(s) in RCA: 347] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The association of histones with specific chaperone complexes is important for their folding, oligomerization, post-translational modification, nuclear import, stability, assembly and genomic localization. In this way, the chaperoning of soluble histones is a key determinant of histone availability and fate, which affects all chromosomal processes, including gene expression, chromosome segregation and genome replication and repair. Here, we review the distinct structural and functional properties of the expanding network of histone chaperones. We emphasize how chaperones cooperate in the histone chaperone network and via co-chaperone complexes to match histone supply with demand, thereby promoting proper nucleosome assembly and maintaining epigenetic information by recycling modified histones evicted from chromatin.
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Affiliation(s)
- Colin M Hammond
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Caroline B Strømme
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Hongda Huang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
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23
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Talbert PB, Henikoff S. Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016; 18:115-126. [PMID: 27924075 DOI: 10.1038/nrm.2016.148] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most histones are assembled into nucleosomes behind the replication fork to package newly synthesized DNA. By contrast, histone variants, which are encoded by separate genes, are typically incorporated throughout the cell cycle. Histone variants can profoundly change chromatin properties, which in turn affect DNA replication and repair, transcription, and chromosome packaging and segregation. Recent advances in the study of histone replacement have elucidated the dynamic processes by which particular histone variants become substrates of histone chaperones, ATP-dependent chromatin remodellers and histone-modifying enzymes. Here, we review histone variant dynamics and the effects of replacing DNA synthesis-coupled histones with their replication-independent variants on the chromatin landscape.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA
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24
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A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function. J Mol Biol 2016; 429:1924-1933. [PMID: 27871933 DOI: 10.1016/j.jmb.2016.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Incorporation of variant histone sequences, in addition to post-translational modification of histones, serves to modulate the chromatin environment. Different histone chaperone proteins mediate the storage and chromatin deposition of variant histones. Although the two non-centromeric histone H3 variants, H3.1 and H3.3, differ by only 5 aa, replacement of histone H3.1 with H3.3 can modulate the transcription for highly expressed and developmentally required genes, lead to the formation of repressive heterochromatin, or aid in DNA and chromatin repair. The human histone cell cycle regulator (HIRA) complex composed of HIRA, ubinuclein-1, CABIN1, and transiently anti-silencing function 1, forms one of the two complexes that bind and deposit H3.3/H4 into chromatin. A number of recent biochemical and structural studies have revealed important details underlying how these proteins assemble and function together as a multiprotein H3.3-specific histone chaperone complex. Here, we present a review of existing data and present a new model for the assembly of the HIRA complex and for the HIRA-mediated incorporation of H3.3/H4 into chromatin.
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25
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Maksimov V, Nakamura M, Wildhaber T, Nanni P, Ramström M, Bergquist J, Hennig L. The H3 chaperone function of NASP is conserved in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:425-436. [PMID: 27402088 DOI: 10.1111/tpj.13263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Histones are abundant cellular proteins but, if not incorporated into chromatin, they are usually bound by histone chaperones. Here, we identify Arabidopsis NASP as a chaperone for histones H3.1 and H3.3. NASP interacts in vitro with monomeric H3.1 and H3.3 as well as with histone H3.1-H4 and H3.3-H4 dimers. However, NASP does not bind to monomeric H4. NASP shifts the equilibrium between histone dimers and tetramers towards tetramers but does not interact with tetramers in vitro. Arabidopsis NASP promotes [H3-H4]2 tetrasome formation, possibly by providing preassembled histone tetramers. However, NASP does not promote disassembly of in vitro preassembled tetrasomes. In contrast to its mammalian homolog, Arabidopsis NASP is a predominantly nuclear protein. In vivo, NASP binds mainly monomeric H3.1 and H3.3. Pulldown experiments indicated that NASP may also interact with the histone chaperone MSI1 and a HSC70 heat shock protein.
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Affiliation(s)
- Vladimir Maksimov
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Miyuki Nakamura
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
| | - Thomas Wildhaber
- Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, CH-8057, Zurich, Switzerland
| | - Margareta Ramström
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, SE-75124, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, SE-75007, Uppsala, Sweden
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26
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Liu WH, Roemer SC, Zhou Y, Shen ZJ, Dennehey BK, Balsbaugh JL, Liddle JC, Nemkov T, Ahn NG, Hansen KC, Tyler JK, Churchill ME. The Cac1 subunit of histone chaperone CAF-1 organizes CAF-1-H3/H4 architecture and tetramerizes histones. eLife 2016; 5. [PMID: 27690308 PMCID: PMC5045291 DOI: 10.7554/elife.18023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/25/2016] [Indexed: 01/16/2023] Open
Abstract
The histone chaperone Chromatin Assembly Factor 1 (CAF-1) deposits tetrameric (H3/H4)2 histones onto newly-synthesized DNA during DNA replication. To understand the mechanism of the tri-subunit CAF-1 complex in this process, we investigated the protein-protein interactions within the CAF-1-H3/H4 architecture using biophysical and biochemical approaches. Hydrogen/deuterium exchange and chemical cross-linking coupled to mass spectrometry reveal interactions that are essential for CAF-1 function in budding yeast, and importantly indicate that the Cac1 subunit functions as a scaffold within the CAF-1-H3/H4 complex. Cac1 alone not only binds H3/H4 with high affinity, but also promotes histone tetramerization independent of the other subunits. Moreover, we identify a minimal region in the C-terminus of Cac1, including the structured winged helix domain and glutamate/aspartate-rich domain, which is sufficient to induce (H3/H4)2 tetramerization. These findings reveal a key role of Cac1 in histone tetramerization, providing a new model for CAF-1-H3/H4 architecture and function during eukaryotic replication. DOI:http://dx.doi.org/10.7554/eLife.18023.001 The DNA of a human, yeast or other eukaryotic cell is bound to proteins called histones to form repeating units called nucleosomes. Every time a eukaryotic cell divides, it must duplicate its DNA. Old histones are first removed from the nucleosomes before being re-assembled onto the newly duplicated DNA along with new histone proteins, producing a full complement of nucleosomes. A group of proteins called the chromatin assembly factor 1 (or CAF-1 for short) helps to assemble the histones onto the DNA. CAF-1 is made up of three proteins, and binds to two copies of each of the histones known as H3 and H4. These are the first histones to be assembled onto the nucleosomes. It was not clear how the components of CAF-1 are organized, or how CAF-1 recognizes histones. Liu et al. have now investigated the structure of CAF-1 and its interactions with the H3 and H4 histones by studying yeast proteins and cells. Yeast is a good model system because yeast CAF-1 is smaller and easier to isolate than human CAF-1, yet still performs the same essential activities. Using a combination of biochemical and biophysical techniques, Liu et al. found that one of the three proteins that makes up yeast CAF-1 – called Cac1 – forms a scaffold that supports the other CAF-1 proteins and histones H3 and H4. Moreover, a specific part of Cac1 is able to bind to these histones and assemble two copies of each of them to prepare for efficient nucleosome assembly. Further experiments revealed the specific areas where the CAF-1 proteins interact with each other and with the histones, determined how strong those interactions are, and confirmed that these interactions play important roles in yeast. Overall, the results presented by Liu et al. provide new insights into the structure of CAF-1 bound to H3 and H4. In order to understand in detail how CAF-1 helps to assemble histones onto DNA, future work needs to capture three-dimensional snapshots of the different steps in this process. Further investigation is also needed to discover how CAF-1 cooperates with other factors that promote DNA duplication. DOI:http://dx.doi.org/10.7554/eLife.18023.002
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Affiliation(s)
- Wallace H Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Sarah C Roemer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Yeyun Zhou
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Zih-Jie Shen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States
| | - Briana K Dennehey
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, Houston, United States
| | - Jeremy L Balsbaugh
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Jennifer C Liddle
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Travis Nemkov
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States.,BioFrontiers Institute, University of Colorado, Boulder, Boulder, United States
| | - Kirk C Hansen
- Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, United States.,Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, Houston, United States
| | - Mair Ea Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States.,Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, United States
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27
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A Quantitative Characterization of Nucleoplasmin/Histone Complexes Reveals Chaperone Versatility. Sci Rep 2016; 6:32114. [PMID: 27558753 PMCID: PMC4997359 DOI: 10.1038/srep32114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023] Open
Abstract
Nucleoplasmin (NP) is an abundant histone chaperone in vertebrate oocytes and embryos involved in storing and releasing maternal histones to establish and maintain the zygotic epigenome. NP has been considered a H2A-H2B histone chaperone, and recently it has been shown that it can also interact with H3-H4. However, its interaction with different types of histones has not been quantitatively studied so far. We show here that NP binds H2A-H2B, H3-H4 and linker histones with Kd values in the subnanomolar range, forming different complexes. Post-translational modifications of NP regulate exposure of the polyGlu tract at the disordered distal face of the protein and induce an increase in chaperone affinity for all histones. The relative affinity of NP for H2A-H2B and linker histones and the fact that they interact with the distal face of the chaperone could explain their competition for chaperone binding, a relevant process in NP-mediated sperm chromatin remodelling during fertilization. Our data show that NP binds H3-H4 tetramers in a nucleosomal conformation and dimers, transferring them to DNA to form disomes and tetrasomes. This finding might be relevant to elucidate the role of NP in chromatin disassembly and assembly during replication and transcription.
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28
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Kim D, Setiaputra D, Jung T, Chung J, Leitner A, Yoon J, Aebersold R, Hebert H, Yip CK, Song JJ. Molecular Architecture of Yeast Chromatin Assembly Factor 1. Sci Rep 2016; 6:26702. [PMID: 27221973 PMCID: PMC4879628 DOI: 10.1038/srep26702] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 05/09/2016] [Indexed: 12/16/2022] Open
Abstract
Chromatin Assembly Complex 1 (CAF-1) is a major histone chaperone involved in deposition of histone H3 and H4 into nucleosome. CAF-1 is composed of three subunits; p150, p60 and p48 for human and Cac1, Cac2 and Cac3 for yeast. Despite of its central role in chromatin formation, structural features of the full CAF-1 in complex with histones and other chaperones have not been well characterized. Here, we dissect molecular architecture of yeast CAF-1 (yCAF-1) by cross-linking mass spectrometry (XL-MS) and negative stain single-particle electron microscopy (EM). Our work revealed that Cac1, the largest subunit of yCAF-1, might serve as a major histone binding platform linking Cac2 and Cac3. In addition, EM analysis showed that yCAF-1 adopts a bilobal shape and Cac1 connecting Cac2 and Cac3 to generate a platform for binding histones. This study provides the first structural glimpse of the full CAF-1 complex and a structural framework to understand histone chaperoning processes.
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Affiliation(s)
- Daegeun Kim
- Department of Biological Sciences, KAIST Institute for the BioCentury, Cancer Metastasis Control Center, KAIST, 291 Daehakro Yuseong Daejeon, 34141, Korea
| | - Dheva Setiaputra
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Taeyang Jung
- Department of Biological Sciences, KAIST Institute for the BioCentury, Cancer Metastasis Control Center, KAIST, 291 Daehakro Yuseong Daejeon, 34141, Korea.,Department of Biosciences and Nutrition, Karolinska Institute, and School of Technology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden
| | - Jaehee Chung
- Department of Biological Sciences, KAIST Institute for the BioCentury, Cancer Metastasis Control Center, KAIST, 291 Daehakro Yuseong Daejeon, 34141, Korea
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jungmin Yoon
- Department of Biological Sciences, KAIST Institute for the BioCentury, Cancer Metastasis Control Center, KAIST, 291 Daehakro Yuseong Daejeon, 34141, Korea
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institute, and School of Technology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Ji-Joon Song
- Department of Biological Sciences, KAIST Institute for the BioCentury, Cancer Metastasis Control Center, KAIST, 291 Daehakro Yuseong Daejeon, 34141, Korea
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29
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Zhang K, Gao Y, Li J, Burgess R, Han J, Liang H, Zhang Z, Liu Y. A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks. Nucleic Acids Res 2016; 44:5083-94. [PMID: 26908650 PMCID: PMC4914081 DOI: 10.1093/nar/gkw106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/15/2016] [Indexed: 02/05/2023] Open
Abstract
Chromatin assembly factor 1 (CAF-1) is a histone H3–H4 chaperone that deposits newly synthesized histone (H3–H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a subunit of yeast CAF-1, and the function of this domain in stabilizing CAF-1 at replication forks. We show that Cac1C forms a winged helix domain (WHD) and binds DNA in a sequence-independent manner. Mutations in Cac1C that abolish DNA binding result in defects in transcriptional silencing and increased sensitivity to DNA damaging agents, and these defects are exacerbated when combined with Cac1 mutations deficient in PCNA binding. Similar phenotypes are observed for corresponding mutations in mouse CAF-1. These results reveal a mechanism conserved in eukaryotic cells whereby the ability of CAF-1 to bind DNA is important for its association with the DNA replication forks and subsequent nucleosome assembly.
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Affiliation(s)
- Kuo Zhang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Gao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jingjing Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Rebecca Burgess
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Division of Abdominal Cancer, West China Hospital, Sichuan University, and National Collaborative innovation Center for Biotherapy, Chengdu 610041, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Zhiguo Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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30
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Yang J, Zhang X, Feng J, Leng H, Li S, Xiao J, Liu S, Xu Z, Xu J, Li D, Wang Z, Wang J, Li Q. The Histone Chaperone FACT Contributes to DNA Replication-Coupled Nucleosome Assembly. Cell Rep 2016; 14:1128-1141. [PMID: 26804921 DOI: 10.1016/j.celrep.2015.12.096] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/17/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022] Open
Abstract
DNA replication-coupled (RC) nucleosome assembly is mediated by histone chaperones and is fundamental for epigenetic inheritance and maintenance of genomic integrity. The mechanisms that promote this process are only partially understood. Here, we show that the histone chaperone FACT (facilitates chromatin transactions), consisting of Spt16 and Pob3, promotes newly synthesized histone H3-H4 deposition. We describe an allele of Spt16 (spt16-m) that has a defect in binding to H3-H4 and impairs their deposition onto DNA. Consistent with a direct role for FACT in RC nucleosome assembly, spt16-m displays synthetic defects with other histone chaperones associated with this process, CAF-1 and Rtt106. Importantly, we show that FACT physically associates with Rtt106 and that the acetylation of H3K56, a mark on newly synthesized H3, modulates this interaction. Therefore, FACT collaborates with CAF-1 and Rtt106 in RC nucleosome assembly.
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Affiliation(s)
- Jiayi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xu Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - He Leng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuqi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shaofeng Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhiyun Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiawei Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Di Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhongshi Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jingyang Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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31
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Haigney A, Ricketts MD, Marmorstein R. Dissecting the Molecular Roles of Histone Chaperones in Histone Acetylation by Type B Histone Acetyltransferases (HAT-B). J Biol Chem 2015; 290:30648-57. [PMID: 26522166 DOI: 10.1074/jbc.m115.688523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Indexed: 12/26/2022] Open
Abstract
The HAT-B enzyme complex is responsible for acetylating newly synthesized histone H4 on lysines K5 and K12. HAT-B is a multisubunit complex composed of the histone acetyltransferase 1 (Hat1) catalytic subunit and the Hat2 (rbap46) histone chaperone. Hat1 is predominantly localized in the nucleus as a member of a trimeric NuB4 complex containing Hat1, Hat2, and a histone H3-H4 specific histone chaperone called Hif1 (NASP). In addition to Hif1 and Hat2, Hat1 interacts with Asf1 (anti-silencing function 1), a histone chaperone that has been reported to be involved in both replication-dependent and -independent chromatin assembly. To elucidate the molecular roles of the Hif1 and Asf1 histone chaperones in HAT-B histone binding and acetyltransferase activity, we have characterized the stoichiometry and binding mode of Hif1 and Asf1 to HAT-B and the effect of this binding on the enzymatic activity of HAT-B. We find that Hif1 and Asf1 bind through different modes and independently to HAT-B, whereby Hif1 binds directly to Hat2, and Asf1 is only capable of interactions with HAT-B through contacts with histones H3-H4. We also demonstrate that HAT-B is significantly more active against an intact H3-H4 heterodimer over a histone H4 peptide, independent of either Hif1 or Asf1 binding. Mutational studies further demonstrate that HAT-B binding to the histone tail regions is not sufficient for this enhanced activity. Based on these data, we propose a model for HAT-B/histone chaperone assembly and acetylation of H3-H4 complexes.
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Affiliation(s)
- Allison Haigney
- From the Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, and
| | - M Daniel Ricketts
- From the Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, and the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ronen Marmorstein
- From the Department of Biochemistry & Biophysics, Abramson Family Cancer Research Institute, and
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32
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Campos EI, Smits AH, Kang YH, Landry S, Escobar TM, Nayak S, Ueberheide BM, Durocher D, Vermeulen M, Hurwitz J, Reinberg D. Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. Mol Cell 2015; 60:697-709. [PMID: 26527279 DOI: 10.1016/j.molcel.2015.08.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/17/2015] [Accepted: 08/07/2015] [Indexed: 11/17/2022]
Abstract
Despite minimal disparity at the sequence level, mammalian H3 variants bind to distinct sets of polypeptides. Although histone H3.1 predominates in cycling cells, our knowledge of the soluble complexes that it forms en route to deposition or following eviction from chromatin remains limited. Here, we provide a comprehensive analysis of the H3.1-binding proteome, with emphasis on its interactions with histone chaperones and components of the replication fork. Quantitative mass spectrometry revealed 170 protein interactions, whereas a large-scale biochemical fractionation of H3.1 and associated enzymatic activities uncovered over twenty stable protein complexes in dividing human cells. The sNASP and ASF1 chaperones play pivotal roles in the processing of soluble histones but do not associate with the active CDC45/MCM2-7/GINS (CMG) replicative helicase. We also find TONSL-MMS22L to function as a H3-H4 histone chaperone. It associates with the regulatory MCM5 subunit of the replicative helicase.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Young-Hoon Kang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Sébastien Landry
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Thelma M Escobar
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Shruti Nayak
- Office of Collaborative Science, New York University School of Medicine, NY 10016, USA
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Molecular Genetics, University of Toronto, Toronto M5G 1X5, Canada
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands 6525 GA
| | - Jerard Hurwitz
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University School of Medicine, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA.
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33
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Ricketts MD, Frederick B, Hoff H, Tang Y, Schultz DC, Singh Rai T, Grazia Vizioli M, Adams PD, Marmorstein R. Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex. Nat Commun 2015; 6:7711. [PMID: 26159857 PMCID: PMC4510971 DOI: 10.1038/ncomms8711] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/01/2015] [Indexed: 01/01/2023] Open
Abstract
Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to mediate H3.3-specific binding and chromatin deposition. Here we demonstrate that the conserved UBN1 Hpc2-related domain (HRD) is a novel H3.3-specific-binding domain. Biochemical and biophysical studies show the UBN1-HRD preferentially binds H3.3/H4 over H3.1/H4. X-ray crystallographic and mutational studies reveal that conserved residues within the UBN1-HRD and H3.3 G90 as key determinants of UBN1–H3.3-binding specificity. Comparison of the structure with the unrelated H3.3-specific chaperone DAXX reveals nearly identical points of contact between the chaperone and histone in the proximity of H3.3 G90, although the mechanism for H3.3 G90 recognition appears to be distinct. This study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA complex. Ubinuclein-1 (UBN1) is a subunit of the HIRA histone chaperone complex that deposits histone H3.3 into chromatin. Here the authors use structural and biochemical studies to show that a conserved domain in UBN1 mediates H3.3-specific binding by the HIRA complex.
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Affiliation(s)
- M Daniel Ricketts
- 1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian Frederick
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Henry Hoff
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Yong Tang
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - David C Schultz
- The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA
| | - Taranjit Singh Rai
- 1] Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK [2] Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, UK
| | - Maria Grazia Vizioli
- Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK
| | - Peter D Adams
- Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK
| | - Ronen Marmorstein
- 1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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34
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Annunziato AT. The Fork in the Road: Histone Partitioning During DNA Replication. Genes (Basel) 2015; 6:353-71. [PMID: 26110314 PMCID: PMC4488668 DOI: 10.3390/genes6020353] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
In the following discussion the distribution of histones at the replication fork is examined, with specific attention paid to the question of H3/H4 tetramer "splitting." After a presentation of early experiments surrounding this topic, more recent contributions are detailed. The implications of these findings with respect to the transmission of histone modifications and epigenetic models are also addressed.
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Affiliation(s)
- Anthony T Annunziato
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
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35
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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36
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Gurard-Levin ZA, Quivy JP, Almouzni G. Histone chaperones: assisting histone traffic and nucleosome dynamics. Annu Rev Biochem 2015; 83:487-517. [PMID: 24905786 DOI: 10.1146/annurev-biochem-060713-035536] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The functional organization of eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. Histone chaperones, which are proteins that escort histones throughout their cellular life, are key actors in all facets of histone metabolism; they regulate the supply and dynamics of histones at chromatin for its assembly and disassembly. Histone chaperones can also participate in the distribution of histone variants, thereby defining distinct chromatin landscapes of importance for genome function, stability, and cell identity. Here, we discuss our current knowledge of the known histone chaperones and their histone partners, focusing on histone H3 and its variants. We then place them into an escort network that distributes these histones in various deposition pathways. Through their distinct interfaces, we show how they affect dynamics during DNA replication, DNA damage, and transcription, and how they maintain genome integrity. Finally, we discuss the importance of histone chaperones during development and describe how misregulation of the histone flow can link to disease.
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Affiliation(s)
- Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche; CNRS UMR 3664; Equipe Labellisée, Ligue contre le Cancer; and Université Pierre et Marie Curie, Paris F-75248, France;
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Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail M, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Res 2015; 43:1905-17. [PMID: 25618846 PMCID: PMC4330383 DOI: 10.1093/nar/gkv021] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.
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Affiliation(s)
- Nicolas Richet
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Danni Liu
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | | | - Christophe Velours
- Laboratoire d'Enzymologie et de Biologie Structurale, CNRS UPR 3082, 1 avenue de la Terrasse, Gif-sur-Yvette, F-91190, France
| | - Armelle Corpet
- Institut Curie, Centre de Recherche, CNRS UMR 3664, Equipe Labellisée Ligue contre le Cancer, and Université Pierre et Marie Curie, Université Sorbonne PSL*, Paris, F-75248, France
| | - Albane Gaubert
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - May Bakail
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Gwenaelle Moal-Raisin
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Raphael Guerois
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Christel Compper
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Arthur Besle
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Berengère Guichard
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
| | - Genevieve Almouzni
- Institut Curie, Centre de Recherche, CNRS UMR 3664, Equipe Labellisée Ligue contre le Cancer, and Université Pierre et Marie Curie, Université Sorbonne PSL*, Paris, F-75248, France
| | - Françoise Ochsenbein
- CEA, iBiTec-S, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, France Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Batiment 144, Gif-sur-Yvette, F-91191, France
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Abstract
A huge amount of information is stored in genomic DNA and this stored information resides inside the nucleus with the aid of chromosomal condensation factors. It has been reported that the repeat nucleosome core particle (NCP) consists of 147-bp of DNA and two copies of H2A, H2B, H3 and H4. Regulation of chromosomal structure is important to many processes inside the cell. In vivo, a group of histone chaperones facilitate and regulate nucleosome assembly. How NCPs are constructed with the aid of histone chaperones remains unclear. In this study, the histone chaperone-mediated nucleosome assembly process was investigated using single-molecule tethered particle motion (TPM) experiments. It was found that Asf1 is able to exert more influence than Nap1 and poly glutamate acid (PGA) on the nucleosome formation process, which highlights Asf1’s specific role in tetrasome formation. Thermodynamic parameters supported a model whereby energetically favored nucleosomal complexes compete with non-nucleosomal complexes. In addition, our kinetic findings propose the model that histone chaperones mediate nucleosome assembly along a path that leads to enthalpy-favored products with free histones as reaction substrates.
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Yu Z, Liu J, Deng WM, Jiao R. Histone chaperone CAF-1: essential roles in multi-cellular organism development. Cell Mol Life Sci 2015; 72:327-37. [PMID: 25292338 PMCID: PMC11114026 DOI: 10.1007/s00018-014-1748-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/16/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
Abstract
More and more studies have shown chromatin remodelers and histone modifiers play essential roles in regulating developmental patterns by organizing specific chromosomal architecture to establish programmed transcriptional profiles, with implications that histone chaperones execute a coordinating role in these processes. Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved three-subunit protein complex, was identified as a histone chaperone coupled with DNA replication and repair in cultured mammalian cells and yeasts. Interestingly, recent findings indicate CAF-1 may have important regulatory roles during development by interacting with specific transcription factors and epigenetic regulators. In this review, we focus on the essential roles of CAF-1 in regulating heterochromatin organization, asymmetric cell division, and specific signal transduction through epigenetic modulations of the chromatin. In the end, we aim at providing a current image of facets of CAF-1 as a histone chaperone to orchestrate cell proliferation and differentiation during multi-cellular organism development.
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Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Jiyong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295 USA
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
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40
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Muchová V, Amiard S, Mozgová I, Dvořáčková M, Gallego ME, White C, Fajkus J. Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:198-209. [PMID: 25359579 PMCID: PMC4309414 DOI: 10.1111/tpj.12718] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 05/19/2023]
Abstract
Arabidopsis thaliana mutants in FAS1 and FAS2 subunits of chromatin assembly factor 1 (CAF1) show progressive loss of 45S rDNA copies and telomeres. We hypothesized that homology-dependent DNA damage repair (HDR) may contribute to the loss of these repeats in fas mutants. To test this, we generated double mutants by crossing fas mutants with knock-out mutants in RAD51B, one of the Rad51 paralogs of A. thaliana. Our results show that the absence of RAD51B decreases the rate of rDNA loss, confirming the implication of RAD51B-dependent recombination in rDNA loss in the CAF1 mutants. Interestingly, this effect is not observed for telomeric repeat loss, which thus differs from that acting in rDNA loss. Involvement of DNA damage repair in rDNA dynamics in fas mutants is further supported by accumulation of double-stranded breaks (measured as γ-H2AX foci) in 45S rDNA. Occurrence of the foci is not specific for S-phase, and is ATM-independent. While the foci in fas mutants occur both in the transcribed (intranucleolar) and non-transcribed (nucleoplasmic) fraction of rDNA, double fas rad51b mutants show a specific increase in the number of the intranucleolar foci. These results suggest that the repair of double-stranded breaks present in the transcribed rDNA region is RAD51B dependent and that this contributes to rDNA repeat loss in fas mutants, presumably via the single-stranded annealing recombination pathway. Our results also highlight the importance of proper chromatin assembly in the maintenance of genome stability.
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Affiliation(s)
- Veronika Muchová
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
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41
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Tessarz P, Kouzarides T. Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 2014; 15:703-8. [PMID: 25315270 DOI: 10.1038/nrm3890] [Citation(s) in RCA: 651] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Post-translational modifications of histones regulate all DNA-templated processes, including replication, transcription and repair. These modifications function as platforms for the recruitment of specific effector proteins, such as transcriptional regulators or chromatin remodellers. Recent data suggest that histone modifications also have a direct effect on nucleosomal architecture. Acetylation, methylation, phosphorylation and citrullination of the histone core may influence chromatin structure by affecting histone-histone and histone-DNA interactions, as well as the binding of histones to chaperones.
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Affiliation(s)
- Peter Tessarz
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK; and the Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Tony Kouzarides
- Gurdon Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QN, UK
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42
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Campos EI, Stafford JM, Reinberg D. Epigenetic inheritance: histone bookmarks across generations. Trends Cell Biol 2014; 24:664-74. [PMID: 25242115 DOI: 10.1016/j.tcb.2014.08.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/22/2022]
Abstract
Multiple circuitries ensure that cells respond correctly to the environmental cues within defined cellular programs. There is increasing evidence suggesting that cellular memory for these adaptive processes can be passed on through cell divisions and generations. However, the mechanisms by which this epigenetic information is transferred remain elusive, largely because it requires that such memory survive through gross chromatin remodeling events during DNA replication, mitosis, meiosis, and developmental reprogramming. Elucidating the processes by which epigenetic information survives and is transmitted is a central challenge in biology. In this review, we consider recent advances in understanding mechanisms of epigenetic inheritance with a focus on histone segregation at the replication fork, and how an epigenetic memory may get passed through the paternal lineage.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - James M Stafford
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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43
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Bošković A, Eid A, Pontabry J, Ishiuchi T, Spiegelhalter C, Raghu Ram EVS, Meshorer E, Torres-Padilla ME. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes Dev 2014; 28:1042-7. [PMID: 24831699 PMCID: PMC4035533 DOI: 10.1101/gad.238881.114] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Torres-Padilla and colleagues investigate the chromatin-based mechanisms behind the transition from totipotency to pluripotency in the developing mouse embryo. Tracking histone dynamics by FRAP in vivo reveals that core histone mobility decreases as development proceeds, defining different cellular states (totipotency, pluripotency, and differentiation). Strikingly, totipotent cells in vitro display the same high chromatin mobility as totipotent cells in the embryo. The data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency. The fusion of the gametes upon fertilization results in the formation of a totipotent cell. Embryonic chromatin is expected to be able to support a large degree of plasticity. However, whether this plasticity relies on a particular conformation of the embryonic chromatin is unknown. Moreover, whether chromatin plasticity is functionally linked to cellular potency has not been addressed. Here, we adapted fluorescence recovery after photobleaching (FRAP) in the developing mouse embryo and show that mobility of the core histones H2A, H3.1, and H3.2 is unusually high in two-cell stage embryos and decreases as development proceeds. The transition toward pluripotency is accompanied by a decrease in histone mobility, and, upon lineage allocation, pluripotent cells retain higher mobility than the differentiated trophectoderm. Importantly, totipotent two-cell-like embryonic stem cells also display high core histone mobility, implying that reprogramming toward totipotency entails changes in chromatin mobility. Our data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency.
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Affiliation(s)
- Ana Bošković
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - André Eid
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Julien Pontabry
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Takashi Ishiuchi
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Coralie Spiegelhalter
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Edupuganti V S Raghu Ram
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Maria-Elena Torres-Padilla
- CNRS/INSERM U964, Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
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DeNizio JE, Elsässer SJ, Black BE. DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues. Nucleic Acids Res 2014; 42:4318-31. [PMID: 24493739 PMCID: PMC3985662 DOI: 10.1093/nar/gku090] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/17/2013] [Accepted: 01/08/2014] [Indexed: 01/08/2023] Open
Abstract
Histone chaperones are a diverse class of proteins that facilitate chromatin assembly. Their ability to stabilize highly abundant histone proteins in the cellular environment prevents non-specific interactions and promotes nucleosome formation, but the various mechanisms for doing so are not well understood. We now focus on the dynamic features of the DAXX histone chaperone that have been elusive from previous structural studies. Using hydrogen/deuterium exchange coupled to mass spectrometry (H/DX-MS), we elucidate the concerted binding-folding of DAXX with histone variants H3.3/H4 and H3.2/H4 and find that high local stability at the variant-specific recognition residues rationalizes its known selectivity for H3.3. We show that the DAXX histone binding domain is largely disordered in solution and that formation of the H3.3/H4/DAXX complex induces folding and dramatic global stabilization of both histone and chaperone. Thus, DAXX uses a novel strategy as a molecular chaperone that paradoxically couples its own folding to substrate recognition and binding. Further, we propose a model for the chromatin assembly reaction it mediates, including a stepwise folding pathway that helps explain the fidelity of DAXX in associating with the H3.3 variant, despite an extensive and nearly identical binding surface on its counterparts, H3.1 and H3.2.
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Affiliation(s)
- Jamie E. DeNizio
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA and MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Simon J. Elsässer
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA and MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA and MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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45
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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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46
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Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication. Nat Commun 2014; 5:3394. [PMID: 24598821 PMCID: PMC3977046 DOI: 10.1038/ncomms4394] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 02/05/2014] [Indexed: 12/25/2022] Open
Abstract
During DNA replication, nucleosomes are rapidly assembled on newly synthesized DNA to restore chromatin organization. Asf1, a key histone H3-H4 chaperone required for this process, is phosphorylated by Tousled-Like Kinases (TLKs). Here, we identify TLK phosphorylation sites by mass spectrometry and dissect how phosphorylation impacts on human Asf1 function. The divergent C-terminal tail of Asf1a is phosphorylated at several sites and this is required for timely progression through S phase. Consistent with this, biochemical analysis of wild-type and phosphomimetic Asf1a shows that phosphorylation enhances binding to histones and the downstream chaperones CAF-1 and HIRA. Moreover, we find that TLK phosphorylation of Asf1a is induced in cells experiencing deficiency of new histones and that TLK interaction with Asf1a involves its histone-binding pocket. We thus propose that TLK signaling promotes histone supply in S phase by targeting histone-free Asf1 and stimulating its ability to shuttle histones to sites of chromatin assembly.
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47
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Han J, Zhang H, Zhang H, Wang Z, Zhou H, Zhang Z. A Cul4 E3 ubiquitin ligase regulates histone hand-off during nucleosome assembly. Cell 2014; 155:817-29. [PMID: 24209620 DOI: 10.1016/j.cell.2013.10.014] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 05/12/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
Abstract
Nucleosome assembly following DNA replication and gene transcription is important to maintain genome stability and epigenetic information. Newly synthesized histones H3-H4 first bind histone chaperone Asf1 and are then transferred to other chaperones for nucleosome assembly. However, it is unknown how H3-H4 is transferred from the Asf1-H3-H4 complex to other chaperones because Asf1 binds H3-H4 with high affinity. Here, we show that yeast Rtt101(Mms1) E3 ubiquitin ligase preferentially binds and ubiquitylates new histone H3 acetylated at lysine 56. Inactivation of Rtt101 or mutating H3 lysine residues ubiquitylated by the Rtt101(Mms1) ligase impairs nucleosome assembly and promotes Asf1-H3 interactions. Similar phenotypes occur in human cells in which the ortholog of Rtt101(Mms1), Cul4A(DDB1), is depleted. These results indicate that the transfer of H3-H4 from the Asf1-H3-H4 complex to other histone chaperones is regulated by a conserved E3 ligase and provide evidence for crosstalk between histone acetylation and ubiquitylation in nucleosome assembly.
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Affiliation(s)
- Junhong Han
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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48
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Latreille D, Bluy L, Benkirane M, Kiernan RE. Identification of histone 3 variant 2 interacting factors. Nucleic Acids Res 2014; 42:3542-50. [PMID: 24393775 PMCID: PMC3973350 DOI: 10.1093/nar/gkt1355] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenome is defined as a type of information that can be transmitted independently of the DNA sequence, at the chromatin level, through post-translational modifications present on histone tails. Recent advances in the identification of histone 3 variants suggest a new model of information transmission through deposition of specific histone variants. To date, several non-centromeric histone 3 variants have been identified in mammals. Despite protein sequence similarity, specific deposition complexes have been characterized for both histone 3.1 (H3.1) and histone 3.3 (H3.3), whereas no deposition complex for histone 3.2 (H3.2) has been identified to date. Here, we identified human H3.2 partners by immunopurification of nuclear H3.2 complexes followed by mass spectrometry analysis. Further biochemical analyses highlighted two major complexes associated with H3.2, one containing chromatin associated factor-1 subunits and the other consisting of a subcomplex of mini chromosome maintenance helicases, together with Asf1. The purified complexes could associate with a DNA template in vitro.
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Affiliation(s)
- Daniel Latreille
- Laboratoire de Régulation des Gènes, Institut de Génétique Humaine, CNRS UPR1142, Montpellier 34396, France and Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS UPR1142, Montpellier 34396, France
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Fang L, Wuptra K, Chen D, Li H, Huang SK, Jin C, Yokoyama KK. Environmental-stress-induced Chromatin Regulation and its Heritability. ACTA ACUST UNITED AC 2014; 5. [PMID: 25045581 PMCID: PMC4101908 DOI: 10.4172/2157-2518.1000156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives.
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Affiliation(s)
- Lei Fang
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Kenly Wuptra
- Center of Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd, San Ming District, Kaohsiung 807, Taiwan ; Division of Environmental Health and Occupational Medicine, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli County 350, Taiwan
| | - Danqi Chen
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Hongjie Li
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Shau-Ku Huang
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, 35 Keyan Rd, Zhunan, Miaoli County 350, Taiwan ; Johns Hopkins Asthma and Allergy Center, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, NYU School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Kazunari K Yokoyama
- Center of Environmental Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd, San Ming District, Kaohsiung 807, Taiwan
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Ramos I, Fernández-Rivero N, Arranz R, Aloria K, Finn R, Arizmendi JM, Ausió J, Valpuesta JM, Muga A, Prado A. The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. Nucleic Acids Res 2013; 42:1311-25. [PMID: 24121686 PMCID: PMC3902905 DOI: 10.1093/nar/gkt899] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics.
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Affiliation(s)
- Isbaal Ramos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del PaísVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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