1
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Dai Z, Yang X. The regulation of liquid-liquid phase separated condensates containing nucleic acids. FEBS J 2024; 291:2320-2331. [PMID: 37735903 DOI: 10.1111/febs.16959] [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: 05/19/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Liquid-liquid phase separation (LLPS) has been recognized as a universal biological phenomenon. It plays an important role in life activities. LLPS is induced by weak interactions between intrinsically disordered regions or low complex domains. Nucleic acids are widely present in cells, and shown to be closely related to LLPS. Their structure and electronegativity provide the excellent platforms for the formation of phase-separated condensates. In this review, we summarize the interconnected regulation between nucleic acids and LLPS demonstrated in in vivo and in vitro studies. Beside homogeneous and single-phase condensates, complicated and multicompartment LLPS induced by nucleic acids is discussed as well. Recent advances about nucleic-acid-induced LLPS as a new pathogenic mechanism and drug design direction are highlighted, especially virus-mediated disease treatment and prevention.
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Affiliation(s)
- Zhuojun Dai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaorong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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2
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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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3
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Lu PYT, Kirlin AC, Aristizabal MJ, Brewis HT, Lévesque N, Setiaputra DT, Avvakumov N, Benschop JJ, Groot Koerkamp M, Holstege FCP, Krogan NJ, Yip CK, Côté J, Kobor MS. A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans. Genetics 2022; 222:iyac136. [PMID: 36066422 PMCID: PMC9630986 DOI: 10.1093/genetics/iyac136] [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: 10/12/2021] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 lysine acetyltransferase complex acetylates histone and nonhistone proteins and functions in transcription regulation, cell cycle progression, and DNA repair. NuA4 harbors an interesting duality in that its catalytic module can function independently and distinctly as picNuA4. At the molecular level, picNuA4 anchors to its bigger brother via physical interactions between the C-terminus of Epl1 and the HSA domain of Eaf1, the NuA4 central scaffolding subunit. This is reflected at the regulatory level, as picNuA4 can be liberated genetically from NuA4 by disrupting the Epl1-Eaf1 interaction. As such, removal of either Eaf1 or the Epl1 C-terminus offers a unique opportunity to elucidate the contributions of Eaf1 and Epl1 to NuA4 biology and in turn their roles in balancing picNuA4 and NuA4 activities. Using high-throughput genetic and gene expression profiling, and targeted functional assays to compare eaf1Δ and epl1-CΔ mutants, we found that EAF1 and EPL1 had both overlapping and distinct roles. Strikingly, loss of EAF1 or its HSA domain led to a significant decrease in the amount of picNuA4, while loss of the Epl1 C-terminus increased picNuA4 levels, suggesting starkly opposing effects on picNuA4 regulation. The eaf1Δ epl1-CΔ double mutants resembled the epl1-CΔ single mutants, indicating that Eaf1's role in picNuA4 regulation depended on the Epl1 C-terminus. Key aspects of this regulation were evolutionarily conserved, as truncating an Epl1 homolog in human cells increased the levels of other picNuA4 subunits. Our findings suggested a model in which distinct aspects of the Epl1-Eaf1 interaction regulated picNuA4 amount and activity.
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Affiliation(s)
- Phoebe Y T Lu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Alyssa C Kirlin
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hilary T Brewis
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nancy Lévesque
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Dheva T Setiaputra
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikita Avvakumov
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Joris J Benschop
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | | | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, The Netherlands
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacques Côté
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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4
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Lai Y, Wang L, Zheng W, Wang S. Regulatory Roles of Histone Modifications in Filamentous Fungal Pathogens. J Fungi (Basel) 2022; 8:jof8060565. [PMID: 35736048 PMCID: PMC9224773 DOI: 10.3390/jof8060565] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungal pathogens have evolved diverse strategies to infect a variety of hosts including plants and insects. The dynamic infection process requires rapid and fine-tuning regulation of fungal gene expression programs in response to the changing host environment and defenses. Therefore, transcriptional reprogramming of fungal pathogens is critical for fungal development and pathogenicity. Histone post-translational modification, one of the main mechanisms of epigenetic regulation, has been shown to play an important role in the regulation of gene expressions, and is involved in, e.g., fungal development, infection-related morphogenesis, environmental stress responses, biosynthesis of secondary metabolites, and pathogenicity. This review highlights recent findings and insights into regulatory mechanisms of histone methylation and acetylation in fungal development and pathogenicity, as well as their roles in modulating pathogenic fungi–host interactions.
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Affiliation(s)
- Yiling Lai
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
| | - Lili Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weilu Zheng
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
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5
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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6
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Zhu J, Huang Q, Peng X, Luo C, Liu S, Liu Z, Wu X, Luo H. Identification of LncRNA Prognostic Signature Associated With Genomic Instability in Pancreatic Adenocarcinoma. Front Oncol 2022; 12:799475. [PMID: 35433487 PMCID: PMC9012103 DOI: 10.3389/fonc.2022.799475] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Genomic instability (GI) is a critical feature of cancer which plays a key role in the occurrence and development of pancreatic adenocarcinoma (PAAD). Long non-coding RNA (LncRNA) is an emerging prognostic biomarker because it is involved in regulating GI. Recently, researchers used such GI-related LncRNAs (GILncRNAs) to establish a prognostic signature for patients with cancer and helped in predicting the overall prognosis of the patients. However, it is evident that patients with PAAD still lack such prognostic signature constructed with GILncRNA. Methods The present study screened GILncRNAs from 83 patients with PAAD. Prognosis-related GILncRNAs were identified by univariate Cox regression analysis. The correlation coefficients of these GILncRNAs were obtained by multivariate Cox regression analysis and used to construct a signature. The signature in the present study was then assessed through survival analysis, mutation correlation analysis, independent prognostic analysis, and clinical stratification analysis in the training set and validated in the testing as well as all TCGA set. The current study performed external clinical relevance validation of the signature and validated the effect of AC108134.2 in GILncSig on PAAD using in vitro experiments. Finally, the function of GILncRNA signature (GILncSig) dependent on Gene Ontology enrichment analysis was explored and chemotherapeutic drug sensitivity analysis was also performed. Results Results of the present study found that a total of 409 GILncRNAs were identified, 5 of which constituted the prognostic risk signature in this study, namely, AC095057.3, AC108134.2, AC124798.1, AL606834.1, and AC104695.4. It was found that the signature of the present study was better than others in predicting the overall survival and applied to patients with PAAD of all ages, genders, and tumor grades. Further, it was noted that the signature of the current study in the GSE102238, was correlated with tumor length, and tumor stage of patients with PAAD. In vitro, functional experiments were used in the present study to validate that AC108134.2 is associated with PAAD genomic instability and progression. Notably, results of the pRRophetic analysis in the current study showed that the high-risk group possessed reverse characteristics and was sensitive to chemotherapy. Conclusions In conclusion, it was evident that the GILncSig used in the present study has good prognostic performance. Therefore, the signature may become a potential sensitive biological indicator of PAAD chemotherapy, which may help in clinical decision-making and management of patients with cancer.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Qian Huang
- Department of General Practice, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Chen Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xun Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongliang Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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7
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Campion CG, Verissimo T, Cossette S, Tremblay J. Does Subtelomeric Position of COMMD5 Influence Cancer Progression? Front Oncol 2021; 11:642130. [PMID: 33768002 PMCID: PMC7985453 DOI: 10.3389/fonc.2021.642130] [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: 12/15/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
The COMMD proteins are a family of ten pleiotropic factors which are widely conserved throughout evolution and are involved in the regulation of many cellular and physiological processes. COMMD proteins are mainly expressed in adult tissue and their downregulation has been correlated with tumor progression and poor prognosis in cancer. Among this family, COMMD5 emerged as a versatile modulator of tumor progression. Its expression can range from being downregulated to highly up regulated in a variety of cancer types. Accordingly, two opposing functions could be proposed for COMMD5 in cancer. Our studies supported a role for COMMD5 in the establishment and maintenance of the epithelial cell phenotype, suggesting a tumor suppressor function. However, genetic alterations leading to amplification of COMMD5 proteins have also been observed in various types of cancer, suggesting an oncogenic function. Interestingly, COMMD5 is the only member of this family that is located at the extreme end of chromosome 8, near its telomere. Here, we review some data concerning expression and role of COMMD5 and propose a novel rationale for the potential link between the subtelomeric position of COMMD5 on chromosome 8 and its contrasting functions in cancer.
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Affiliation(s)
- Carole G Campion
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Thomas Verissimo
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Suzanne Cossette
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Johanne Tremblay
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Département de Médecine, Université de Montréal, Montréal, QC, Canada
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8
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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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9
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Liu JC, Li QJ, He MH, Hu C, Dai P, Meng FL, Zhou BO, Zhou JQ. Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes. Nucleic Acids Res 2021; 48:12792-12803. [PMID: 33270890 PMCID: PMC7736797 DOI: 10.1093/nar/gkaa1150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and examined 195 strains, in which individual non-essential gene deletion causes telomere shortening. We have identified 24 genes whose deletion results in dramatic failure of Cdc13-Est2 function, including those encoding components of telomerase, Yku, KEOPS and NMD complexes, as well as quite a few whose functions are not obvious in telomerase activity regulation. We have characterized Swc4, a shared subunit of histone acetyltransferase NuA4 and chromatin remodeling SWR1 (SWR1-C) complexes, in telomere length regulation. Deletion of SWC4, but not other non-essential subunits of either NuA4 or SWR1-C, causes significant telomere shortening. Consistently, simultaneous disassembly of NuA4 and SWR1-C does not affect telomere length. Interestingly, inactivation of Swc4 in telomerase null cells accelerates both telomere shortening and senescence rates. Swc4 associates with telomeric DNA in vivo, suggesting a direct role of Swc4 at telomeres. Taken together, our work reveals a distinct role of Swc4 in telomere length regulation, separable from its canonical roles in both NuA4 and SWR1-C.
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Affiliation(s)
- Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian-Jin Li
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Fei-Long Meng
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo O Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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10
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Jezek M, Green EM. Histone Modifications and the Maintenance of Telomere Integrity. Cells 2019; 8:E199. [PMID: 30823596 PMCID: PMC6407025 DOI: 10.3390/cells8020199] [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: 01/01/2019] [Revised: 02/09/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022] Open
Abstract
Telomeres, the nucleoprotein structures at the ends of eukaryotic chromosomes, play an integral role in protecting linear DNA from degradation. Dysregulation of telomeres can result in genomic instability and has been implicated in increased rates of cellular senescence and many diseases, including cancer. The integrity of telomeres is maintained by a coordinated network of proteins and RNAs, such as the telomerase holoenzyme and protective proteins that prevent the recognition of the telomere ends as a DNA double-strand breaks. The structure of chromatin at telomeres and within adjacent subtelomeres has been implicated in telomere maintenance pathways in model systems and humans. Specific post-translational modifications of histones, including methylation, acetylation, and ubiquitination, have been shown to be necessary for maintaining a chromatin environment that promotes telomere integrity. Here we review the current knowledge regarding the role of histone modifications in maintaining telomeric and subtelomeric chromatin, discuss the implications of histone modification marks as they relate to human disease, and highlight key areas for future research.
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Affiliation(s)
- Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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11
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Thakre PK, SV A, Golla U, Chauhan S, Tomar RS. Previously uncharacterized amino acid residues in histone H3 and H4 mutants with roles in
DNA
damage repair response and cellular aging. FEBS J 2018; 286:1154-1173. [DOI: 10.1111/febs.14723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/01/2018] [Accepted: 12/04/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Pilendra K. Thakre
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Athira SV
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Upendarrao Golla
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Bethesda MD USA
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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12
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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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13
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Jezek M, Gast A, Choi G, Kulkarni R, Quijote J, Graham-Yooll A, Park D, Green EM. The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance. Epigenetics 2016; 12:93-104. [PMID: 27911222 DOI: 10.1080/15592294.2016.1265712] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of Saccharomyces cerevisiae have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
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Affiliation(s)
- Meagan Jezek
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Alison Gast
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Grace Choi
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Rushmie Kulkarni
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Jeremiah Quijote
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Andrew Graham-Yooll
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
| | - DoHwan Park
- b Department of Mathematics and Statistics , University of Maryland Baltimore County , Baltimore , MD , USA
| | - Erin M Green
- a Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , MD , USA
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Epigenetic engineering reveals a balance between histone modifications and transcription in kinetochore maintenance. Nat Commun 2016; 7:13334. [PMID: 27841270 PMCID: PMC5114538 DOI: 10.1038/ncomms13334] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/22/2016] [Indexed: 01/12/2023] Open
Abstract
Centromeres consist of specialized centrochromatin containing CENP-A nucleosomes intermingled with H3 nucleosomes carrying transcription-associated modifications. We have designed a novel synthetic biology 'in situ epistasis' analysis in which H3 dimethylated on lysine 4 (H3K4me2) demethylase LSD2 plus synthetic modules with competing activities are simultaneously targeted to a synthetic alphoidtetO HAC centromere. This allows us to uncouple transcription from histone modifications at the centromere. Here, we report that H3K4me2 loss decreases centromeric transcription, CENP-A assembly and stability and causes spreading of H3K9me3 across the HAC, ultimately inactivating the centromere. Surprisingly, CENP-28/Eaf6-induced transcription of the alphoidtetO array associated with H4K12 acetylation does not rescue the phenotype, whereas p65-induced transcription associated with H3K9 acetylation does rescue. Thus mitotic transcription plus histone modifications including H3K9ac constitute the 'epigenetic landscape' allowing CENP-A assembly and centrochromatin maintenance. H3K4me2 is required for the transcription and H3K9ac may form a barrier to prevent heterochromatin spreading and kinetochore inactivation at human centromeres.
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Cameron AM, Lawless SJ, Pearce EJ. Metabolism and acetylation in innate immune cell function and fate. Semin Immunol 2016; 28:408-416. [PMID: 28340958 PMCID: PMC10911065 DOI: 10.1016/j.smim.2016.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
Innate immunity is the first line of defense against invading pathogens. Changes in both metabolism and chromatin accessibility contribute to the shaping of these innate immune responses, and we are beginning to appreciate that cross-talk between these two systems plays an important role in determining innate immune cell differentiation and function. In this review we focus on acetylation, a post-translational modification important for both regulating chromatin accessibility by modulating histone function, and for functional regulation of non-histone proteins, which has many links to both immune signaling and metabolism. We discuss the interactions between metabolism and acetylation, including the requirement for metabolic intermediates as substrates and co-factors for acetylation, and the regulation of metabolic proteins and enzymes by acetylation. Here we highlight recent findings, which demonstrate the role that the metabolism-acetylation axis has in coordinating the responses of innate immune cells to the availability of nutrients and the microenvironment.
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Affiliation(s)
- Alanna M Cameron
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Simon J Lawless
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
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16
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Su CH, Cheng C, Tzeng TY, Lin IH, Hsu MT. An H2A Histone Isotype, H2ac, Associates with Telomere and Maintains Telomere Integrity. PLoS One 2016; 11:e0156378. [PMID: 27228173 PMCID: PMC4882029 DOI: 10.1371/journal.pone.0156378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/13/2016] [Indexed: 11/19/2022] Open
Abstract
Telomeres are capped at the ends of eukaryotic chromosomes and are composed of TTAGGG repeats bound to the shelterin complex. Here we report that a replication-dependent histone H2A isotype, H2ac, was associated with telomeres in human cells and co-immunoprecipitates with telomere repeat factor 2 (TRF2) and protection of telomeres protein 1 (POT1), whereas other histone H2A isotypes and mutations of H2ac did not bind to telomeres or these two proteins. The amino terminal basic domain of TRF2 was necessary for the association with H2ac and for the recruitment of H2ac to telomeres. Depletion of H2ac led to loss of telomeric repeat sequences, the appearance of dysfunctional telomeres, and chromosomal instability, including chromosomal breaks and anaphase bridges, as well as accumulation of telomere-associated DNA damage factors in H2ac depleted cells. Additionally, knockdown of H2ac elicits an ATM-dependent DNA damage response at telomeres and depletion of XPF protects telomeres against H2ac-deficiency-induced G-strand overhangs loss and DNA damage response, and prevents chromosomal instability. These findings suggest that the H2A isotype, H2ac, plays an essential role in maintaining telomere functional integrity.
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Affiliation(s)
- Chia-Hsin Su
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, 11221, Taiwan, Republic of China
| | - Ching Cheng
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, 11221, Taiwan, Republic of China
| | - Tsai-Yu Tzeng
- VYM Genome Research Center, National Yang-Ming University, University System of Taiwan, Taipei, 11221, Taiwan, Republic of China
| | - I-Hsuan Lin
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, 11221, Taiwan, Republic of China
| | - Ming-Ta Hsu
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei, 11221, Taiwan, Republic of China
- VYM Genome Research Center, National Yang-Ming University, University System of Taiwan, Taipei, 11221, Taiwan, Republic of China
- Chien-Tien Hsu Cancer Research Foundation, Taipei, 11221, Taiwan, Republic of China
- * E-mail:
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17
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Zhou T, Chung YH, Chen J, Chen Y. Site-Specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells. J Proteome Res 2016; 15:1103-13. [DOI: 10.1021/acs.jproteome.5b01097] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Zhou
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ying-hua Chung
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Jianji Chen
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Yue Chen
- Department of Biochemistry,
Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, Minnesota 55455, United States
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18
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Grézy A, Chevillard-Briet M, Trouche D, Escaffit F. Control of genetic stability by a new heterochromatin compaction pathway involving the Tip60 histone acetyltransferase. Mol Biol Cell 2015; 27:599-607. [PMID: 26700317 PMCID: PMC4750920 DOI: 10.1091/mbc.e15-05-0316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 12/18/2015] [Indexed: 02/02/2023] Open
Abstract
A new compaction pathway of mammalian pericentric heterochromatin is identified, which relies on H4K12ac by Tip60, probably followed by recruitment of BRD2, and therefore chromatin compaction, which can contribute to genetic stability. Pericentric heterochromatin is a highly compacted structure required for accurate chromosome segregation in mitosis. In mammals, it relies on methylation of histone H3K9 by Suv39H enzymes, which provides a docking site for HP1 proteins, therefore mediating heterochromatin compaction. Here we show that, when this normal compaction pathway is defective, the histone acetyltransferase Tip60 is recruited to pericentric heterochromatin, where it mediates acetylation of histone H4K12. Furthermore, in such a context, depletion of Tip60 leads to derepression of satellite transcription, decompaction of pericentric heterochromatin, and defects in chromosome segregation in mitosis. Finally, we show that depletion of BRD2, a double bromodomain–containing protein that binds H4K12ac, phenocopies the Tip60 depletion with respect to heterochromatin decompaction and defects in chromosome segregation. Taking the results together, we identify a new compaction pathway of mammalian pericentric heterochromatin relying on Tip60 that might be dependent on BRD2 recruitment by H4K12 acetylation. We propose that the underexpression of Tip60 observed in many human tumors can promote genetic instability via defective pericentric heterochromatin.
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Affiliation(s)
- Aude Grézy
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Center for Integrative Biology, Université de Toulouse, UPS and CNRS, F-31062 Toulouse, France
| | - Martine Chevillard-Briet
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Center for Integrative Biology, Université de Toulouse, UPS and CNRS, F-31062 Toulouse, France
| | - Didier Trouche
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Center for Integrative Biology, Université de Toulouse, UPS and CNRS, F-31062 Toulouse, France
| | - Fabrice Escaffit
- Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération, Center for Integrative Biology, Université de Toulouse, UPS and CNRS, F-31062 Toulouse, France
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19
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Robin JD, Ludlow AT, Batten K, Gaillard MC, Stadler G, Magdinier F, Wright WE, Shay JW. SORBS2 transcription is activated by telomere position effect-over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy. Genome Res 2015; 25:1781-90. [PMID: 26359233 PMCID: PMC4665000 DOI: 10.1101/gr.190660.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/09/2015] [Indexed: 01/05/2023]
Abstract
DNA is organized into complex three-dimensional chromatin structures, but how this spatial organization regulates gene expression remains a central question. These DNA/chromatin looping structures can range in size from 10-20 kb (enhancers/repressors) to many megabases during intra- and inter-chromosomal interactions. Recently, the influence of telomere length on chromatin organization prior to senescence has revealed the existence of long-distance chromatin loops that dictate the expression of genes located up to 10 Mb from the telomeres (Telomere Position Effect-Over Long Distances [TPE-OLD]). Here, we demonstrate the existence of a telomere loop at the 4q35 locus involving the sorbin and SH3 domain-containing protein 2 gene, SORBS2, a skeletal muscle protein using a modification of the chromosome conformation capture method. The loop reveals a cis-acting mechanism modifying SORBS2 transcription. The expression of this gene is altered by TPE-OLD in myoblasts from patients affected with the age-associated genetic disease, facioscapulohumeral muscular dystrophy (FSHD1A, MIM 158900). SORBS2 is expressed in FSHD myoblasts with short telomeres, while not detectable in FSHD myoblasts with long telomeres or in healthy myoblasts regardless of telomere length. This indicates that TPE-OLD may modify the regulation of the 4q35 locus in a pathogenic context. Upon differentiation, both FSHD and healthy myotubes express SORBS2, suggesting that SORBS2 is normally up-regulated by maturation/differentiation of skeletal muscle and is misregulated by TPE-OLD-dependent variegation in FSHD myoblasts. These findings provide additional insights for the complexity and age-related symptoms of FSHD.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Biopsy
- Chromosome Deletion
- Chromosomes, Human, Pair 4
- DNA Methylation
- Epistasis, Genetic
- Gene Expression Regulation
- Genetic Loci
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- In Situ Hybridization, Fluorescence
- Muscle Cells/metabolism
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- MyoD Protein/genetics
- MyoD Protein/metabolism
- Myoblasts
- RNA-Binding Proteins
- Telomere/genetics
- Telomere Shortening
- Transcriptional Activation
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Affiliation(s)
- Jérôme D Robin
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew T Ludlow
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kimberly Batten
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | - Guido Stadler
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | | | - Woodring E Wright
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA; Center for Excellence in Genomics Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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20
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Identification of chromatin marks at TERRA promoter and encoding region. Biochem Biophys Res Commun 2015; 467:1052-7. [PMID: 26449455 DOI: 10.1016/j.bbrc.2015.09.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 09/30/2015] [Indexed: 12/27/2022]
Abstract
TERRA is a long non-coding RNA that is essential for telomere integrity. Although it is transcribed from subtelomeres and telomeres, how it is expressed in heterochromatic region is currently unknown. In this study, we focused our analysis on TERRA-encoding region TelBam3.4 and TelBam3.4-like sequences, and determined their transcription start sites, as well as enrichment of RNA polymerase II and histone modifications. We found that H3K4me3 and H3K9me3 are present at TERRA promoters, whereas H3K27ac and H3K9me3 are present at telomeric repeats. Consistently, we show that presence of active histone modifications H3K4me3 and H3K27ac are correlated to TERRA expression. These results mark an important step towards understanding telomere maintenance and transcription.
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21
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Weng L, Greenberg MM. Rapid Histone-Catalyzed DNA Lesion Excision and Accompanying Protein Modification in Nucleosomes and Nucleosome Core Particles. J Am Chem Soc 2015; 137:11022-31. [PMID: 26290445 DOI: 10.1021/jacs.5b05478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
C5'-Hydrogen atoms are frequently abstracted during DNA oxidation. The oxidized abasic lesion 5'-(2-phosphoryl-1,4-dioxobutane) (DOB) is an electrophilic product of the C5'-radical. DOB is a potent irreversible inhibitor of DNA polymerase β, and forms interstrand cross-links in free DNA. We examined the reactivity of DOB within nucleosomes and nucleosome core particles (NCPs), the monomeric component of chromatin. Depending upon the position at which DOB is generated within a NCP, it is excised from nucleosomal DNA at a rate 275-1500-fold faster than that in free DNA. The half-life of DOB (7.0-16.8 min) in NCPs is shorter than any other abasic lesion. DOB's lifetime in NCPs is also significantly shorter than the estimated lifetime of an abasic site within a cell, suggesting that the observed chemistry would occur intracellularly. Histones also catalyze DOB excision when the lesion is present in the DNA linker region of a nucleosome. Schiff-base formation between DOB and histone proteins is detected in nucleosomes and NCPs, resulting in pyrrolone formation at the lysine residues. The lysines modified by DOB are often post-translationally modified. Consequently, the histone modifications described herein could affect the regulation of gene expression and may provide a chemical basis for the cytotoxicity of the DNA damaging agents that produce this lesion.
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Affiliation(s)
- Liwei Weng
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States
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22
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Dhall A, Wei S, Fierz B, Woodcock CL, Lee TH, Chatterjee C. Sumoylated human histone H4 prevents chromatin compaction by inhibiting long-range internucleosomal interactions. J Biol Chem 2014; 289:33827-37. [PMID: 25294883 DOI: 10.1074/jbc.m114.591644] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of eukaryotic chromatin directly influences gene function, and is regulated by chemical modifications of the core histone proteins. Modification of the human histone H4 N-terminal tail region by the small ubiquitin-like modifier protein, SUMO-3, is associated with transcription repression. However, the direct effect of sumoylation on chromatin structure and function remains unknown. Therefore, we employed a disulfide-directed strategy to generate H4 homogenously and site-specifically sumoylated at Lys-12 (suH4ss). Chromatin compaction and oligomerization assays with nucleosomal arrays containing suH4ss established that SUMO-3 inhibits array folding and higher order oligomerization, which underlie chromatin fiber formation. Moreover, the effect of sumoylation differed from that of acetylation, and could be recapitulated with the structurally similar protein ubiquitin. Mechanistic studies at the level of single nucleosomes revealed that, unlike acetylation, the effect of SUMO-3 arises from the attenuation of long-range internucleosomal interactions more than from the destabilization of a compacted dinucleosome state. Altogether, our results present the first insight on the direct structural effects of histone H4 sumoylation and reveal a novel mechanism by which SUMO-3 inhibits chromatin compaction.
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Affiliation(s)
- Abhinav Dhall
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Sijie Wei
- the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Beat Fierz
- the Institute of Chemical Sciences and Engineering, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and
| | | | - Tae-Hee Lee
- the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802,
| | - Champak Chatterjee
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195,
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23
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House NCM, Yang JH, Walsh SC, Moy JM, Freudenreich CH. NuA4 initiates dynamic histone H4 acetylation to promote high-fidelity sister chromatid recombination at postreplication gaps. Mol Cell 2014; 55:818-828. [PMID: 25132173 PMCID: PMC4169719 DOI: 10.1016/j.molcel.2014.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 04/16/2014] [Accepted: 07/10/2014] [Indexed: 11/24/2022]
Abstract
CAG/CTG trinucleotide repeats are unstable, fragile sequences that strongly position nucleosomes, but little is known about chromatin modifications required to prevent genomic instability at these or other structure-forming sequences. We discovered that regulated histone H4 acetylation is required to maintain CAG repeat stability and promote gap-induced sister chromatid recombination. CAG expansions in the absence of H4 HATs NuA4 and Hat1 and HDACs Sir2, Hos2, and Hst1 depended on Rad52, Rad57, and Rad5 and were therefore arising through homology-mediated postreplication repair (PRR) events. H4K12 and H4K16 acetylation were required to prevent Rad5-dependent CAG repeat expansions, and H4K16 acetylation was enriched at CAG repeats during S phase. Genetic experiments placed the RSC chromatin remodeler in the same PRR pathway, and Rsc2 recruitment was coincident with H4K16 acetylation. Here we have utilized a repetitive DNA sequence that induces endogenous DNA damage to identify histone modifications that regulate recombination efficiency and fidelity during postreplication gap repair.
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Affiliation(s)
| | - Jiahui H Yang
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Stephen C Walsh
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jonathan M Moy
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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24
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Zhang H, Gao L, Anandhakumar J, Gross DS. Uncoupling transcription from covalent histone modification. PLoS Genet 2014; 10:e1004202. [PMID: 24722509 PMCID: PMC3983032 DOI: 10.1371/journal.pgen.1004202] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/08/2014] [Indexed: 12/04/2022] Open
Abstract
It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast Saccharomyces cerevisiae can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, hsp82-2001, and a natural drug-inducible subtelomeric gene, YFR057w, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since hsp82-ΔTATA, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic hsp82-2001, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, dot1Δ cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation. The proper regulation of gene expression is of fundamental importance in the maintenance of normal growth and development. Misregulation of genes can lead to such outcomes as cancer, diabetes and neurodegenerative disease. A key step in gene regulation occurs during the transcription of the chromosomal DNA into messenger RNA by the enzyme, RNA polymerase II. Histones are small, positively charged proteins that package genomic DNA into arrays of bead-like particles termed nucleosomes, the principal components of chromatin. Increasing evidence suggests that nucleosomal histones play an active role in regulating transcription, and that this is derived in part from reversible chemical (“covalent”) modifications that take place on their amino acids. These histone modifications create novel surfaces on nucleosomes that can serve as docking sites for other proteins that control a gene's expression state. In this study we present evidence that contrary to the general case, covalent modifications typically associated with transcription are minimally used by genes embedded in a specialized, condensed chromatin structure termed heterochromatin in the model organism baker's yeast. Our observations are significant, for they suggest that gene transcription can occur in a living cell in the virtual absence of covalent modification of the chromatin template.
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Affiliation(s)
- Hesheng Zhang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Lu Gao
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Jayamani Anandhakumar
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - David S. Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
- * E-mail:
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25
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Wan Y, Zuo X, Zhuo Y, Zhu M, Danziger SA, Zhou Z. The functional role of SUMO E3 ligase Mms21p in the maintenance of subtelomeric silencing in budding yeast. Biochem Biophys Res Commun 2013; 438:746-52. [PMID: 23911609 DOI: 10.1016/j.bbrc.2013.07.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 12/11/2022]
Abstract
In Saccharomyces cerevisiae, subtelomeric silencing is involved in the propagation of Silent Information Regulator (SIR) proteins toward euchromatin. Numerous mechanisms are involved in antagonizing the local spread of Sir-dependent silent chromatin into neighboring euchromatin. Here, we identified a novel role for sumoylation E3 ligase Mms21 in the maintenance of subtelomeric silencing. We found that disruption of E3 ligase activity of Mms21 results in the de-repression of subtelomeric silencing. Deletion of E3 ligase domain of Mms21 led to decreased binding of Sir2p, Sir3p and Sir4 at subtelomeric chromatins and increased H3K4 tri-methylation at telomere-distal euchromatin regions, correlating with increased gene expression in two subtelomeric reporter genes. In addition, a mms21Δsl mutant caused a severe growth defect in combination with htz1Δ deletion and showed an enhanced association of Htz1 with telomere proximal regions. Taken together, our findings suggest an important role of Mms21p; it contributes to subtelomeric silencing during the formation of a heterochromatin boundary.
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Affiliation(s)
- Yakun Wan
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing 210096, China.
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26
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Galati A, Micheli E, Cacchione S. Chromatin structure in telomere dynamics. Front Oncol 2013; 3:46. [PMID: 23471416 PMCID: PMC3590461 DOI: 10.3389/fonc.2013.00046] [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] [Received: 12/31/2012] [Accepted: 02/21/2013] [Indexed: 11/13/2022] Open
Abstract
The establishment of a specific nucleoprotein structure, the telomere, is required to ensure the protection of chromosome ends from being recognized as DNA damage sites. Telomere shortening below a critical length triggers a DNA damage response that leads to replicative senescence. In normal human somatic cells, characterized by telomere shortening with each cell division, telomere uncapping is a regulated process associated with cell turnover. Nevertheless, telomere dysfunction has also been associated with genomic instability, cell transformation, and cancer. Despite the essential role telomeres play in chromosome protection and in tumorigenesis, our knowledge of the chromatin structure involved in telomere maintenance is still limited. Here we review the recent findings on chromatin modifications associated with the dynamic changes of telomeres from protected to deprotected state and their role in telomere functions.
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Affiliation(s)
- Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza Università di Roma Rome, Italy
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27
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Abshiru N, Ippersiel K, Tang Y, Yuan H, Marmorstein R, Verreault A, Thibault P. Chaperone-mediated acetylation of histones by Rtt109 identified by quantitative proteomics. J Proteomics 2012; 81:80-90. [PMID: 23036725 DOI: 10.1016/j.jprot.2012.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 09/23/2012] [Indexed: 02/04/2023]
Abstract
Rtt109 is a fungal-specific histone acetyltransferase (HAT) that associates with either Vps75 or Asf1 to acetylate histone H3. Recent biochemical and structural studies suggest that site-specific acetylation of H3 by Rtt109 is dictated by the binding chaperone where Rtt109-Asf1 acetylates K56, while Rtt109-Vps75 acetylates K9 and K27. To gain further insights into the roles of Vps75 and Asf1 in directing site-specific acetylation of H3, we used quantitative proteomics to profile the global and site-specific changes in H3 and H4 during in vitro acetylation assays with Rtt109 and its chaperones. Our analyses showed that Rtt109-Vps75 preferentially acetylates H3 K9 and K23, the former residue being the major acetylation site. At high enzyme-to-substrate ratio, Rtt109 also acetylated K14, K18, K27 and to a lower extent K56 of histone H3. Importantly, this study revealed that in contrast to Rtt109-Vps75, Rtt109-Asf1 displayed a far greater site-specificity, with K56 being the primary site of acetylation. For the first time, we also report the acetylation of histone H4 K12 by Rtt109-Vps75, whereas Rtt109-Asf1 showed no detectable activity toward H4. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Nebiyu Abshiru
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
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28
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Soukup AA, Chiang YM, Bok JW, Reyes-Dominguez Y, Oakley BR, Wang CCC, Strauss J, Keller NP. Overexpression of the Aspergillus nidulans histone 4 acetyltransferase EsaA increases activation of secondary metabolite production. Mol Microbiol 2012; 86:314-30. [PMID: 22882998 PMCID: PMC3514908 DOI: 10.1111/j.1365-2958.2012.08195.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Regulation of secondary metabolite (SM) gene clusters in Aspergillus nidulans has been shown to occur through cluster-specific transcription factors or through global regulators of chromatin structure such as histone methyltransferases, histone deacetylases, or the putative methyltransferase LaeA. A multicopy suppressor screen for genes capable of returning SM production to the SM deficient ΔlaeA mutant resulted in identification of the essential histone acetyltransferase EsaA, able to complement an esa1 deletion in Saccharomyces cereviseae. Here we report that EsaA plays a novel role in SM cluster activation through histone 4 lysine 12 (H4K12) acetylation in four examined SM gene clusters (sterigmatocystin, penicillin, terrequinone and orsellinic acid), in contrast to no increase in H4K12 acetylation of the housekeeping tubA promoter. This augmented SM cluster acetylation requires LaeA for full effect and correlates with both increased transcript levels and metabolite production relative to wild type. H4K12 levels may thus represent a unique indicator of relative production potential, notably of SMs.
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Affiliation(s)
- Alexandra A. Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yi-Ming Chiang
- Graduate Institute of Pharmaceutical Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan, ROC 71710,Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Jin Woo Bok
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706
| | - Yazmid Reyes-Dominguez
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, USA 66045
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033,Department of Chemistry, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, USA 90033
| | - Joseph Strauss
- Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna, and Austrian Institute of Technology GmbH, University and Research Center Campus Tulln, Konrad Lorenz Strasse 24, Tulln/Donau, Austria A-3430
| | - Nancy P. Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, USA 53706,Corresponding author: 3476 Microbial Sciences, 1550 Linden Drive, Madison, WI, USA 53706 Phone: (608) 262-9795 Fax: (608)262-8418
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Yao H, Rahman I. Role of histone deacetylase 2 in epigenetics and cellular senescence: implications in lung inflammaging and COPD. Am J Physiol Lung Cell Mol Physiol 2012; 303:L557-66. [PMID: 22842217 DOI: 10.1152/ajplung.00175.2012] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that regulates various cellular processes, such as cell cycle, senescence, proliferation, differentiation, development, apoptosis, and glucocorticoid function in inhibiting inflammatory response. HDAC2 has been shown to protect against DNA damage response and cellular senescence/premature aging via an epigenetic mechanism in response to oxidative stress. These phenomena are observed in patients with chronic obstructive pulmonary disease (COPD). HDAC2 is posttranslationally modified by oxidative/carbonyl stress imposed by cigarette smoke and oxidants, leading to its reduction via an ubiquitination-proteasome dependent degradation in lungs of patients with COPD. In this perspective, we have discussed the role of HDAC2 posttranslational modifications and its role in regulation of inflammation, histone/DNA epigenetic modifications, DNA damage response, and cellular senescence, particularly in inflammaging, and during the development of COPD. We have also discussed the potential directions for future translational research avenues in modulating lung inflammaging and cellular senescence based on epigenetic chromatin modifications in diseases associated with increased oxidative stress.
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Affiliation(s)
- Hongwei Yao
- Dept. of Environmental Medicine, Lung Biology and Disease Program, Univ. of Rochester Medical Center, Rochester, NY 14642, USA
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30
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Schizosaccharomyces pombe Hat1 (Kat1) is associated with Mis16 and is required for telomeric silencing. EUKARYOTIC CELL 2012; 11:1095-103. [PMID: 22771823 DOI: 10.1128/ec.00123-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Hat1 histone acetyltransferase has been implicated in the acetylation of histone H4 during chromatin assembly. In this study, we have characterized the Hat1 complex from the fission yeast Schizosaccharomyces pombe and have examined its role in telomeric silencing. Hat1 is found associated with the RbAp46 homologue Mis16, an essential protein. The Hat1 complex acetylates lysines 5 and 12 of histone H4, the sites that are acetylated in newly synthesized H4 in a wide range of eukaryotes. Deletion of hat1 in S. pombe is itself sufficient to cause the loss of silencing at telomeres. This is in contrast to results obtained with an S. cerevisiae hat1Δ strain, which must also carry mutations of specific acetylatable lysines in the H3 tail domain for loss of telomeric silencing to occur. Notably, deletion of hat1 from S. pombe resulted in an increase of acetylation of histone H4 in subtelomeric chromatin, concomitant with derepression of this region. A similar loss of telomeric silencing was also observed after growing cells in the presence of the deacetylase inhibitor trichostatin A. However, deleting hat1 did not cause loss of silencing at centromeres or the silent mating type locus. These results point to a direct link between Hat1, H4 acetylation, and the establishment of repressed telomeric chromatin in fission yeast.
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31
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Green EM, Morrison AJ, Gozani O. New marks on the block: Set5 methylates H4 lysines 5, 8 and 12. Nucleus 2012; 3:335-9. [PMID: 22688645 DOI: 10.4161/nucl.20695] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The methylation of lysine residues in the N-terminal tails of histones is a highly conserved mechanism that regulates critical functions of chromatin, such as the control of gene expression. Using a biochemical approach, we recently identified new methylation marks on the histone H4 tail in budding yeast at lysines 5, 8 and 12, catalyzed by the previously-uncharacterized enzyme Set5. Genetic studies revealed that Set5 functions in cellular processes that also rely on the global chromatin modifying complexes COMPASS and NuA4, which methylate H3 lysine 4 and acetylate H4 lysines 5, 8 and 12, respectively. The identification of new methylation events on the H4 tail raises many intriguing questions regarding their function and their interaction with known histone modifications. Here, we analyze the insights gained about the new enzyme Set5 and the implications for new functionality added to the H4 tail.
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Affiliation(s)
- Erin M Green
- Department of Biology, Stanford University, Stanford, CA, USA.
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32
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Peng J, Zhou JQ. The tail-module of yeast Mediator complex is required for telomere heterochromatin maintenance. Nucleic Acids Res 2012; 40:581-93. [PMID: 21930512 PMCID: PMC3258146 DOI: 10.1093/nar/gkr757] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/15/2011] [Accepted: 08/30/2011] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic chromosome ends have a DNA-protein complex structure termed telomere. Integrity of telomeres is essential for cell proliferation. Genome-wide screenings for telomere length maintenance genes identified several components of the transcriptional regulator, the Mediator complex. Our work provides evidence that Mediator is involved in telomere length regulation and telomere heterochromatin maintenance. Tail module of Mediator is required for telomere silencing by promoting or stabilizing Sir protein binding and spreading on telomeres. Mediator binds on telomere and may be a component of telomeric chromatin. Our study reveals a specific role of Mediator complex at the heterochromatic telomere and this function is specific to telomeres as it has no effect on the HMR locus.
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Affiliation(s)
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, Shanghai, China
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Pan MH, Lai CS, Tsai ML, Wu JC, Ho CT. Molecular mechanisms for anti-aging by natural dietary compounds. Mol Nutr Food Res 2011; 56:88-115. [PMID: 22083941 DOI: 10.1002/mnfr.201100509] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/20/2011] [Accepted: 09/02/2011] [Indexed: 12/11/2022]
Abstract
Aging is defined as a normal decline in survival with advancing age; however, the recent researches have showed that physiological functions of the body change during the aging process. Majority of the changes are often subject to a higher risk of developing diseases, such as cardiovascular disease, type II diabetes, Alzheimer's disease, Parkinson's disease, as well as the dysregulated immune and inflammatory disorders. Aging process is controlled by a complicated and precise signaling network that involved in energy homeostasis, cellular metabolism and stress resistance. Over the past few decades, research in natural dietary compounds by various organism and animal models provides a new strategy for anti-aging. Natural dietary compounds act through a variety mechanisms to extend lifespan and prevent age-related diseases. This review summarizes the current understanding on signaling pathways of aging and knowledge and underlying mechanism of natural dietary compounds that provide potential application on anti-aging and improve heath in human.
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Affiliation(s)
- Min-Hsiung Pan
- Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan.
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34
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Ribaud V, Ribeyre C, Damay P, Shore D. DNA-end capping by the budding yeast transcription factor and subtelomeric binding protein Tbf1. EMBO J 2011; 31:138-49. [PMID: 21952045 DOI: 10.1038/emboj.2011.349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 09/01/2011] [Indexed: 11/09/2022] Open
Abstract
Telomere repeats in budding yeast are maintained at a constant average length and protected ('capped'), in part, by mechanisms involving the TG(1-3) repeat-binding protein Rap1. However, metazoan telomere repeats (T(2)AG(3)) can be maintained in yeast through a Rap1-independent mechanism. Here, we examine the dynamics of capping and telomere formation at an induced DNA double-strand break flanked by varying lengths of T(2)AG(3) repeats. We show that a 60-bp T(2)AG(3) repeat array induces a transient G2/M checkpoint arrest, but is rapidly elongated by telomerase to generate a stable T(2)AG(3)/TG(1-3) hybrid telomere. In contrast, a 230-bp T(2)AG(3) array induces neither G2/M arrest nor telomerase elongation. This capped state requires the T(2)AG(3)-binding protein Tbf1, but is independent of two Tbf1-interacting factors, Vid22 and Ygr071c. Arrays of binding sites for three other subtelomeric or Myb/SANT domain-containing proteins fail to display a similar end-protection effect, indicating that Tbf1 capping is an evolved function. Unexpectedly, we observed strong telomerase association with non-telomeric ends, whose elongation is blocked by a Mec1-dependent mechanism, apparently acting at the level of Cdc13 binding.
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Affiliation(s)
- Virginie Ribaud
- Department of Molecular Biology, NCCR Program Frontiers in Genetics, University of Geneva, Geneva, Switzerland
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35
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Zhou BO, Zhou JQ. Recent transcription-induced histone H3 lysine 4 (H3K4) methylation inhibits gene reactivation. J Biol Chem 2011; 286:34770-6. [PMID: 21849496 DOI: 10.1074/jbc.m111.273128] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent transcription of GAL genes transiently leaves an H3K4 methylation mark at their promoters, providing an epigenetic memory for the recent transcriptional activity. However, the physiological significance of this mark is enigmatic. In our study, we show that the transient H3K4 di- and trimethylation at recently transcribed GAL1 inhibited the reinduction of GAL1. The H3K4 methylation functioned by recruiting the Isw1 ATPase onto GAL1 and thereby limiting the action of RNA polymerase II during GAL1 reactivation. Strikingly, the H3K4 methylation was also observed at the promoters of inositol- and fatty acid-responsive genes after recent transcription and played a negative role in their reinduction. Taken together, our data present a new mechanism by which H3K4 methylation regulates gene transcription.
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Affiliation(s)
- Bo O Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China.
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The C-terminus of histone H2B is involved in chromatin compaction specifically at telomeres, independently of its monoubiquitylation at lysine 123. PLoS One 2011; 6:e22209. [PMID: 21829450 PMCID: PMC3146481 DOI: 10.1371/journal.pone.0022209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 06/17/2011] [Indexed: 12/11/2022] Open
Abstract
Telomeric heterochromatin assembly in budding yeast propagates through the association of Silent Information Regulator (SIR) proteins with nucleosomes, and the nucleosome array has been assumed to fold into a compacted structure. It is believed that the level of compaction and gene repression within heterochromatic regions can be modulated by histone modifications, such as acetylation of H3 lysine 56 and H4 lysine 16, and monoubiquitylation of H2B lysine 123. However, it remains unclear as to whether or not gene silencing is a direct consequence of the compaction of chromatin. Here, by investigating the role of the carboxy-terminus of histone H2B in heterochromatin formation, we identify that the disorderly compaction of chromatin induced by a mutation at H2B T122 specifically hinders telomeric heterochromatin formation. H2B T122 is positioned within the highly conserved AVTKY motif of the αC helix of H2B. Heterochromatin containing the T122E substitution in H2B remains inaccessible to ectopic dam methylase with dramatically increased mobility in sucrose gradients, indicating a compacted chromatin structure. Genetic studies indicate that this unique phenotype is independent of H2B K123 ubiquitylation and Sir4. In addition, using ChIP analysis, we demonstrate that telomere structure in the mutant is further disrupted by a defect in Sir2/Sir3 binding and the resulting invasion of euchromatic histone marks. Thus, we have revealed that the compaction of chromatin per se is not sufficient for heterochromatin formation. Instead, these results suggest that an appropriately arrayed chromatin mediated by H2B C-terminus is required for SIR binding and the subsequent formation of telomeric chromatin in yeast, thereby identifying an intrinsic property of the nucleosome that is required for the establishment of telomeric heterochromatin. This requirement is also likely to exist in higher eukaryotes, as the AVTKY motif of H2B is evolutionarily conserved.
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Wan Y, Chen W, Xing J, Tan J, Li B, Chen H, Lin Z, Chiang JH, Ramsey S. Transcriptome profiling reveals a novel role for trichostatin A in antagonizing histone chaperone Chz1 mediated telomere anti-silencing. FEBS Lett 2011; 585:2519-25. [DOI: 10.1016/j.febslet.2011.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 06/12/2011] [Accepted: 06/20/2011] [Indexed: 01/06/2023]
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