1
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Fang Y, Hua X, Shan CM, Toda T, Qiao F, Zhang Z, Jia S. Coordination of histone chaperones for parental histone segregation and epigenetic inheritance. Genes Dev 2024; 38:189-204. [PMID: 38479839 PMCID: PMC10982699 DOI: 10.1101/gad.351278.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Chromatin-based epigenetic memory relies on the accurate distribution of parental histone H3-H4 tetramers to newly replicated DNA strands. Mcm2, a subunit of the replicative helicase, and Dpb3/4, subunits of DNA polymerase ε, govern parental histone H3-H4 deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here, using fission yeast heterochromatin inheritance systems that eliminate interference from initiation pathways, we show that a Mcm2 histone binding mutation severely disrupts heterochromatin inheritance, while mutations in Dpb3/4 cause only moderate defects. Surprisingly, simultaneous mutations of Mcm2 and Dpb3/4 stabilize heterochromatin inheritance. eSPAN (enrichment and sequencing of protein-associated nascent DNA) analyses confirmed the conservation of Mcm2 and Dpb3/4 functions in parental histone H3-H4 segregation, with their combined absence showing a more symmetric distribution of parental histone H3-H4 than either single mutation alone. Furthermore, the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance. These results underscore the importance of both symmetric distribution of parental histones and their density at daughter strands for epigenetic inheritance and unveil distinctive properties of parental histone chaperones during DNA replication.
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Affiliation(s)
- Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University, New York, New York 10027, USA
- Department of Pediatrics, Columbia University, New York, New York 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, New York 10027, USA;
- Department of Pediatrics, Columbia University, New York, New York 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA;
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2
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Lee H, Kim S, Lee D. The versatility of the proteasome in gene expression and silencing: Unraveling proteolytic and non-proteolytic functions. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194978. [PMID: 37633648 DOI: 10.1016/j.bbagrm.2023.194978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The 26S proteasome consists of a 20S core particle and a 19S regulatory particle and critically regulates gene expression and silencing through both proteolytic and non-proteolytic functions. The 20S core particle mediates proteolysis, while the 19S regulatory particle performs non-proteolytic functions. The proteasome plays a role in regulating gene expression in euchromatin by modifying histones, activating transcription, initiating and terminating transcription, mRNA export, and maintaining transcriptome integrity. In gene silencing, the proteasome modulates the heterochromatin formation, spreading, and subtelomere silencing by degrading specific proteins and interacting with anti-silencing factors such as Epe1, Mst2, and Leo1. This review discusses the proteolytic and non-proteolytic functions of the proteasome in regulating gene expression and gene silencing-related heterochromatin formation. This article is part of a special issue on the regulation of gene expression and genome integrity by the ubiquitin-proteasome system.
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Affiliation(s)
- Hyesu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sungwook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
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3
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Seman M, Levashkevich A, Larkin A, Huang F, Ragunathan K. Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance. Cell Rep 2023; 42:113428. [PMID: 37952152 DOI: 10.1016/j.celrep.2023.113428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023] Open
Abstract
H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. HP1 proteins are required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how these different HP1 properties are involved in establishing and maintaining transcriptional silencing. Here, we demonstrate that the S. pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1, and an H3K14 acetyltransferase, Mst2, are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identify a genetically separable function in maintaining epigenetic memory.
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Affiliation(s)
- Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | | | - Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | - Fengting Huang
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
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4
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MacKinnon S, Pagé V, Chen JJ, Shariat-Panahi A, Martin RD, Hébert TE, Tanny JC. Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms. PLoS Genet 2023; 19:e1010492. [PMID: 37939109 PMCID: PMC10659198 DOI: 10.1371/journal.pgen.1010492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/20/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
Heterochromatin is a condensed chromatin structure that represses transcription of repetitive DNA elements and developmental genes, and is required for genome stability. Paradoxically, transcription of heterochromatic sequences is required for establishment of heterochromatin in diverse eukaryotic species. As such, components of the transcriptional machinery can play important roles in establishing heterochromatin. How these factors coordinate with heterochromatin proteins at nascent heterochromatic transcripts remains poorly understood. In the model eukaryote Schizosaccharomyces pombe (S. pombe), heterochromatin nucleation can be coupled to processing of nascent transcripts by the RNA interference (RNAi) pathway, or to other post-transcriptional mechanisms that are RNAi-independent. Here we show that the RNA polymerase II processivity factor Spt5 negatively regulates heterochromatin in S. pombe through its C-terminal domain (CTD). The Spt5 CTD is analogous to the CTD of the RNA polymerase II large subunit, and is comprised of multiple repeats of an amino acid motif that is phosphorylated by Cdk9. We provide evidence that genetic ablation of Spt5 CTD phosphorylation results in aberrant RNAi-dependent nucleation of heterochromatin at an ectopic location, as well as inappropriate spread of heterochromatin proximal to centromeres. In contrast, truncation of Spt5 CTD repeat number enhanced RNAi-independent heterochromatin formation and bypassed the requirement for RNAi. We relate these phenotypes to the known Spt5 CTD-binding factor Prf1/Rtf1. This separation of function argues that Spt5 CTD phosphorylation and CTD length restrict heterochromatin through unique mechanisms. More broadly, our findings argue that length and phosphorylation of the Spt5 CTD repeat array have distinct regulatory effects on transcription.
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Affiliation(s)
- Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jennifer J. Chen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ali Shariat-Panahi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ryan D. Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Terence E. Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
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5
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Seman M, Levashkevich A, Larkin A, Huang F, Ragunathan K. Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.30.538869. [PMID: 37961629 PMCID: PMC10634687 DOI: 10.1101/2023.04.30.538869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
H3K9 methylation (H3K9me) marks transcriptionally silent genomic regions called heterochromatin. HP1 proteins are required to establish and maintain heterochromatin. HP1 proteins bind to H3K9me, recruit factors that promote heterochromatin formation, and oligomerize to form phase-separated condensates. We do not understand how HP1 protein binding to heterochromatin establishes and maintains transcriptional silencing. Here, we demonstrate that the S.pombe HP1 homolog, Swi6, can be completely bypassed to establish silencing at ectopic and endogenous loci when an H3K4 methyltransferase, Set1 and an H3K14 acetyltransferase, Mst2 are deleted. Deleting Set1 and Mst2 enhances Clr4 enzymatic activity, leading to higher H3K9me levels and spreading. In contrast, Swi6 and its capacity to oligomerize were indispensable during epigenetic maintenance. Our results demonstrate the role of HP1 proteins in regulating histone modification crosstalk during establishment and identifies a genetically separable function in maintaining epigenetic memory.
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Affiliation(s)
- Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
| | | | - Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
| | - Fengting Huang
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
| | - Kaushik Ragunathan
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
- Lead Contact
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6
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Grewal SIS. The molecular basis of heterochromatin assembly and epigenetic inheritance. Mol Cell 2023; 83:1767-1785. [PMID: 37207657 PMCID: PMC10309086 DOI: 10.1016/j.molcel.2023.04.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023]
Abstract
Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are essential for the establishment of heterochromatin domains, which is initiated by the recruitment of histone-modifying enzymes to nucleation sites. This leads to the deposition of histone H3 lysine-9 methylation (H3K9me), which provides the foundation for building high-concentration territories of heterochromatin proteins and the spread of heterochromatin across extended domains. Moreover, heterochromatin can be epigenetically inherited during cell division in a self-templating manner. This involves a "read-write" mechanism where pre-existing modified histones, such as tri-methylated H3K9 (H3K9me3), support chromatin association of the histone methyltransferase to promote further deposition of H3K9me. Recent studies suggest that a critical density of H3K9me3 and its associated factors is necessary for the propagation of heterochromatin domains across multiple generations. In this review, I discuss the key experiments that have highlighted the importance of modified histones for epigenetic inheritance.
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Affiliation(s)
- Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Shan CM, Fang Y, Jia S. Leaving histone unturned for epigenetic inheritance. FEBS J 2023; 290:310-320. [PMID: 34726351 PMCID: PMC9058036 DOI: 10.1111/febs.16260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/09/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Post-translational modifications in histones play important roles in regulating chromatin structure and gene expression programs, and the modified histones can be passed on to subsequent generations as an epigenetic memory. The fission yeast has been a great model organism for studying histone modifications in heterochromatin assembly and epigenetic inheritance. Here, we review findings in this organism that cemented the idea of chromatin-based inheritance and highlight recent studies that reveal the role of histone turnover in regulating this process.
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Affiliation(s)
- Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Present address: State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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8
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Du W, Shi G, Shan CM, Li Z, Zhu B, Jia S, Li Q, Zhang Z. Mechanisms of chromatin-based epigenetic inheritance. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2162-2190. [PMID: 35792957 DOI: 10.1007/s11427-022-2120-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Multi-cellular organisms such as humans contain hundreds of cell types that share the same genetic information (DNA sequences), and yet have different cellular traits and functions. While how genetic information is passed through generations has been extensively characterized, it remains largely obscure how epigenetic information encoded by chromatin regulates the passage of certain traits, gene expression states and cell identity during mitotic cell divisions, and even through meiosis. In this review, we will summarize the recent advances on molecular mechanisms of epigenetic inheritance, discuss the potential impacts of epigenetic inheritance during normal development and in some disease conditions, and outline future research directions for this challenging, but exciting field.
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Affiliation(s)
- Wenlong Du
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guojun Shi
- 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
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiming Li
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - 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.
| | - Zhiguo Zhang
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
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9
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Biswas S, Chen Z, Karslake JD, Farhat A, Ames A, Raiymbek G, Freddolino PL, Biteen JS, Ragunathan K. HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization. SCIENCE ADVANCES 2022; 8:eabk0793. [PMID: 35857444 PMCID: PMC9269880 DOI: 10.1126/sciadv.abk0793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 05/24/2022] [Indexed: 05/31/2023]
Abstract
HP1 proteins traverse a complex and crowded chromatin landscape to bind with low affinity but high specificity to histone H3K9 methylation (H3K9me) and form transcriptionally inactive genomic compartments called heterochromatin. Here, we visualize single-molecule dynamics of an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By tracking single Swi6 molecules, we identify mobility states that map to discrete biochemical intermediates. Using Swi6 mutants that perturb H3K9me recognition, oligomerization, or nucleic acid binding, we determine how each biochemical property affects protein dynamics. We estimate that Swi6 recognizes H3K9me3 with ~94-fold specificity relative to unmodified nucleosomes in living cells. While nucleic acid binding competes with Swi6 oligomerization, as few as four tandem chromodomains can overcome these inhibitory effects to facilitate Swi6 localization at heterochromatin formation sites. Our studies indicate that HP1 oligomerization is essential to form dynamic, higher-order complexes that outcompete nucleic acid binding to enable specific H3K9me recognition.
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Affiliation(s)
- Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Joshua D. Karslake
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda Ames
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Julie S. Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48104, USA
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Kim SM, Forsburg SL. Determinants of RPA megafoci localization to the nuclear periphery in response to replication stress. G3 (BETHESDA, MD.) 2022; 12:jkac116. [PMID: 35567482 PMCID: PMC9258583 DOI: 10.1093/g3journal/jkac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Upon replication stress, ssDNA, coated by the ssDNA-binding protein RPA, accumulates and generates a signal to activate the replication stress response. Severe replication stress induced by the loss of minichromosome maintenance helicase subunit Mcm4 in the temperature-sensitive Schizosaccharomyces pombe degron mutant (mcm4-dg) results in the formation of a large RPA focus that is translocated to the nuclear periphery. We show that resection and repair processes and chromatin remodeler Swr1/Ino80 are involved in the large RPA foci formation and its relocalization to nuclear periphery. This concentrated accumulation of RPA increases the recruitment of Cds1 to chromatin and results in an aberrant cell cycle that lacks MBF-mediated G1/S accumulation of Tos4. These findings reveal a distinct replication stress response mediated by localized accumulation of RPA that allows the evasion of cell cycle arrest.
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Affiliation(s)
- Seong Min Kim
- Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Susan L Forsburg
- Corresponding author: Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA.
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11
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Dicer promotes genome stability via the bromodomain transcriptional co-activator BRD4. Nat Commun 2022; 13:1001. [PMID: 35194019 PMCID: PMC8863982 DOI: 10.1038/s41467-022-28554-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
RNA interference is required for post-transcriptional silencing, but also has additional roles in transcriptional silencing of centromeres and genome stability. However, these roles have been controversial in mammals. Strikingly, we found that Dicer-deficient embryonic stem cells have strong proliferation and chromosome segregation defects as well as increased transcription of centromeric satellite repeats, which triggers the interferon response. We conducted a CRISPR-Cas9 genetic screen to restore viability and identified transcriptional activators, histone H3K9 methyltransferases, and chromosome segregation factors as suppressors, resembling Dicer suppressors identified in independent screens in fission yeast. The strongest suppressors were mutations in the transcriptional co-activator Brd4, which reversed the strand-specific transcription of major satellite repeats suppressing the interferon response, and in the histone acetyltransferase Elp3. We show that identical mutations in the second bromodomain of Brd4 rescue Dicer-dependent silencing and chromosome segregation defects in both mammalian cells and fission yeast. This remarkable conservation demonstrates that RNA interference has an ancient role in transcriptional silencing and in particular of satellite repeats, which is essential for cell cycle progression and proper chromosome segregation. Our results have pharmacological implications for cancer and autoimmune diseases characterized by unregulated transcription of satellite repeats. While RNA interference is conserved across species, small RNA pathways are very diverse. In this study, Gutbrod et al. find that non-canonical roles of Dicer in genome stability are in fact deeply conserved from yeast to humans.
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12
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Gene Amplification and the Extrachromosomal Circular DNA. Genes (Basel) 2021; 12:genes12101533. [PMID: 34680928 PMCID: PMC8535887 DOI: 10.3390/genes12101533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Oncogene amplification is closely linked to the pathogenesis of a broad spectrum of human malignant tumors. The amplified genes localize either to the extrachromosomal circular DNA, which has been referred to as cytogenetically visible double minutes (DMs), or submicroscopic episome, or to the chromosomal homogeneously staining region (HSR). The extrachromosomal circle from a chromosome arm can initiate gene amplification, resulting in the formation of DMs or HSR, if it had a sequence element required for replication initiation (the replication initiation region/matrix attachment region; the IR/MAR), under a genetic background that permits gene amplification. In this article, the nature, intracellular behavior, generation, and contribution to cancer genome plasticity of such extrachromosomal circles are summarized and discussed by reviewing recent articles on these topics. Such studies are critical in the understanding and treating human cancer, and also for the production of recombinant proteins such as biopharmaceuticals by increasing the recombinant genes in the cells.
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13
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SIRT1 stabilizes extrachromosomal gene amplification and contributes to repeat-induced gene silencing. J Biol Chem 2021; 296:100356. [PMID: 33539925 PMCID: PMC7949162 DOI: 10.1016/j.jbc.2021.100356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/15/2021] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Sirtuin 1 (SIRT1) is a protein deacetylase that maintains genome stability by preventing the activation of latent replication origins. Amplified genes in cancer cells localize on either extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region. Previously, we found that a plasmid with a mammalian replication initiation region and a matrix attachment region spontaneously mimics gene amplification in cultured animal cells and efficiently generates DMs and/or an homogeneously staining region. Here, we addressed the possibility that SIRT1 might be involved in initiation region/matrix attachment region–mediated gene amplification using SIRT1-knockout human COLO 320DM cells. Consequently, we found that extrachromosomal amplification was infrequent in SIRT1-deficient cells, suggesting that DNA breakage caused by latent origin activation prevented the formation of stable extrachromosomal amplicons. Moreover, we serendipitously found that reporter gene expression from the amplified repeats, which is commonly silenced by repeat-induced gene silencing (RIGS) in SIRT1-proficient cells, was strikingly higher in SIRT1-deficient cells, especially in the culture treated with the histone deacetylase inhibitor butyrate. Compared with the SIRT1-proficient cells, the gene expression per copy was up to thousand-fold higher in the sorter-isolated highest 10% cells among the SIRT1-deficient cells. These observations suggest that SIRT1 depletion alleviates RIGS. Thus, SIRT1 may stabilize extrachromosomal amplicons and facilitate RIGS. This result could have implications in cancer malignancy and protein expression.
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14
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Shan CM, Bao K, Diedrich J, Chen X, Lu C, Yates JR, Jia S. The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin. Cell Rep 2020; 33:108561. [PMID: 33378674 PMCID: PMC7896557 DOI: 10.1016/j.celrep.2020.108561] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/31/2020] [Accepted: 12/03/2020] [Indexed: 12/21/2022] Open
Abstract
One key aspect of epigenetic inheritance is that chromatin structures can be stably inherited through generations after the removal of the signals that establish such structures. In fission yeast, the RNA interference (RNAi) pathway is critical for the targeting of histone methyltransferase Clr4 to pericentric repeats to establish heterochromatin. However, pericentric heterochromatin cannot be properly inherited in the absence of RNAi, suggesting the existence of mechanisms that counteract chromatin structure inheritance. Here, we show that mutations of components of the INO80 chromatin-remodeling complex allow pericentric heterochromatin inheritance in RNAi mutants. The ability of INO80 to counter heterochromatin inheritance is attributed to one subunit, Iec5, which promotes histone turnover at heterochromatin but has little effects on nucleosome positioning at heterochromatin, gene expression, or the DNA damage response. These analyses demonstrate the importance of the INO80 chromatin-remodeling complex in controlling heterochromatin inheritance and maintaining the proper heterochromatin landscape of the genome.
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Affiliation(s)
- Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kehan Bao
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jolene Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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15
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Sun L, Liu XM, Li WZ, Yi YY, He X, Wang Y, Jin QW. The molecular chaperone Hsp90 regulates heterochromatin assembly through stabilizing multiple complexes in fission yeast. J Cell Sci 2020; 133:jcs244863. [PMID: 32499408 DOI: 10.1242/jcs.244863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, both RNAi machinery and RNAi-independent factors mediate transcriptional and posttranscriptional silencing and heterochromatin formation. Here, we show that the silencing of reporter genes at major native heterochromatic loci (centromeres, telomeres, mating-type locus and rDNA regions) and an artificially induced heterochromatin locus is alleviated in a fission yeast hsp90 mutant, hsp90-G84C Also, H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects. We further discovered that Hsp90 is required for stabilization or assembly of the RNA-induced transcriptional silencing (RITS) and Argonaute siRNA chaperone (ARC) RNAi effector complexes, the RNAi-independent factor Fft3, the shelterin complex subunit Poz1 and the Snf2/HDAC-containing repressor complex (SHREC). Our ChIP data suggest that Hsp90 regulates the efficient recruitment of the methyltransferase/ubiquitin ligase complex CLRC by shelterin to chromosome ends and targeting of the SHREC and Fft3 to mating type locus and/or rDNA region. Finally, our genetic analyses demonstrated that increased heterochromatin spreading restores silencing at subtelomeres in the hsp90-G84C mutant. Thus, this work uncovers a conserved factor critical for promoting RNAi-dependent and -independent heterochromatin assembly and gene silencing through stabilizing multiple effectors and effector complexes.
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Affiliation(s)
- Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiao-Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wen-Zhu Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yuan-Yuan Yi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiangwei He
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Quan-Wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
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16
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Ogaki Y, Fukuma M, Shimizu N. Repeat induces not only gene silencing, but also gene activation in mammalian cells. PLoS One 2020; 15:e0235127. [PMID: 32579599 PMCID: PMC7313748 DOI: 10.1371/journal.pone.0235127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/08/2020] [Indexed: 11/19/2022] Open
Abstract
Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32–3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5’-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.
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Affiliation(s)
- Yusuke Ogaki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Miki Fukuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
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17
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Raiymbek G, An S, Khurana N, Gopinath S, Larkin A, Biswas S, Trievel RC, Cho US, Ragunathan K. An H3K9 methylation-dependent protein interaction regulates the non-enzymatic functions of a putative histone demethylase. eLife 2020; 9:53155. [PMID: 32195666 PMCID: PMC7192584 DOI: 10.7554/elife.53155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
H3K9 methylation (H3K9me) specifies the establishment and maintenance of transcriptionally silent epigenetic states or heterochromatin. The enzymatic erasure of histone modifications is widely assumed to be the primary mechanism that reverses epigenetic silencing. Here, we reveal an inversion of this paradigm where a putative histone demethylase Epe1 in fission yeast, has a non-enzymatic function that opposes heterochromatin assembly. Mutations within the putative catalytic JmjC domain of Epe1 disrupt its interaction with Swi6HP1 suggesting that this domain might have other functions besides enzymatic activity. The C-terminus of Epe1 directly interacts with Swi6HP1, and H3K9 methylation stimulates this protein-protein interaction in vitro and in vivo. Expressing the Epe1 C-terminus is sufficient to disrupt heterochromatin by outcompeting the histone deacetylase, Clr3 from sites of heterochromatin formation. Our results underscore how histone modifying proteins that resemble enzymes have non-catalytic functions that regulate the assembly of epigenetic complexes in cells. A cell’s identity depends on which of its genes are active. One way for cells to control this process is to change how accessible their genes are to the molecular machinery that switches them on and off. Special proteins called histones determine how accessible genes are by altering how loosely or tightly DNA is packed together. Histones can be modified by enzymes, which are proteins that add or remove specific chemical ‘tags’. These tags regulate how accessible genes are and provide cells with a memory of gene activity. For example, a protein found in yeast called Epe1 helps reactivate large groups of genes after cell division, effectively ‘re-setting’ the yeast’s genome and eliminating past memories of the genes being inactive. For a long time, Epe1 was thought to do this by removing methyl groups, a ‘tag’ that indicates a gene is inactive, from histones – that is, by acting like an enzyme. However, no direct evidence to support this hypothesis has been found. Raiymbek et al. therefore set out to determine exactly how Epe1 worked, and whether or not it did indeed behave like an enzyme. Initial experiments testing mutant versions of Epe1 in yeast cells showed that the changes expected to stop Epe1 from removing methyl groups instead prevented the protein from ‘homing’ to the sections of DNA it normally activates. Detailed microscope imaging, using live yeast cells engineered to produce proteins with fluorescent markers, revealed that this inability to ‘home’ was due to a loss of interaction with Epe1’s main partner, a protein called Swi6. This protein recognizes and binds histones that have methyl tags. Swi6 also acts as a docking site for proteins involved in deactivating genes in close proximity to these histones. Further biochemical studies revealed how the interaction between Epe1 and Swi6 can help in gene reactivation. The methyl tag on histones in inactive regions of the genome inadvertently helps Epe1 interact more efficiently with Swi6. Then, Epe1 can simply block every other protein that binds to Swi6 from participating in gene deactivation. This observation contrasts with the prevailing view where the active removal of methyl tags by proteins such as Epe1 switches genes from an inactive to an active state. This work shows for the first time that Epe1 influences the state of the genome through a process that does not involve enzyme activity. In other words, although the protein may ‘moonlight’ as an enzyme, its main job uses a completely different mechanism. More broadly, these results increase the understanding of the many different ways that gene activity, and ultimately cell identity, can be controlled.
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Affiliation(s)
- Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Nidhi Khurana
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Saarang Gopinath
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Ajay Larkin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.,Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.,Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
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18
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Georgescu PR, Capella M, Fischer-Burkart S, Braun S. The euchromatic histone mark H3K36me3 preserves heterochromatin through sequestration of an acetyltransferase complex in fission yeast. MICROBIAL CELL 2020; 7:80-92. [PMID: 32161768 PMCID: PMC7052950 DOI: 10.15698/mic2020.03.711] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Maintaining the identity of chromatin states requires mechanisms that ensure their structural integrity through the concerted actions of histone modifiers, readers, and erasers. Histone H3K9me and H3K27me are hallmarks of repressed heterochromatin, whereas H3K4me and H3K36me are associated with actively transcribed euchromatin. Paradoxically, several studies have reported that loss of Set2, the methyltransferase responsible for H3K36me, causes de-repression of heterochromatin. Here we show that unconstrained activity of the acetyltransferase complex Mst2C, which antagonizes heterochromatin, is the main cause of the silencing defects observed in Set2-deficient cells. As previously shown, Mst2C is sequestered to actively transcribed chromatin via binding to H3K36me3 that is recognized by the PWWP domain protein Pdp3. We demonstrate that combining deletions of set2+ and pdp3+ results in an epistatic silencing phenotype. In contrast, deleting mst2+, or other members of Mst2C, fully restores silencing in Set2-deficient cells. Suppression of the silencing defect in set2Δ cells is specific for pericentromeres and subtelomeres, which are marked by H3K9me, but is not seen for loci that lack genuine heterochromatin. Mst2 is known to acetylate histone H3K14 redundantly with the HAT Gnc5. Further, it is involved in the acetylation of the non-histone substrate and E3 ubiquitin ligase Brl1, resulting in increased H2B-K119 ubiquitylation at euchromatin. However, we reveal that none of these mechanisms are responsible for the Set2-dependent silencing pathway, implying that Mst2 targets another, unknown substrate critical for heterochromatin silencing. Our findings demonstrate that maintenance of chromatin states requires spatial constraint of opposing chromatin activities.
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Affiliation(s)
- Paula R Georgescu
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Matías Capella
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Sabine Fischer-Burkart
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Sigurd Braun
- Department of Physiological Chemistry, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
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19
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Bhattacharjee S, Roche B, Martienssen RA. RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol 2019; 16:1133-1146. [PMID: 31213126 DOI: 10.1080/15476286.2019.1621624] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'. In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the RNA interference pathway. The key effector complex of the RNA interference pathway consists of small interfering RNA molecules (siRNAs) associated with Argonaute, assembled into the RNA-induced transcriptional silencing (RITS) complex. This review focuses on our current understanding of how RITS promotes heterochromatin formation, and in particular on the role of Argonaute-containing complexes in many other functions such as quelling, release of RNA polymerases, cellular quiescence and genome defense.
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Affiliation(s)
- Sonali Bhattacharjee
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Benjamin Roche
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Robert A Martienssen
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
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20
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Regulation of centromeric heterochromatin in the cell cycle by phosphorylation of histone H3 tyrosine 41. Curr Genet 2019; 65:829-836. [DOI: 10.1007/s00294-019-00962-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/23/2022]
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21
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Bao K, Shan CM, Moresco J, Yates J, Jia S. Anti-silencing factor Epe1 associates with SAGA to regulate transcription within heterochromatin. Genes Dev 2018; 33:116-126. [PMID: 30573453 PMCID: PMC6317313 DOI: 10.1101/gad.318030.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
In this study, Bao et al. investigated how transcription is regulated within heterochromatin in fission yeast. They show that overexpressed Epe1 associates with SAGA and recruits SAGA to heterochromatin regions (which leads to an increase in histone acetylation, transcription of repeats, and the disruption of heterochromatin) and that Epe1 recruits SAGA to regulate transcription within heterochromatin when expressed at normal levels. Heterochromatin is a highly condensed form of chromatin that silences gene transcription. Although high levels of transcriptional activities disrupt heterochromatin, transcription of repetitive DNA elements and subsequent processing of the transcripts by the RNAi machinery are required for heterochromatin assembly. In fission yeast, a JmjC domain protein, Epe1, promotes transcription of DNA repeats to facilitate heterochromatin formation, but overexpression of Epe1 leads to heterochromatin defects. However, the molecular function of Epe1 is not well understood. By screening the fission yeast deletion library, we found that heterochromatin defects associated with Epe1 overexpression are alleviated by mutations of the SAGA histone acetyltransferase complex. Overexpressed Epe1 associates with SAGA and recruits SAGA to heterochromatin regions, which leads to increased histone acetylation, transcription of repeats, and the disruption of heterochromatin. At its normal expression levels, Epe1 also associates with SAGA, albeit weakly. Such interaction regulates histone acetylation levels at heterochromatin and promotes transcription of repeats for heterochromatin assembly. Our results also suggest that increases of certain chromatin protein levels, which frequently occur in cancer cells, might strengthen relatively weak interactions to affect the epigenetic landscape.
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Affiliation(s)
- Kehan Bao
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James Moresco
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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22
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Ebrahimi H, Masuda H, Jain D, Cooper JP. Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions. eLife 2018; 7:32911. [PMID: 29722648 PMCID: PMC5933923 DOI: 10.7554/elife.32911] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/30/2018] [Indexed: 12/24/2022] Open
Abstract
Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are beginning to be mapped out. Here we delineate distinct domains of the fission yeast nuclear envelope (NE), focusing on regions enriched for the inner NE protein, Bqt4, or the lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 tethers chromosome termini and the mat locus to the NE specifically while these regions are replicating. This positioning is required for accurate heterochromatin replication. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE to promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are 'safe zones' in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully.
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Affiliation(s)
- Hani Ebrahimi
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Hirohisa Masuda
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Devanshi Jain
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
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23
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The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly. Cell Rep 2018. [PMID: 28636937 DOI: 10.1016/j.celrep.2017.05.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNAi factors and their catalytic activities are essential for heterochromatin assembly in S. pombe. This has led to the idea that siRNAs can promote H3K9 methylation by recruiting the cryptic loci regulator complex (CLRC), also known as recombination in K complex (RIKC), to the nucleation site. The conserved RNA-binding protein Rct1 (AtCyp59/SIG-7) interacts with splicing factors and RNA polymerase II. Here we show that Rct1 promotes processing of pericentromeric transcripts into siRNAs via the RNA recognition motif. Surprisingly, loss of siRNA in rct1 mutants has no effect on H3K9 di- or tri-methylation, resembling other splicing mutants, suggesting that post-transcriptional gene silencing per se is not required to maintain heterochromatin. Splicing of the Argonaute gene is also defective in rct1 mutants and contributes to loss of silencing but not to loss of siRNA. Our results suggest that Rct1 guides transcripts to the RNAi machinery by promoting splicing of elongating non-coding transcripts.
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24
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Bartholomew B. Proteasomes beyond proteolysis: Roles in heterochromatin maintenance. J Biol Chem 2017; 292:17156-17157. [PMID: 29030538 DOI: 10.1074/jbc.h117.790824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In addition to its proteolytic roles, the 26S proteasome is involved in regulating transcription and in promoting sites of active chromatin. In this report, Seo et al. provide evidence that the non-proteolytic 19S subunit of the 26S proteasome also regulates the spreading of inactive chromatin referred to as heterochromatin, suggesting further non-canonical roles of the proteasome in gene expression.
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Affiliation(s)
- Blaine Bartholomew
- From the Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
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25
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Seo HD, Choi Y, Kim M, Kang K, Urano T, Lee D. The 19S proteasome is directly involved in the regulation of heterochromatin spreading in fission yeast. J Biol Chem 2017; 292:17144-17155. [PMID: 28784663 DOI: 10.1074/jbc.m117.790824] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/17/2017] [Indexed: 01/12/2023] Open
Abstract
Cumulative evidence suggests that non-proteolytic functions of the proteasome are involved in transcriptional regulation, mRNA export, and ubiquitin-dependent histone modification and thereby modulate the intracellular levels of regulatory proteins implicated in controlling key cellular functions. To date, the non-proteolytic roles of the proteasome have been mainly investigated in euchromatin; their effects on heterochromatin are largely unknown. Here, using fission yeast as a model, we randomly mutagenized the subunits of the 19S proteasome subcomplex and sought to uncover a direct role of the proteasome in heterochromatin regulation. We identified a mutant allele, rpt4-1, that disrupts a non-proteolytic function of the proteasome, also known as a non-proteolytic allele. Experiments performed using rpt4-1 cells revealed that the proteasome is involved in the regulation of heterochromatin spreading to prevent its uncontrolled invasion into neighboring euchromatin regions. Intriguingly, the phenotype of the non-proteolytic rpt4-1 mutant resembled that of epe1Δ cells, which lack the Epe1 protein that counteracts heterochromatin spreading. Both mutants exhibited variegated gene-silencing phenotypes across yeast colonies, spreading of heterochromatin, bypassing of the requirement for RNAi in heterochromatin formation at the outer repeat region (otr), and up-regulation of RNA polymerase II. Further analysis revealed Mst2, another factor that antagonizes heterochromatin spreading, may function redundantly with Rpt4. These observations suggest that the 19S proteasome may be involved in modulating the activities of Epe1 and Mst2. In conclusion, our findings indicate that the proteasome appears to have a heterochromatin-regulating function that is independent of its canonical function in proteolysis.
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Affiliation(s)
- Hogyu David Seo
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Yoonjung Choi
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Minhoo Kim
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, Chungnam 31116, South Korea, and
| | - Takeshi Urano
- Department of Biochemistry, Faculty of Medicine, Shimane University, Shimane 690-8504, Izumo, Japan
| | - Daeyoup Lee
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea,
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26
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Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M. The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1. Mol Cell 2017. [PMID: 28648780 PMCID: PMC5526834 DOI: 10.1016/j.molcel.2017.05.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Faithful propagation of functionally distinct chromatin states is crucial for maintaining cellular identity, and its breakdown can lead to diseases such as cancer. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report a positive feedback loop that preserves the transcription-competent state of RNA polymerase II-transcribed genes. We found that Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3-marked chromatin. Thereby, Mst2 binds to all transcriptionally active regions genome-wide. Besides acetylating histone H3K14, Mst2 also acetylates Brl1, a component of the histone H2B ubiquitin ligase complex. Brl1 acetylation increases histone H2B ubiquitination, which positively feeds back on transcription and prevents ectopic heterochromatin assembly. Our work uncovers a molecular pathway that secures epigenome integrity and highlights the importance of opposing feedback loops for the partitioning of chromatin into transcriptionally active and inactive states.
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Affiliation(s)
- Valentin Flury
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Paula Raluca Georgescu
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Yukiko Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Sigurd Braun
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany.
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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27
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Roche B, Arcangioli B, Martienssen RA. RNA interference is essential for cellular quiescence. Science 2016; 354:science.aah5651. [PMID: 27738016 DOI: 10.1126/science.aah5651] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 12/19/2022]
Abstract
Quiescent cells play a predominant role in most organisms. Here we identify RNA interference (RNAi) as a major requirement for quiescence (G0 phase of the cell cycle) in Schizosaccharomyces pombe RNAi mutants lose viability at G0 entry and are unable to maintain long-term quiescence. We identified suppressors of G0 defects in cells lacking Dicer (dcr1Δ), which mapped to genes involved in chromosome segregation, RNA polymerase-associated factors, and heterochromatin formation. We propose a model in which RNAi promotes the release of RNA polymerase in cycling and quiescent cells: (i) RNA polymerase II release mediates heterochromatin formation at centromeres, allowing proper chromosome segregation during mitotic growth and G0 entry, and (ii) RNA polymerase I release prevents heterochromatin formation at ribosomal DNA during quiescence maintenance. Our model may account for the codependency of RNAi and histone H3 lysine 9 methylation throughout eukaryotic evolution.
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Affiliation(s)
- B Roche
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - B Arcangioli
- Dynamics of the Genome Unit, Department of Genomes and Genetics, Institut Pasteur, UMR3525, 25-28 rue du Docteur Roux, Paris 75015, France
| | - R A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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28
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Ohzeki JI, Shono N, Otake K, Martins NMC, Kugou K, Kimura H, Nagase T, Larionov V, Earnshaw WC, Masumoto H. KAT7/HBO1/MYST2 Regulates CENP-A Chromatin Assembly by Antagonizing Suv39h1-Mediated Centromere Inactivation. Dev Cell 2016; 37:413-27. [PMID: 27270040 PMCID: PMC4906249 DOI: 10.1016/j.devcel.2016.05.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 01/01/2023]
Abstract
Centromere chromatin containing histone H3 variant CENP-A is required for accurate chromosome segregation as a foundation for kinetochore assembly. Human centromere chromatin assembles on a part of the long α-satellite (alphoid) DNA array, where it is flanked by pericentric heterochromatin. Heterochromatin spreads into adjacent chromatin and represses gene expression, and it can antagonize centromere function or CENP-A assembly. Here, we demonstrate an interaction between CENP-A assembly factor M18BP1 and acetyltransferase KAT7/HBO1/MYST2. Knocking out KAT7 in HeLa cells reduced centromeric CENP-A assembly. Mitotic chromosome misalignment and micronuclei formation increased in the knockout cells and were enhanced when the histone H3-K9 trimethylase Suv39h1 was overproduced. Tethering KAT7 to an ectopic alphoid DNA integration site removed heterochromatic H3K9me3 modification and was sufficient to stimulate new CENP-A or histone H3.3 assembly. Thus, KAT7-containing acetyltransferases associating with the Mis18 complex provides competence for histone turnover/exchange activity on alphoid DNA and prevents Suv39h1-mediated heterochromatin invasion into centromeres.
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Affiliation(s)
- Jun-Ichirou Ohzeki
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Nobuaki Shono
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Koichiro Otake
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Nuno M C Martins
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kazuto Kugou
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takahiro Nagase
- Public Relations Team, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Vladimir Larionov
- Genome Structure and Function Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan.
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Wang J, Jia ST, Jia S. New Insights into the Regulation of Heterochromatin. Trends Genet 2016; 32:284-294. [PMID: 27005444 DOI: 10.1016/j.tig.2016.02.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
All living organisms are constantly exposed to stresses from internal biological processes and surrounding environments, which induce many adaptive changes in cellular physiology and gene expression programs. Unexpectedly, constitutive heterochromatin, which is generally associated with the stable maintenance of gene silencing, is also dynamically regulated in response to stimuli. In this review we discuss the mechanism of constitutive heterochromatin assembly, its dynamic nature, and its responses to environmental changes.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sharon T Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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Wang J, Cohen AL, Letian A, Tadeo X, Moresco JJ, Liu J, Yates JR, Qiao F, Jia S. The proper connection between shelterin components is required for telomeric heterochromatin assembly. Genes Dev 2016; 30:827-39. [PMID: 26988418 PMCID: PMC4826398 DOI: 10.1101/gad.266718.115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 02/24/2016] [Indexed: 12/31/2022]
Abstract
Telomeric regions contain prominent sites of heterochromatin, which is associated with unique histone modification profiles such as the methylation of histone H3 at Lys9 (H3K9me). In fission yeast, the conserved telomeric shelterin complex recruits the histone H3K9 methyltransferase complex CLRC to establish subtelomeric heterochromatin. Although many shelterin mutations affect subtelomeric heterochromatin assembly, the mechanism remains elusive due to the diverse functions of shelterin. Through affinity purification, we found that shelterin directly associates with CLRC through the Ccq1 subunit. Surprisingly, mutations that disrupt interactions between shelterin subunits compromise subtelomeric heterochromatin without affecting CLRC interaction with shelterin component Pot1, located at chromosome ends. We further discovered that telomeric repeats are refractory to heterochromatin spreading and that artificial restoration of shelterin connections or increased heterochromatin spreading rescued heterochromatin defects in these shelterin mutants. Thus, subtelomeric heterochromatin assembly requires both the recruitment of CLRC by shelterin to chromosome ends and the proper connection of shelterin components, which allows CLRC to skip telomeric repeats to internal regions.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Allison L Cohen
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Anudari Letian
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jinqiang Liu
- Department of Biological Chemistry, University of California at Irvine, Irvine, California 92697, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Feng Qiao
- Department of Biological Chemistry, University of California at Irvine, Irvine, California 92697, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO Rep 2015; 16:1673-87. [PMID: 26518661 PMCID: PMC4687421 DOI: 10.15252/embr.201541214] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/05/2015] [Indexed: 11/21/2022] Open
Abstract
The maintenance of open and repressed chromatin states is crucial for the regulation of gene expression. To study the genes involved in maintaining chromatin states, we generated a random mutant library in Schizosaccharomyces pombe and monitored the silencing of reporter genes inserted into the euchromatic region adjacent to the heterochromatic mating type locus. We show that Leo1–Paf1 [a subcomplex of the RNA polymerase II‐associated factor 1 complex (Paf1C)] is required to prevent the spreading of heterochromatin into euchromatin by mapping the heterochromatin mark H3K9me2 using high‐resolution genomewide ChIP (ChIP–exo). Loss of Leo1–Paf1 increases heterochromatin stability at several facultative heterochromatin loci in an RNAi‐independent manner. Instead, deletion of Leo1 decreases nucleosome turnover, leading to heterochromatin stabilization. Our data reveal that Leo1–Paf1 promotes chromatin state fluctuations by enhancing histone turnover.
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Affiliation(s)
- Laia Sadeghi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Punit Prasad
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Amikam Cohen
- Department of Microbiology and Molecular Genetics, IMRIC The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Bayne EH, Bijos DA, White SA, de Lima Alves F, Rappsilber J, Allshire RC. A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast. Genome Biol 2015; 15:481. [PMID: 25274039 PMCID: PMC4210515 DOI: 10.1186/s13059-014-0481-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 12/20/2022] Open
Abstract
Background Heterochromatin plays important roles in the regulation and stability of eukaryotic genomes. Both heterochromatin components and pathways that promote heterochromatin assembly, including RNA interference, RNAi, are broadly conserved between the fission yeast Schizosaccharomyces pombe and humans. As a result, fission yeast has emerged as an important model system for dissecting mechanisms governing heterochromatin integrity. Thus far, over 50 proteins have been found to contribute to heterochromatin assembly at fission yeast centromeres. However, previous studies have not been exhaustive, and it is therefore likely that further factors remain to be identified. Results To gain a more complete understanding of heterochromatin assembly pathways, we have performed a systematic genetic screen for factors required for centromeric heterochromatin integrity. In addition to known RNAi and chromatin modification components, we identified several proteins with previously undescribed roles in heterochromatin regulation. These included both known and newly characterised splicing-associated proteins, which are required for proper processing of centromeric transcripts by the RNAi pathway, and COP9 signalosome components Csn1 and Csn2, whose role in heterochromatin assembly can be explained at least in part by a role in the Ddb1-dependent degradation of the heterochromatin regulator Epe1. Conclusions This work has revealed new factors involved in RNAi-directed heterochromatin assembly in fission yeast. Our findings support and extend previous observations that implicate components of the splicing machinery as a platform for RNAi, and demonstrate a novel role for the COP9 signalosome in heterochromatin regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0481-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth H Bayne
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK.
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33
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Allshire RC, Ekwall K. Epigenetic Regulation of Chromatin States in Schizosaccharomyces pombe. Cold Spring Harb Perspect Biol 2015; 7:a018770. [PMID: 26134317 DOI: 10.1101/cshperspect.a018770] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article discusses the advances made in epigenetic research using the model organism fission yeast Schizosaccharomyces pombe. S. pombe has been used for epigenetic research since the discovery of position effect variegation (PEV). This is a phenomenon in which a transgene inserted within heterochromatin is variably expressed, but can be stably inherited in subsequent cell generations. PEV occurs at centromeres, telomeres, ribosomal DNA (rDNA) loci, and mating-type regions of S. pombe chromosomes. Heterochromatin assembly in these regions requires enzymes that modify histones and the RNA interference (RNAi) machinery. One of the key histone-modifying enzymes is the lysine methyltransferase Clr4, which methylates histone H3 on lysine 9 (H3K9), a classic hallmark of heterochromatin. The kinetochore is assembled on specialized chromatin in which histone H3 is replaced by the variant CENP-A. Studies in fission yeast have contributed to our understanding of the establishment and maintenance of CENP-A chromatin and the epigenetic activation and inactivation of centromeres.
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Affiliation(s)
- Robin C Allshire
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, NOVUM, S-141 83, Huddinge, Sweden
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34
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Yang XJ. MOZ and MORF acetyltransferases: Molecular interaction, animal development and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1818-26. [PMID: 25920810 DOI: 10.1016/j.bbamcr.2015.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023]
Abstract
Lysine residues are subject to many forms of covalent modification and one such modification is acetylation of the ε-amino group. Initially identified on histone proteins in the 1960s, lysine acetylation is now considered as an important form of post-translational modification that rivals phosphorylation. However, only about a dozen of human lysine acetyltransferases have been identified. Among them are MOZ (monocytic leukemia zinc finger protein; a.k.a. MYST3 and KAT6A) and its paralog MORF (a.k.a. MYST4 and KAT6B). Although there is a distantly related protein in Drosophila and sea urchin, these two enzymes are vertebrate-specific. They form tetrameric complexes with BRPF1 (bromodomain- and PHD finger-containing protein 1) and two small non-catalytic subunits. These two acetyltransferases and BRPF1 play key roles in various developmental processes; for example, they are important for development of hematopoietic and neural stem cells. The human KAT6A and KAT6B genes are recurrently mutated in leukemia, non-hematologic malignancies, and multiple developmental disorders displaying intellectual disability and various other abnormalities. In addition, the BRPF1 gene is mutated in childhood leukemia and adult medulloblastoma. Therefore, these two acetyltransferases and their partner BRPF1 are important in animal development and human disease.
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Affiliation(s)
- Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada; McGill University Health Center, Montreal, Quebec H3A 1A3, Canada.
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35
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Wang J, Reddy BD, Jia S. Rapid epigenetic adaptation to uncontrolled heterochromatin spreading. eLife 2015; 4. [PMID: 25774602 PMCID: PMC4395908 DOI: 10.7554/elife.06179] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
Heterochromatin, a highly compact chromatin state characterized by histone H3K9 methylation and HP1 protein binding, silences the underlying DNA and influences the expression of neighboring genes. However, the mechanisms that regulate heterochromatin spreading are not well understood. In this study, we show that the conserved Mst2 histone acetyltransferase complex in fission yeast regulates histone turnover at heterochromatin regions to control heterochromatin spreading and prevents ectopic heterochromatin assembly. The combined loss of Mst2 and the JmjC domain protein Epe1 results in uncontrolled heterochromatin spreading and massive ectopic heterochromatin, leading to severe growth defects due to the inactivation of essential genes. Interestingly, these cells quickly recover by accumulating heterochromatin at genes essential for heterochromatin assembly, leading to their reduced expression to restrain heterochromatin spreading. Our studies discover redundant pathways that control heterochromatin spreading and prevent ectopic heterochromatin assembly and reveal a fast epigenetic adaptation response to changes in heterochromatin landscape. DOI:http://dx.doi.org/10.7554/eLife.06179.001 The DNA in the nucleus of a cell is wrapped around histone proteins to form a compact structure known as chromatin. Chromatin's structure can control how the genes in DNA are expressed. Loosely packed chromatin contains active genes, whereas densely packed chromatin (also called ‘heterochromatin’) contains silenced genes that are not expressed. The assembly of DNA into heterochromatin needs to be carefully controlled. Otherwise, the DNA next to heterochromatin regions can become densely packed as well (via a process called ‘heterochromatin spreading’), and the genes within this DNA are incorrectly silenced. Incorrect gene silencing is often associated with diseases such as cancer. Cells add chemical groups onto the histone proteins to influence how chromatin is compacted. Densely packed chromatin contains histones with many methyl groups but few acetyl groups. A protein called Epe1, which potentially removes methyl groups, helps to prevent heterochromatin spreading in yeast cells. Wang et al. found that an enzyme called Mst2, which adds acetyl groups onto histones, also limits heterochromatin spreading and prevents extra heterochromatin from assembling at undesirable locations. Wang et al. then generated yeast cells that lacked both Epe1 and Mst2. At first, these cells were sickly and unable to grow, because several essential genes were incorrectly silenced due to rampant heterochromatin spreading. However, the cells quickly overcame this growth defect by gaining an additional mutation. Normally mutations occur through changes in DNA sequences. However, Wang et al. found that the cells acquired this mutation by packing a gene required for heterochromatin assembly into heterochromatin. This in turn stopped more chromatin from becoming packed too densely. Changes to chromatin can also be passed on to the yeast's offspring, and such a change could help the offspring to better cope with changes in heterochromatin levels. Future work could test how often inheritable changes to chromatin modification help organisms adapt to environmental stresses, or if similar changes allow cancer cells to become tolerant to anticancer drugs. DOI:http://dx.doi.org/10.7554/eLife.06179.002
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Bharat D Reddy
- Department of Biological Sciences, Columbia University, New York, United States
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, United States
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36
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Ragunathan K, Jih G, Moazed D. Epigenetics. Epigenetic inheritance uncoupled from sequence-specific recruitment. Science 2014; 348:1258699. [PMID: 25831549 DOI: 10.1126/science.1258699] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/13/2014] [Indexed: 11/03/2022]
Abstract
Changes in histone posttranslational modifications are associated with epigenetic states that define distinct patterns of gene expression. It remains unclear whether epigenetic information can be transmitted through histone modifications independently of specific DNA sequence, DNA methylation, or RNA interference. Here we show that, in the fission yeast Schizosaccharomyces pombe, ectopically induced domains of histone H3 lysine 9 methylation (H3K9me), a conserved marker of heterochromatin, are inherited through several mitotic and meiotic cell divisions after removal of the sequence-specific initiator. The putative JmjC domain H3K9 demethylase, Epe1, and the chromodomain of the H3K9 methyltransferase, Clr4/Suv39h, play opposing roles in maintaining silent H3K9me domains. These results demonstrate how a direct "read-write" mechanism involving Clr4 propagates histone modifications and allows histones to act as carriers of epigenetic information.
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Affiliation(s)
- Kaushik Ragunathan
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Gloria Jih
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Danesh Moazed
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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37
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Kallgren SP, Andrews S, Tadeo X, Hou H, Moresco JJ, Tu PG, Yates JR, Nagy PL, Jia S. The proper splicing of RNAi factors is critical for pericentric heterochromatin assembly in fission yeast. PLoS Genet 2014; 10:e1004334. [PMID: 24874881 PMCID: PMC4038458 DOI: 10.1371/journal.pgen.1004334] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin preferentially assembles at repetitive DNA elements, playing roles in transcriptional silencing, recombination suppression, and chromosome segregation. The RNAi machinery is required for heterochromatin assembly in a diverse range of organisms. In fission yeast, RNA splicing factors are also required for pericentric heterochromatin assembly, and a prevailing model is that splicing factors provide a platform for siRNA generation independently of their splicing activity. Here, by screening the fission yeast deletion library, we discovered four novel splicing factors that are required for pericentric heterochromatin assembly. Sequencing total cellular RNAs from the strongest of these mutants, cwf14Δ, showed intron retention in mRNAs of several RNAi factors. Moreover, introducing cDNA versions of RNAi factors significantly restored pericentric heterochromatin in splicing mutants. We also found that mutations of splicing factors resulted in defective telomeric heterochromatin assembly and mis-splicing the mRNA of shelterin component Tpz1, and that replacement of tpz1+ with its cDNA partially rescued heterochromatin defects at telomeres in splicing mutants. Thus, proper splicing of RNAi and shelterin factors contributes to heterochromatin assembly at pericentric regions and telomeres.
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Affiliation(s)
- Scott P. Kallgren
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Stuart Andrews
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Haitong Hou
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Patricia G. Tu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Peter L. Nagy
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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38
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The Mi-2 homolog Mit1 actively positions nucleosomes within heterochromatin to suppress transcription. Mol Cell Biol 2014; 34:2046-61. [PMID: 24662054 DOI: 10.1128/mcb.01609-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mit1 is the putative chromatin remodeling subunit of the fission yeast Snf2/histone deacetylase (HDAC) repressor complex (SHREC) and is known to repress transcription at regions of heterochromatin. However, how Mit1 modifies chromatin to silence transcription is largely unknown. Here we report that Mit1 mobilizes histone octamers in vitro and requires ATP hydrolysis and conserved chromatin tethering domains, including a previously unrecognized chromodomain, to remodel nucleosomes and silence transcription. Loss of Mit1 remodeling activity results in nucleosome depletion at specific DNA sequences that display low intrinsic affinity for the histone octamer, but its contribution to antagonizing RNA polymerase II (Pol II) access and transcription is not restricted to these sites. Genetic epistasis analyses demonstrate that SHREC subunits and the transcription-coupled Set2 histone methyltransferase, which is involved in suppression of cryptic transcription at actively transcribed regions, cooperate to silence heterochromatic transcripts. In addition, we have demonstrated that Mit1's remodeling activity contributes to SHREC function independently of Clr3's histone deacetylase activity on histone H3 K14. We propose that Mit1 is a chromatin remodeling factor that cooperates with the Clr3 histone deacetylase of SHREC and other chromatin modifiers to stabilize heterochromatin structure and to prevent access to the transcriptional machinery.
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39
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Tadeo X, Wang J, Kallgren SP, Liu J, Reddy BD, Qiao F, Jia S. Elimination of shelterin components bypasses RNAi for pericentric heterochromatin assembly. Genes Dev 2014; 27:2489-99. [PMID: 24240238 PMCID: PMC3841737 DOI: 10.1101/gad.226118.113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The RNAi pathway is required for heterochromatin assembly, and loss of RNAi causes pericentric heterochromatin defects. Tadeo et al. show that deletion of telomere shelterin components in RNAi mutants restores pericentric heterochromatin. Shelterin component Poz1 mutant analysis reveals that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Furthermore, heterochromatin protein Swi6 is redistributed to pericentric regions in RNAi mutants. Heterochromatin domains thus use multiple pathways to restrain Swi6 and avoid promiscuous heterochromatin formation. The RNAi pathway is required for heterochromatin assembly at repetitive DNA elements in diverse organisms. In fission yeast, loss of RNAi causes pericentric heterochromatin defects, compromising gene silencing and chromosome segregation. Here we show that deletion of telomere shelterin components restores pericentric heterochromatin and its functions in RNAi mutants. We further isolated a separation-of-function mutant of Poz1 and revealed that defective telomere silencing, but not telomere length control, is critical for bypassing RNAi. Further analyses demonstrated that compromising shelterin-mediated heterochromatin assembly in RNAi mutants releases heterochromatin protein Swi6, which is redistributed to pericentric regions through RNAi-independent heterochromatin assembly pathways. Given the high mobility of Swi6 protein and that increased levels of Swi6 facilitates heterochromatin spreading as well as ectopic heterochromatin assembly, our results suggest that constitutive heterochromatin domains use multiple pathways to form high-affinity platforms to restrain Swi6, thus limiting its availability and avoiding promiscuous heterochromatin formation.
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Affiliation(s)
- Xavier Tadeo
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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40
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Wang J, Tadeo X, Hou H, Tu PG, Thompson J, Yates JR, Jia S. Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries. Genes Dev 2013; 27:1886-902. [PMID: 24013502 PMCID: PMC3778242 DOI: 10.1101/gad.221010.113] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heterochromatin spreading leads to gene silencing, and boundary elements constrain such spreading. IRC inverted repeats are required for boundary function at centromeric heterochromatin in fission yeast. Jia and colleagues now identify BET family homolog Bdf2 as required for heterochromatin boundary function at IRCs. Bdf2 interacts with boundary protein Epe1, recognizes acetylated histone H4 tails, and antagonizes Sir2-mediated deacetylation of histone H4K16. This study illustrates a mechanism for establishing chromosome boundaries through recruitment of a factor that protects euchromatic histone modifications. Heterochromatin spreading leads to the silencing of genes within its path, and boundary elements have evolved to constrain such spreading. In fission yeast, heterochromatin at centromeres I and III is flanked by inverted repeats termed IRCs, which are required for proper boundary functions. However, the mechanisms by which IRCs prevent heterochromatin spreading are unknown. Here, we identified Bdf2, which is homologous to the mammalian bromodomain and extraterminal (BET) family double bromodomain proteins involved in diverse types of cancers, as a factor required for proper boundary function at IRCs. Bdf2 is enriched at IRCs through its interaction with the boundary protein Epe1. The bromodomains of Bdf2 recognize acetylated histone H4 tails and antagonize Sir2-mediated deacetylation of histone H4K16. Furthermore, abolishing H4K16 acetylation (H4K16ac) with an H4K16R mutation promotes heterochromatin spreading, and mimicking H4K16ac by an H4K16Q mutation blocks heterochromatin spreading at IRCs. Our results thus illustrate a mechanism of establishing chromosome boundaries at specific sites through the recruitment of a factor that protects euchromatic histone modifications. They also reveal a previously unappreciated function of H4K16ac in cooperation with H3K9 methylation to regulate heterochromatin spreading.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Alper BJ, Lowe BR, Partridge JF. Centromeric heterochromatin assembly in fission yeast--balancing transcription, RNA interference and chromatin modification. Chromosome Res 2012; 20:521-34. [PMID: 22733402 DOI: 10.1007/s10577-012-9288-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Distinct regions of the eukaryotic genome are packaged into different types of chromatin, with euchromatin representing gene rich, transcriptionally active regions and heterochromatin more condensed and gene poor. The assembly and maintenance of heterochromatin is important for many aspects of genome control, including silencing of gene transcription, suppression of recombination, and to ensure proper chromosome segregation. The precise mechanisms underlying heterochromatin establishment and maintenance are still unclear, but much progress has been made towards understanding this process during the last few years, particularly from studies performed in fission yeast. In this review, we hope to provide a conceptual model of centromeric heterochromatin in fission yeast that integrates our current understanding of the competing forces of transcription, replication, and RNA decay that influence its assembly and propagation.
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Affiliation(s)
- Benjamin J Alper
- Department of Biochemistry, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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42
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Chen Z, McCroskey S, Guo W, Li H, Gerton JL. A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors. G3 (BETHESDA, MD.) 2012; 2:1161-8. [PMID: 23050226 PMCID: PMC3464108 DOI: 10.1534/g3.112.003327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 07/23/2012] [Indexed: 11/23/2022]
Abstract
Cohesion, the force that holds sister chromatids together from the time of DNA replication until separation at the metaphase to anaphase transition, is mediated by the cohesin complex. This complex is also involved in DNA damage repair, chromosomes condensation, and gene regulation. To learn more about the cellular functions of cohesin, we conducted a genetic screen in Schizosaccharomyces pombe with two different cohesin mutants (eso1-G799D and mis4-242). We found synthetic negative interactions with deletions of genes involved in DNA replication and heterochromatin formation. We also found a few gene deletions that rescued the growth of eso1-G799D at the nonpermissive temperature, and these genes partially rescue the lagging chromosome phenotype. These genes are all chromatin effectors. Overall, our screen revealed an intimate association between cohesin and chromatin.
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Affiliation(s)
- Zhiming Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Weichao Guo
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
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Sasaki T, Kobayashi A, Saze H, Kakutani T. RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:750-758. [PMID: 22269081 DOI: 10.1111/j.1365-313x.2012.04911.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Methylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. Transposon-specific non-CpG methylation in plants is controlled by small RNAs and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly demonstrated in plants. We have previously shown that a mutation in the chromatin remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1) induces a global decrease but a local increase of cytosine methylation and accumulation of small RNA at a locus called BONSAI. Here we show that de novo BONSAI methylation does not depend on RNAi but does depend on H3K9me. In mutants of H3K9 methyltransferase gene KRYPTONITE or the H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts (CpG, CpHpG and CpHpH). Furthermore, RNAi mutants showed strong developmental defects when combined with the ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications that may be conserved among diverse eukaryotes.
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Affiliation(s)
- Taku Sasaki
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Reyes-Turcu FE, Grewal SI. Different means, same end-heterochromatin formation by RNAi and RNAi-independent RNA processing factors in fission yeast. Curr Opin Genet Dev 2012; 22:156-63. [PMID: 22243696 PMCID: PMC3331891 DOI: 10.1016/j.gde.2011.12.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 12/19/2011] [Indexed: 11/28/2022]
Abstract
The assembly of heterochromatin in eukaryotic genomes is critical for diverse chromosomal events including regulation of gene expression, silencing of repetitive DNA elements, proper segregation of chromosomes and maintenance of genomic integrity. Previous studies have shown that noncoding RNAs and the RNA interference (RNAi) machinery promote the assembly of heterochromatin that serves as a multipurpose platform for targeting effectors involved in various chromosomal processes. Recent work has revealed that RNAi-independent mechanisms, involving RNA processing activities that utilize both noncoding and coding RNAs, operate in the assembly of heterochromatin. These findings have established that, in addition to coding for proteins, mRNAs also function as signaling molecules that modify chromatin structure by targeting heterochromatin assembly factors.
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Affiliation(s)
- Francisca E Reyes-Turcu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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45
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Sarkies P, Sale JE. Cellular epigenetic stability and cancer. Trends Genet 2012; 28:118-27. [PMID: 22226176 DOI: 10.1016/j.tig.2011.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/30/2011] [Accepted: 11/30/2011] [Indexed: 10/14/2022]
Abstract
When a cell divides, it must not only accurately duplicate its genome, but also restore its previous levels of gene expression. The information determining gene expression is often not directly encoded in the DNA and is hence termed 'epigenetic'. The molecular basis of epigenetic memory remains a subject of intense debate, but is likely to arise from the collaboration of several mechanisms, including histone post-translational modifications, transcription factors, DNA methylation and noncoding RNAs. In this article, we look at how these mechanisms interact to generate robust epigenetic states. We then consider recent observations that mitotic inheritance of stable gene expression can be compromised by interruption of DNA replication. We discuss how these data may provide direct evidence for a central role for histone modifications in transcriptional memory and how they could potentially provide an explanation for the some of the widespread alterations in transcription seen in cancer cells.
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Affiliation(s)
- Peter Sarkies
- Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Hills Road, Cambridge, CB2 0QH, UK
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Wang Y, Kallgren SP, Reddy BD, Kuntz K, López-Maury L, Thompson J, Watt S, Ma C, Hou H, Shi Y, Yates JR, Bähler J, O'Connell MJ, Jia S. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast. J Biol Chem 2011; 287:4386-93. [PMID: 22184112 DOI: 10.1074/jbc.m111.329417] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histone lysine acetylation has emerged as a key regulator of genome organization. However, with a few exceptions, the contribution of each acetylated lysine to cellular functions is not well understood because of the limited specificity of most histone acetyltransferases and histone deacetylases. Here we show that the Mst2 complex in Schizosaccharomyces pombe is a highly specific H3 lysine 14 (H3K14) acetyltransferase that functions together with Gcn5 to regulate global levels of H3K14 acetylation (H3K14ac). By analyzing the effect of H3K14ac loss through both enzymatic inactivation and histone mutations, we found that H3K14ac is critical for DNA damage checkpoint activation by directly regulating the compaction of chromatin and by recruiting chromatin remodeling protein complex RSC.
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Affiliation(s)
- Yu Wang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol 2011; 31:4193-204. [PMID: 21844224 DOI: 10.1128/mcb.05568-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spt6 is a conserved factor, critically required for several transcription- and chromatin-related processes. We now show that Spt6 and its binding partner, Iws1, are required for heterochromatic silencing in Schizosaccharomyces pombe. Our studies demonstrate that Spt6 is required for silencing of all heterochromatic loci and that an spt6 mutant has an unusual combination of heterochromatic phenotypes compared to previously studied silencing mutants. Unexpectedly, we find normal nucleosome positioning over heterochromatin and normal levels of histone H3K9 dimethylation at the endogenous pericentric repeats. However, we also find greatly reduced levels of H3K9 trimethylation, elevated levels of H3K14 acetylation, reduced recruitment of several silencing factors, and defects in heterochromatin spreading. Our evidence suggests that Spt6 plays a role at both the transcriptional and posttranscriptional levels; in an spt6 mutant, RNA polymerase II (RNAPII) occupancy at the pericentric regions is only modestly increased, while production of small interfering RNAs (siRNAs) is lost. Taken together, our results suggest that Spt6 is required for multiple steps in heterochromatic silencing by controlling chromatin, transcriptional, and posttranscriptional processes.
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