1
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Mei Q, Yu Q, Li X, Chen J, Yu X. Regulation of telomere silencing by the core histones-autophagy-Sir2 axis. Life Sci Alliance 2023; 6:6/3/e202201614. [PMID: 36585257 PMCID: PMC9806677 DOI: 10.26508/lsa.202201614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022] Open
Abstract
Telomeres contain compacted heterochromatin, and genes adjacent to telomeres are subjected to transcription silencing. Maintaining telomere structure integrity and transcription silencing is important to prevent the occurrence of premature aging and aging-related diseases. How telomere silencing is regulated during aging is not well understood. Here, we find that the four core histones are reduced during yeast chronological aging, leading to compromised telomere silencing. Mechanistically, histone loss promotes the nuclear export of Sir2 and its degradation by autophagy. Meanwhile, reducing core histones enhances the autophagy pathway, which further accelerates autophagy-mediated Sir2 degradation. By screening the histone mutant library, we identify eight histone mutants and one histone modification (histone methyltransferase Set1-catalyzed H3K4 trimethylation) that regulate telomere silencing by modulating the core histones-autophagy-Sir2 axis. Overall, our findings reveal core histones and autophagy as causes of aging-coupled loss of telomere silencing and shed light on dynamic regulation of telomere structure during aging.
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Affiliation(s)
- Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Jianguo Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
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2
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Fukuda Y, Akematsu T, Bando H, Kato K. Snf2 Proteins Are Required to Generate Gamete Pronuclei in Tetrahymena thermophila. Microorganisms 2022; 10:microorganisms10122426. [PMID: 36557679 PMCID: PMC9786623 DOI: 10.3390/microorganisms10122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
During sexual reproduction/conjugation of the ciliate Tetrahymena thermophila, the germinal micronucleus undergoes meiosis resulting in four haploid micronuclei (hMICs). All hMICs undergo post-meiotic DNA double-strand break (PM-DSB) formation, cleaving their genome. DNA lesions are subsequently repaired in only one ‘selected’ hMIC, which eventually produces gametic pronuclei. DNA repair in the selected hMIC involves chromatin remodeling by switching from the heterochromatic to the euchromatic state of its genome. Here, we demonstrate that, among the 15 Tetrahymena Snf2 family proteins, a core of the ATP-dependent chromatin remodeling complex in Tetrahymena, the germline nucleus specific Iswi in Tetrahymena IswiGTt and Rad5Tt is crucial for the generation of gametic pronuclei. In either gene knockout, the selected hMIC which shows euchromatin markers such as lysine-acetylated histone H3 does not appear, but all hMICs in which markers for DNA lesions persist are degraded, indicating that both IswiGTt and Rad5Tt have important roles in repairing PM-DSB DNA lesions and remodeling chromatin for the euchromatic state in the selected hMIC.
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Affiliation(s)
- Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
- Correspondence: ; Tel.: +81-229-84-7387
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan
| | - Hironori Bando
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
| | - Kentaro Kato
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
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3
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Peng Q, Zhou M, Zuo S, Liu Y, Li X, Yang Y, He Q, Yu X, Zhou J, He Z, He Q. Nuclear Factor Related to KappaB Binding Protein ( NFRKB) Is a Telomere-Associated Protein and Involved in Liver Cancer Development. DNA Cell Biol 2021; 40:1298-1307. [PMID: 34591601 DOI: 10.1089/dna.2021.0486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism activated in 10-15% of human cancers. Although significant progress has been made, the key regulators of the ALT pathway and its role in cancer development remain elusive. Bioinformatics methods were used to predict novel telomere-associated proteins (TAPs) by analysis of large-scale ChIP-Seq data. Immunostaining and fluorescence in situ hybridization experiments were applied to detect the subcellular location of target genes and telomeres. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) were used to examine the expression of targeting genes. Overall survival (OS) analyses were used to evaluate the relationship between gene expression and survival time; immunohistochemistry was used to detect the distribution of target genes in liver cancer tissues. We found that nuclear factor related to kappaB binding protein (NFRKB), a metazoan-specific subunit of the INO80 complex, can associate with telomeres in human ALT cells. Loss of NFRKB induces dysfunction of telomeres and less PML bodies in U2OS cells. In addition, NFRKB is low/moderately expressed in cytoplasm of normal hepatocytes but heavily accumulating in the nucleus of liver cancer cells. Finally, the high expression of NFRKB is associated with short OS time and poor prognosis. NFRKB is a TAP and protects telomeres from DNA damage in ALT cells. It is highly expressed in hepatocellular carcinoma (HCC) cells and predicts a poor prognosis. NFRKB may be a promising prognostic biomarker for the treatment of HCC in the future.
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Affiliation(s)
- Qiyao Peng
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Mingqing Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Shanru Zuo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Yucong Liu
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Quanze He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xing Yu
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Zuping He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University School of Medicine, Changsha, China
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4
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INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins. Cell Rep 2021; 32:108106. [PMID: 32905765 PMCID: PMC7540730 DOI: 10.1016/j.celrep.2020.108106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/26/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast· INO80C recruitment requires origin sequences but does not require ORC· suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs· INO80C co-localizes at origins with Mot1 and NC2 transcription factors· and genetic studies suggest that they function together to promote genome stability. Interestingly· nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences· and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription· maintaining genomic stability. The INO80C chromatin remodeler is known to regulate transcription and genomic stability. Topal et al. find that INO80C functions with Mot1 repressor to prevent pervasive transcription at replication origins in yeast and mESCs. Increased ncRNAs lead to new DNA double-strand breaks at origins, linking transcriptional regulation to genomic stability.
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5
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Cardoso da Silva R, Vader G. Getting there: understanding the chromosomal recruitment of the AAA+ ATPase Pch2/TRIP13 during meiosis. Curr Genet 2021; 67:553-565. [PMID: 33712914 PMCID: PMC8254700 DOI: 10.1007/s00294-021-01166-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
The generally conserved AAA+ ATPase Pch2/TRIP13 is involved in diverse aspects of meiosis, such as prophase checkpoint function, DNA break regulation, and meiotic recombination. The controlled recruitment of Pch2 to meiotic chromosomes allows it to use its ATPase activity to influence HORMA protein-dependent signaling. Because of the connection between Pch2 chromosomal recruitment and its functional roles in meiosis, it is important to reveal the molecular details that govern Pch2 localization. Here, we review the current understanding of the different factors that control the recruitment of Pch2 to meiotic chromosomes, with a focus on research performed in budding yeast. During meiosis in this organism, Pch2 is enriched within the nucleolus, where it likely associates with the specialized chromatin of the ribosomal (r)DNA. Pch2 is also found on non-rDNA euchromatin, where its recruitment is contingent on Zip1, a component of the synaptonemal complex (SC) that assembles between homologous chromosomes. We discuss recent findings connecting the recruitment of Pch2 with its association with the Origin Recognition Complex (ORC) and reliance on RNA Polymerase II-dependent transcription. In total, we provide a comprehensive overview of the pathways that control the chromosomal association of an important meiotic regulator.
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Affiliation(s)
- Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Clinical Genetics, Section of Oncogenetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
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6
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Zhang S, Yu X, Zhang Y, Xue X, Yu Q, Zha Z, Gogol M, Workman JL, Li S. Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation. Nat Commun 2021; 12:594. [PMID: 33500413 PMCID: PMC7838282 DOI: 10.1038/s41467-020-20711-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Telomeres are organized into a heterochromatin structure and maintenance of silent heterochromatin is required for chromosome stability. How telomere heterochromatin is dynamically regulated in response to stimuli remains unknown. Pyruvate kinase Pyk1 forms a complex named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex) to regulate gene expression by phosphorylating histone H3T11 (H3pT11). Here, we identify a function of SESAME in regulating telomere heterochromatin structure. SESAME phosphorylates H3T11 at telomeres, which maintains SIR (silent information regulator) complex occupancy at telomeres and protects Sir2 from degradation by autophagy. Moreover, SESAME-catalyzed H3pT11 directly represses autophagy-related gene expression to further prevent autophagy-mediated Sir2 degradation. By promoting H3pT11, serine increases Sir2 protein levels and enhances telomere silencing. Loss of H3pT11 leads to reduced Sir2 and compromised telomere silencing during chronological aging. Together, our study provides insights into dynamic regulation of silent heterochromatin by histone modifications and autophagy in response to cell metabolism and aging.
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Affiliation(s)
- Shihao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xiangyan Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Zitong Zha
- Human Aging Research Institute (HARI), School of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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7
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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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8
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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. BIOLOGY 2020; 9:E213. [PMID: 32784701 PMCID: PMC7465399 DOI: 10.3390/biology9080213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions.
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Affiliation(s)
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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9
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Hocher A, Taddei A. Subtelomeres as Specialized Chromatin Domains. Bioessays 2020; 42:e1900205. [PMID: 32181520 DOI: 10.1002/bies.201900205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. However, current definitions of subtelomeres are generally based on synteny and are largely gene-centered. Taking into consideration both the peculiar gene content and dynamics as well as the chromatin properties of those domains, it is discussed how chromatin features can contribute to subtelomeric properties and functions, and play a pivotal role in the emergence of subtelomeres.
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Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, F-75005, France.,Sorbonne Université, UPMC University Paris 06, CNRS, UMR3664, Paris, F-75005, France
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10
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Singh PP, Shukla M, White SA, Lafos M, Tong P, Auchynnikava T, Spanos C, Rappsilber J, Pidoux AL, Allshire RC. Hap2-Ino80-facilitated transcription promotes de novo establishment of CENP-A chromatin. Genes Dev 2020; 34:226-238. [PMID: 31919190 PMCID: PMC7000912 DOI: 10.1101/gad.332536.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
Centromeres are maintained epigenetically by the presence of CENP-A, an evolutionarily conserved histone H3 variant, which directs kinetochore assembly and hence centromere function. To identify factors that promote assembly of CENP-A chromatin, we affinity-selected solubilized fission yeast CENP-ACnp1 chromatin. All subunits of the Ino80 complex were enriched, including the auxiliary subunit Hap2. Chromatin association of Hap2 is Ies4-dependent. In addition to a role in maintenance of CENP-ACnp1 chromatin integrity at endogenous centromeres, Hap2 is required for de novo assembly of CENP-ACnp1 chromatin on naïve centromere DNA and promotes H3 turnover on centromere regions and other loci prone to CENP-ACnp1 deposition. Prior to CENP-ACnp1 chromatin assembly, Hap2 facilitates transcription from centromere DNA. These analyses suggest that Hap2-Ino80 destabilizes H3 nucleosomes on centromere DNA through transcription-coupled histone H3 turnover, driving the replacement of resident H3 nucleosomes with CENP-ACnp1 nucleosomes. These inherent properties define centromere DNA by directing a program that mediates CENP-ACnp1 assembly on appropriate sequences.
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Affiliation(s)
- Puneet P. Singh
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Manu Shukla
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Sharon A. White
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Marcel Lafos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Pin Tong
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Tatsiana Auchynnikava
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Alison L. Pidoux
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Robin C. Allshire
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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11
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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12
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Vlaming H, McLean CM, Korthout T, Alemdehy MF, Hendriks S, Lancini C, Palit S, Klarenbeek S, Kwesi‐Maliepaard EM, Molenaar TM, Hoekman L, Schmidlin TT, Altelaar AFM, van Welsem T, Dannenberg J, Jacobs H, van Leeuwen F. Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO J 2019; 38:e101564. [PMID: 31304633 PMCID: PMC6627229 DOI: 10.15252/embj.2019101564] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
DOT1L methylates histone H3K79 and is aberrantly regulated in MLL-rearranged leukemia. Inhibitors have been developed to target DOT1L activity in leukemia, but cellular mechanisms that regulate DOT1L are still poorly understood. We have identified the histone deacetylase Rpd3 as a negative regulator of budding yeast Dot1. At its target genes, the transcriptional repressor Rpd3 restricts H3K79 methylation, explaining the absence of H3K79me3 at a subset of genes in the yeast genome. Similar to the crosstalk in yeast, inactivation of the murine Rpd3 homolog HDAC1 in thymocytes led to an increase in H3K79 methylation. Thymic lymphomas that arise upon genetic deletion of Hdac1 retained the increased H3K79 methylation and were sensitive to reduced DOT1L dosage. Furthermore, cell lines derived from Hdac1Δ/Δ thymic lymphomas were sensitive to a DOT1L inhibitor, which induced apoptosis. In summary, we identified an evolutionarily conserved crosstalk between HDAC1 and DOT1L with impact in murine thymic lymphoma development.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMAUSA
| | - Chelsea M McLean
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tessy Korthout
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mir Farshid Alemdehy
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Hendriks
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Cesare Lancini
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sander Palit
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Thom M Molenaar
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Thierry T Schmidlin
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
- Proteomics FacilityNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tibor van Welsem
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jan‐Hermen Dannenberg
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Genmab B.V.Antibody SciencesUtrechtThe Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Fred van Leeuwen
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
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13
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Knezevic I, González-Medina A, Gaspa L, Hidalgo E, Ayté J. The INO80 complex activates the transcription of S-phase genes in a cell cycle-regulated manner. FEBS J 2018; 285:3870-3881. [PMID: 30134042 DOI: 10.1111/febs.14640] [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] [Received: 05/11/2018] [Revised: 07/30/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022]
Abstract
Chromatin structure is an essential factor in the proper regulation of DNA repair, DNA replication and transcription. The INO80 complex and the SWR complex have been shown to play a fundamental role in transcription regulation through remodeling chromatin at specific genes and loci. Here, we report that the Schizosaccharomyces pombe INO80 complex physically interacts with the mlui-binding factor (MBF) complex. Furthermore, we are able to detect the INO80 complex in MBF-regulated promoters. Binding of INO80 to these genes is cell cycle regulated, with a maximum binding preceding their transcription and accumulation of their mRNAs. In fact, the INO80 complex is required to fully and timely activate the transcription of these genes. We also show that the accumulation of acetylated H2A.Z at the +1 nucleosome is cell cycle regulated. Cells in which H2A.Z acetylation is abolished still have some cell cycle-regulated transcription of MBF-dependent genes, although to a much lesser extent.
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Affiliation(s)
- Iva Knezevic
- Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alberto González-Medina
- Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura Gaspa
- Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - José Ayté
- Departament de Ciències, Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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14
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Sun J, Shi L, Kinomura A, Fukuto A, Horikoshi Y, Oma Y, Harata M, Ikura M, Ikura T, Kanaar R, Tashiro S. Distinct roles of ATM and ATR in the regulation of ARP8 phosphorylation to prevent chromosome translocations. eLife 2018; 7:e32222. [PMID: 29759113 PMCID: PMC5953535 DOI: 10.7554/elife.32222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/25/2018] [Indexed: 12/26/2022] Open
Abstract
Chromosomal translocations are hallmarks of various types of cancers and leukemias. However, the molecular mechanisms of chromosome translocations remain largely unknown. The ataxia-telangiectasia mutated (ATM) protein, a DNA damage signaling regulator, facilitates DNA repair to prevent chromosome abnormalities. Previously, we showed that ATM deficiency led to the 11q23 chromosome translocation, the most frequent chromosome abnormalities in secondary leukemia. Here, we show that ARP8, a subunit of the INO80 chromatin remodeling complex, is phosphorylated after etoposide treatment. The etoposide-induced phosphorylation of ARP8 is regulated by ATM and ATR, and attenuates its interaction with INO80. The ATM-regulated phosphorylation of ARP8 reduces the excessive loading of INO80 and RAD51 onto the breakpoint cluster region. These findings suggest that the phosphorylation of ARP8, regulated by ATM, plays an important role in maintaining the fidelity of DNA repair to prevent the etoposide-induced 11q23 abnormalities.
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Affiliation(s)
- Jiying Sun
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
| | - Lin Shi
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
| | - Aiko Kinomura
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
| | - Atsuhiko Fukuto
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
- Department of Ophthalmology and Visual Science, Graduate School of Biomedical SciencesHiroshima UniversityHiroshimaJapan
| | - Yasunori Horikoshi
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
| | - Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Masae Ikura
- Laboratory of Chromatin Regulatory Network, Department of MutagenesisRadiation Biology Center, Kyoto UniversityKyotoJapan
| | - Tsuyoshi Ikura
- Laboratory of Chromatin Regulatory Network, Department of MutagenesisRadiation Biology Center, Kyoto UniversityKyotoJapan
| | - Roland Kanaar
- Department of Molecular GeneticsOncode InstituteRotterdamNetherlands
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and MedicineHiroshima UniversityHiroshimaJapan
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15
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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16
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Morrison AJ. Genome maintenance functions of the INO80 chromatin remodeller. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0289. [PMID: 28847826 DOI: 10.1098/rstb.2016.0289] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin modification is conserved in all eukaryotes and is required to facilitate and regulate DNA-templated processes. For example, chromatin manipulation, such as histone post-translational modification and nucleosome positioning, play critical roles in genome stability pathways. The INO80 chromatin-remodelling complex, which regulates the abundance and positioning of nucleosomes, is particularly important for proper execution of inducible responses to DNA damage. This review discusses the participation and activity of the INO80 complex in DNA repair and cell cycle checkpoint pathways, with emphasis on the Saccharomyces cerevisiae model system. Furthermore, the role of ATM/ATR kinases, central regulators of DNA damage signalling, in the regulation of INO80 function will be reviewed. In addition, emerging themes of chromatin remodelling in mitotic stability pathways and chromosome segregation will be introduced. These studies are critical to understanding the dynamic chromatin landscape that is rapidly and reversibly modified to maintain the integrity of the genome.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
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17
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Identification of Two Distinct Classes of the Human INO80 Complex Genome-Wide. G3-GENES GENOMES GENETICS 2018; 8:1095-1102. [PMID: 29432129 PMCID: PMC5873900 DOI: 10.1534/g3.117.300504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin remodeling and histone modifying enzymes play a critical role in shaping the regulatory output of a cell. Although much is known about these classes of proteins, identifying the mechanisms by which they coordinate gene expression programs remains an exciting topic of investigation. One factor that may contribute to the targeting and activity of chromatin regulators is local chromatin landscape. We leveraged genomic approaches and publically-available datasets to characterize the chromatin landscape at targets of the human INO80 chromatin remodeling complex (INO80-C). Our data revealed two classes of INO80-C targets with distinct chromatin signatures. The predominant INO80-C class was enriched for open chromatin, H3K27ac, and representative subunits from each of the three INO80-C modules (RUVBL1, RUVBL2, MCRS1, YY1). We named this class Canonical INO80. Notably, we identified an unexpected class of INO80-C targets that contained only the INO80 ATPase and harbored a repressive chromatin signature characterized by inaccessible chromatin, H3K27me3, and the methyltransferase EZH2. We named this class Non-Canonical INO80 (NC-INO80). Biochemical approaches indicated that INO80-C and the H3K27 acetyltransferase P300 physically interact, suggesting INO80-C and P300 may jointly coordinate chromatin accessibility at Canonical INO80 sites. No interaction was detected between INO80-C and EZH2, indicating INO80-C and EZH2 may engage in a separate form of regulatory crosstalk at NC-INO80 targets. Our data indicate that INO80-C is more compositionally heterogenous at its genomic targets than anticipated. Moreover, our data suggest there is an important link between INO80-C and histone modifying enzymes that may have consequences in developmental and pathological contexts.
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18
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Beckwith SL, Schwartz EK, García-Nieto PE, King DA, Gowans GJ, Wong KM, Eckley TL, Paraschuk AP, Peltan EL, Lee LR, Yao W, Morrison AJ. The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation. PLoS Genet 2018; 14:e1007216. [PMID: 29462149 PMCID: PMC5834206 DOI: 10.1371/journal.pgen.1007216] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/02/2018] [Accepted: 01/23/2018] [Indexed: 12/16/2022] Open
Abstract
Chromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators in Saccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis. In particular, mitochondrial maintenance is disrupted in ies6 mutants. INO80 is also needed to communicate TORC1-mediated signaling to chromatin, as ino80 mutants exhibit defective transcriptional profiles and altered histone acetylation of TORC1-responsive genes. Furthermore, comparative analysis reveals subunits of INO80 and mTORC1 have high co-occurrence of alterations in human cancers. Collectively, these results demonstrate that the INO80 complex is a central component of metabolic homeostasis that influences histone acetylation and may contribute to disease when disrupted.
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Affiliation(s)
- Sean L. Beckwith
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Erin K. Schwartz
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Devin A. King
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Graeme J. Gowans
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Ka Man Wong
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Tessa L. Eckley
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Egan L. Peltan
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Laura R. Lee
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Wei Yao
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Ashby J. Morrison
- Department of Biology, Stanford University, Stanford, CA, United States of America
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19
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Endothelial deletion of Ino80 disrupts coronary angiogenesis and causes congenital heart disease. Nat Commun 2018; 9:368. [PMID: 29371594 PMCID: PMC5785521 DOI: 10.1038/s41467-017-02796-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 12/28/2017] [Indexed: 12/18/2022] Open
Abstract
During development, the formation of a mature, well-functioning heart requires transformation of the ventricular wall from a loose trabecular network into a dense compact myocardium at mid-gestation. Failure to compact is associated in humans with congenital diseases such as left ventricular non-compaction (LVNC). The mechanisms regulating myocardial compaction are however still poorly understood. Here, we show that deletion of the Ino80 chromatin remodeler in vascular endothelial cells prevents ventricular compaction in the developing mouse heart. This correlates with defective coronary vascularization, and specific deletion of Ino80 in the two major coronary progenitor tissues—sinus venosus and endocardium—causes intermediate phenotypes. In vitro, endothelial cells promote myocardial expansion independently of blood flow in an Ino80-dependent manner. Ino80 deletion increases the expression of E2F-activated genes and endothelial cell S-phase occupancy. Thus, Ino80 is essential for coronary angiogenesis and allows coronary vessels to support proper compaction of the heart wall. Heart development requires compaction of the ventricular wall into a dense myocardium at mid-gestation. Here, Rhee and colleagues show that the chromatin remodeller Ino80 is critical for the formation of the coronary vasculature, and show that coronary vessels are needed for successful cardiac compaction during embryonic development.
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20
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Klopf E, Schmidt HA, Clauder-Münster S, Steinmetz LM, Schüller C. INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res 2017; 45:3752-3766. [PMID: 28025392 PMCID: PMC5397147 DOI: 10.1093/nar/gkw1292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The conserved INO80 chromatin remodeling complex is involved in regulation of DNA damage repair, replication and transcription. It is commonly recruited to the transcription start region and contributes to the establishment of promoter-proximal nucleosomes. We find a substantial influence of INO80 on nucleosome dynamics and gene expression during stress induced transcription. Transcription induced by osmotic stress leads to genome-wide remodeling of promoter proximal nucleosomes. INO80 function is required for timely return of evicted nucleosomes to the 5΄ end of induced genes. Reduced INO80 function in Arp8-deficient cells leads to correlated prolonged transcription and nucleosome eviction. INO80 and the related complex SWR1 regulate incorporation of the H2A.Z isoform at promoter proximal nucleosomes. However, H2A.Z seems not to influence osmotic stress induced gene regulation. Furthermore, we show that high rates of transcription promote INO80 recruitment to promoter regions, suggesting a connection between active transcription and promoter proximal nucleosome remodeling. In addition, we find that absence of INO80 enhances bidirectional promoter activity at highly induced genes and expression of a number of stress induced transcripts. We suggest that INO80 has a direct repressive role via promoter proximal nucleosome remodeling to limit high levels of transcription in yeast.
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Affiliation(s)
- Eva Klopf
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Campus Vienna Biocenter 5 (VBC5), 1030 Vienna, Austria
| | - Sandra Clauder-Münster
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
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21
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Yau EH, Kummetha IR, Lichinchi G, Tang R, Zhang Y, Rana TM. Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers. Cancer Res 2017; 77:6330-6339. [PMID: 28954733 DOI: 10.1158/0008-5472.can-17-2043] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022]
Abstract
Targeting mutant KRAS signaling pathways continues to attract attention as a therapeutic strategy for KRAS-driven tumors. In this study, we exploited the power of the CRISPR-Cas9 system to identify genes affecting the tumor xenograft growth of human mutant KRAS (KRASMUT) colorectal cancers. Using pooled lentiviral single-guide RNA libraries, we conducted a genome-wide loss-of-function genetic screen in an isogenic pair of human colorectal cancer cell lines harboring mutant or wild-type KRAS. The screen identified novel and established synthetic enhancers or synthetic lethals for KRASMUT colorectal cancer, including targetable metabolic genes. Notably, genetic disruption or pharmacologic inhibition of the metabolic enzymes NAD kinase or ketohexokinase was growth inhibitory in vivo In addition, the chromatin remodeling protein INO80C was identified as a novel tumor suppressor in KRASMUT colorectal and pancreatic tumor xenografts. Our findings define a novel targetable set of therapeutic targets for KRASMUT tumors. Cancer Res; 77(22); 6330-9. ©2017 AACR.
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Affiliation(s)
- Edwin H Yau
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California.,Division of Hematology-Oncology, Department of Internal Medicine, University of California San Diego School of Medicine, La Jolla, California.,Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Indrasena Reddy Kummetha
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Gianluigi Lichinchi
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Rachel Tang
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Yunlin Zhang
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Tariq M Rana
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California. .,Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, La Jolla, California
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22
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The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3. Nat Commun 2017; 8:529. [PMID: 28904333 PMCID: PMC5597579 DOI: 10.1038/s41467-017-00704-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 07/19/2017] [Indexed: 12/25/2022] Open
Abstract
The centromere is the chromosomal locus at which the kinetochore is assembled to direct chromosome segregation. The histone H3 variant, centromere protein A (CENP-A), is known to epigenetically mark active centromeres, but the mechanism by which CENP-A propagates at the centromere, replacing histone H3, remains poorly understood. Using fission yeast, here we show that the Ino80 adenosine triphosphate (ATP)-dependent chromatin-remodeling complex, which removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. CENP-ACnp1 chromatin actively recruits the Ino80 complex to centromeres to elicit eviction of histone H3-containing nucleosomes. Artificial targeting of Ino80 subunits to a non-centromeric DNA sequence placed in a native centromere enhances the spreading of CENP-ACnp1 chromatin into the non-centromeric DNA. Based on these results, we propose that CENP-ACnp1 chromatin employs the Ino80 complex to mediate the replacement of histone H3 with CENP-ACnp1, and thereby reinforces itself. The histone variant CENP-A marks active centromeres and replaces H3 at centromeres through a poorly understood mechanism. Here, the authors provide evidence that the chromatin remodeller Ino80 promotes CENP-A chromatin assembly at the centromere in fission yeast.
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23
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Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals. Mol Cell 2017; 67:594-607.e4. [PMID: 28735899 DOI: 10.1016/j.molcel.2017.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/12/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023]
Abstract
Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C, or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.
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Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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24
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INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun 2017; 8:15616. [PMID: 28604691 PMCID: PMC5472786 DOI: 10.1038/ncomms15616] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
ATP-dependent chromatin remodellers modulate nucleosome dynamics by mobilizing or disassembling nucleosomes, as well as altering nucleosome composition. These chromatin remodellers generally function by translocating along nucleosomal DNA at the H3–H4 interface of nucleosomes. Here we show that, unlike other remodellers, INO80 translocates along DNA at the H2A–H2B interface of nucleosomes and persistently displaces DNA from the surface of H2A–H2B. DNA translocation and DNA torsional strain created near the entry site of nucleosomes by INO80 promotes both the mobilization of nucleosomes and the selective exchange of H2A.Z–H2B dimers out of nucleosomes and replacement by H2A–H2B dimers without any additional histone chaperones. We find that INO80 translocates and mobilizes H2A.Z-containing nucleosomes more efficiently than those containing H2A, partially accounting for the preference of INO80 to replace H2A.Z with H2A. Our data suggest that INO80 has a mechanism for dimer exchange that is distinct from other chromatin remodellers including its paralogue SWR1. Chromatin remodellers usually mobilize or disassemble nucleosomes by translocating along the nucleosomal DNA at the H3-H4 interface. Here, the authors provide evidence chromatin remodeller INO80 translocates along DNA at the H2A-H2B interface and displaces DNA from the surface of H2A-H2B.
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25
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The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae. Genetics 2017; 203:1563-99. [PMID: 27516616 DOI: 10.1534/genetics.112.145243] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/30/2016] [Indexed: 12/31/2022] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae occurs at several genomic sites including the silent mating-type loci, telomeres, and the ribosomal DNA (rDNA) tandem array. Epigenetic silencing at each of these domains is characterized by the absence of nearly all histone modifications, including most prominently the lack of histone H4 lysine 16 acetylation. In all cases, silencing requires Sir2, a highly-conserved NAD(+)-dependent histone deacetylase. At locations other than the rDNA, silencing also requires additional Sir proteins, Sir1, Sir3, and Sir4 that together form a repressive heterochromatin-like structure termed silent chromatin. The mechanisms of silent chromatin establishment, maintenance, and inheritance have been investigated extensively over the last 25 years, and these studies have revealed numerous paradigms for transcriptional repression, chromatin organization, and epigenetic gene regulation. Studies of Sir2-dependent silencing at the rDNA have also contributed to understanding the mechanisms for maintaining the stability of repetitive DNA and regulating replicative cell aging. The goal of this comprehensive review is to distill a wide array of biochemical, molecular genetic, cell biological, and genomics studies down to the "nuts and bolts" of silent chromatin and the processes that yield transcriptional silencing.
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Gai K, Cao X, Dong Q, Ding Z, Wei Y, Liu Y, Liu X, He Q. Transcriptional repression of frequency by the IEC-1-INO80 complex is required for normal Neurospora circadian clock function. PLoS Genet 2017; 13:e1006732. [PMID: 28403234 PMCID: PMC5406019 DOI: 10.1371/journal.pgen.1006732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 04/26/2017] [Accepted: 04/03/2017] [Indexed: 12/02/2022] Open
Abstract
Rhythmic activation and repression of the frequency (frq) gene are essential for normal function of the Neurospora circadian clock. WHITE COLLAR (WC) complex, the positive element of the Neurospora circadian system, is responsible for stimulation of frq transcription. We report that a C2H2 finger domain-containing protein IEC-1 and its associated chromatin remodeling complex INO80 play important roles in normal Neurospora circadian clock function. In iec-1KO strains, circadian rhythms are abolished, and the frq transcript levels are increased compared to that of the wild-type strain. Similar results are observed in mutant strains of the INO80 subunits. Furthermore, ChIP data show that recruitment of the INO80 complex to the frq promoter is IEC-1-dependent. WC-mediated transcription of frq contributes to the rhythmic binding of the INO80 complex at the frq promoter. As demonstrated by ChIP analysis, the INO80 complex is required for the re-establishment of the dense chromatin environment at the frq promoter. In addition, WC-independent frq transcription is present in ino80 mutants. Altogether, our data indicate that the INO80 complex suppresses frq transcription by re-assembling the suppressive mechanisms at the frq promoter after transcription of frq. Circadian clocks organize inner physiology to anticipate changes in the external environment. These clocks are controlled by the oscillation of central clock proteins which form the central oscillator. Transcriptional regulation is a critical step in the regulation of the oscillation of these core proteins. In eukaryotes, chromatin remodeling is a common mechanism to regulate gene transcription by conquering or establishing nucleosomal barriers for the transcription machinery. Here, we showed that a C2H2 finger domain-containing protein IEC-1 and its associated chromatin remodeling complex INO80 are required for transcriptional repression of the core clock gene frq in the Neurospora circadian system. Moreover, the activator WHITE COLLAR (WC) complex is responsible for the transcriptional activation of frq; thus, considering the different timing of the transcriptional activation and suppression of frq, there must be a mechanism that coordinates the two opposite processes. We also demonstrated that the WC-mediated open state of the frq promoter facilitates the binding of INO80 to this region, which prepares for subsequent transcriptional suppression. Collectively, our data provide novel insights into the regulation of the frq gene and the circadian clock.
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Affiliation(s)
- Kexin Gai
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuemei Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Dong
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhaolan Ding
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yashang Wei
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yingchun Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiao Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail:
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27
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Huang C, Su T, Xue Y, Cheng C, Lay FD, McKee RA, Li M, Vashisht A, Wohlschlegel J, Novitch BG, Plath K, Kurdistani SK, Carey M. Cbx3 maintains lineage specificity during neural differentiation. Genes Dev 2017; 31:241-246. [PMID: 28270516 PMCID: PMC5358721 DOI: 10.1101/gad.292169.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/27/2017] [Indexed: 02/05/2023]
Abstract
Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) stimulates cell differentiation, but its mechanism is unknown. We found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26. RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.
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Affiliation(s)
- Chengyang Huang
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Trent Su
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Yong Xue
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Fides D Lay
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Robin A McKee
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Meiyang Li
- Department of Neurobiology, Shantou University Medical College, Shantou 515041, China
| | - Ajay Vashisht
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Bennett G Novitch
- Department of Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
| | - Michael Carey
- Department of Biological Chemistry, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles California 90095, USA
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28
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Mendiratta S, Bhatia S, Jain S, Kaur T, Brahmachari V. Interaction of the Chromatin Remodeling Protein hINO80 with DNA. PLoS One 2016; 11:e0159370. [PMID: 27428271 PMCID: PMC4948845 DOI: 10.1371/journal.pone.0159370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/01/2016] [Indexed: 11/18/2022] Open
Abstract
The presence of a highly conserved DNA binding domain in INO80 subfamily predicted that INO80 directly interacts with DNA and we demonstrated its DNA binding activity in vitro. Here we report the consensus motif recognized by the DBINO domain identified by SELEX method and demonstrate the specific interaction of INO80 with the consensus motif. We show that INO80 significantly down regulates the reporter gene expression through its binding motif, and the repression is dependent on the presence of INO80 but not YY1 in the cell. The interaction is lost if specific residues within the consensus motif are altered. We identify a large number of potential target sites of INO80 in the human genome through in silico analysis that can grouped into three classes; sites that contain the recognition sequence for INO80 and YY1, only YY1 and only INO80. We demonstrate the binding of INO80 to a representative set of sites in HEK cells and the correlated repressive histone modifications around the binding motif. In the light of the role of INO80 in homeotic gene regulation in Drosophila as an Enhancer of trithorax and polycomb protein (ETP) that can modify the effect of both repressive complexes like polycomb as well as the activating complex like trithorax, it remains to be seen if INO80 can act as a recruiter of chromatin modifying complexes.
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Affiliation(s)
- Shweta Mendiratta
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Shipra Bhatia
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Shruti Jain
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Taniya Kaur
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- * E-mail: ;
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29
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Poli J, Gerhold CB, Tosi A, Hustedt N, Seeber A, Sack R, Herzog F, Pasero P, Shimada K, Hopfner KP, Gasser SM. Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress. Genes Dev 2016; 30:337-54. [PMID: 26798134 PMCID: PMC4743062 DOI: 10.1101/gad.273813.115] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022]
Abstract
Poli et al. present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C, and the transcription complex PAF1C. A subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea. Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription–replication fork collision.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | | | - Alessandro Tosi
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Franz Herzog
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Philippe Pasero
- UPR 1142, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 30396 Montpellier, France
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Karl-Peter Hopfner
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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30
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The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation. Mol Cell Biol 2016; 36:979-91. [PMID: 26755556 DOI: 10.1128/mcb.00801-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/30/2015] [Indexed: 11/20/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80-regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5Δ, ies6Δ, and ino80Δ mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability.
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31
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Abstract
Base Excision Repair (BER) is a conserved, intracellular DNA repair system that recognizes and removes chemically modified bases to insure genomic integrity and prevent mutagenesis. Aberrant BER has been tightly linked with a broad spectrum of human pathologies, such as several types of cancer, neurological degeneration, developmental abnormalities, immune dysfunction and aging. In the cell, BER must recognize and remove DNA lesions from the tightly condensed, protein-coated chromatin. Because chromatin is necessarily refractory to DNA metabolic processes, like transcription and replication, the compaction of the genomic material is also inhibitory to the repair systems necessary for its upkeep. Multiple ATP-dependent chromatin remodelling (ACR) complexes play essential roles in modulating the protein-DNA interactions within chromatin, regulating transcription and promoting activities of some DNA repair systems, including double-strand break repair and nucleotide excision repair. However, it remains unclear how BER operates in the context of chromatin, and if the chromatin remodelling processes that govern transcription and replication also actively regulate the efficiency of BER. In this review we highlight the emerging role of ACR in regulation of BER.
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Affiliation(s)
- John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA.
| | - Wioletta Czaja
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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32
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An RNAi-Based Candidate Screen for Modifiers of the CHD1 Chromatin Remodeler and Assembly Factor in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2015; 6:245-54. [PMID: 26596648 PMCID: PMC4751545 DOI: 10.1534/g3.115.021691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conserved chromatin remodeling and assembly factor CHD1 (chromodomains, helicase, DNA-binding domain) is present at active genes where it participates in histone turnover and recycling during transcription. In order to gain a more complete understanding of the mechanism of action of CHD1 during development, we created a novel genetic assay in Drosophila melanogaster to evaluate potential functional interactions between CHD1 and other chromatin factors. We found that overexpression of CHD1 results in defects in wing development and utilized this fully penetrant and reliable phenotype to conduct a small-scale RNAi-based candidate screen to identify genes that functionally interact with chd1 in vivo. Our results indicate that CHD1 may act in opposition to other remodeling factors, including INO80, and that the recruitment of CHD1 to active genes by RTF1 is conserved in flies.
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33
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Rege M, Subramanian V, Zhu C, Hsieh THS, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 2015; 13:1610-22. [PMID: 26586442 PMCID: PMC4662874 DOI: 10.1016/j.celrep.2015.10.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/02/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
The histone variant H2A.Z is a hallmark of nucleosomes flanking promoters of protein-coding genes and is often found in nucleosomes that carry lysine 56-acetylated histone H3 (H3-K56Ac), a mark that promotes replication-independent nucleosome turnover. Here, we find that H3-K56Ac promotes RNA polymerase II occupancy at many protein-coding and noncoding loci, yet neither H3-K56Ac nor H2A.Z has a significant impact on steady-state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on RNA levels are revealed only in the absence of the nuclear RNA exosome. H2A.Z is also necessary for the expression of divergent, promoter-proximal non-coding RNAs (ncRNAs) in mouse embryonic stem cells. Finally, we show that H2A.Z functions with H3-K56Ac to facilitate formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher-order chromatin structures.
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Affiliation(s)
- Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chenchen Zhu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Tsung-Han S Hsieh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laurie A Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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34
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Yao W, Beckwith SL, Zheng T, Young T, Dinh VT, Ranjan A, Morrison AJ. Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities. J Biol Chem 2015; 290:25700-9. [PMID: 26306040 DOI: 10.1074/jbc.m115.674887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
ATP-dependent chromatin remodeling, which repositions and restructures nucleosomes, is essential to all DNA-templated processes. The INO80 chromatin remodeling complex is an evolutionarily conserved complex involved in diverse cellular processes, including transcription, DNA repair, and replication. The functional diversity of the INO80 complex can, in part, be attributed to specialized activities of distinct subunits that compose the complex. Furthermore, structural analyses have identified biochemically discrete subunit modules that assemble along the Ino80 ATPase scaffold. Of particular interest is the Saccharomyces cerevisiae Arp5-Ies6 module located proximal to the Ino80 ATPase and the Rvb1-Rvb2 helicase module needed for INO80-mediated in vitro activity. In this study we demonstrate that the previously uncharacterized Ies2 subunit is required for Arp5-Ies6 association with the catalytic components of the INO80 complex. In addition, Arp5-Ies6 module assembly with the INO80 complex is dependent on distinct conserved domains within Arp5, Ies6, and Ino80, including the spacer region within the Ino80 ATPase domain. Arp5-Ies6 interacts with chromatin via assembly with the INO80 complex, as IES2 and INO80 deletion results in loss of Arp5-Ies6 chromatin association. Interestingly, ectopic addition of the wild-type Arp5-Ies6 module stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro. However, the addition of mutant Arp5 lacking unique insertion domains facilitates ATP hydrolysis in the absence of nucleosome sliding. Collectively, these results define the requirements of Arp5-Ies6 assembly, which are needed to couple ATP hydrolysis to productive nucleosome movement.
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Affiliation(s)
- Wei Yao
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Sean L Beckwith
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Tina Zheng
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Thomas Young
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Van T Dinh
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ashby J Morrison
- From the Department of Biology, Stanford University, Stanford California 94305 and
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