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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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2
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Chen Q, Yang B, Liu X, Zhang XD, Zhang L, Liu T. Histone acetyltransferases CBP/p300 in tumorigenesis and CBP/p300 inhibitors as promising novel anticancer agents. Am J Cancer Res 2022; 12:4935-4948. [PMID: 35836809 PMCID: PMC9274749 DOI: 10.7150/thno.73223] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/23/2022] [Indexed: 01/12/2023] Open
Abstract
The histone acetyltransferases CBP and p300, often referred to as CBP/p300 due to their sequence homology and functional overlap and co-operation, are emerging as critical drivers of oncogenesis in the past several years. CBP/p300 induces histone H3 lysine 27 acetylation (H3K27ac) at target gene promoters, enhancers and super-enhancers, thereby activating gene transcription. While earlier studies indicate that CBP/p300 deletion/loss can promote tumorigenesis, CBP/p300 have more recently been shown to be over-expressed in cancer cells and drug-resistant cancer cells, activate oncogene transcription and induce cancer cell proliferation, survival, tumorigenesis, metastasis, immune evasion and drug-resistance. Small molecule CBP/p300 histone acetyltransferase inhibitors, bromodomain inhibitors, CBP/p300 and BET bromodomain dual inhibitors and p300 protein degraders have recently been discovered. The CBP/p300 inhibitors and degraders reduce H3K27ac, down-regulate oncogene transcription, induce cancer cell growth inhibition and cell death, activate immune response, overcome drug resistance and suppress tumor progression in vivo. In addition, CBP/p300 inhibitors enhance the anticancer efficacy of chemotherapy, radiotherapy and epigenetic anticancer agents, including BET bromodomain inhibitors; and the combination therapies exert substantial anticancer effects in mouse models of human cancers including drug-resistant cancers. Currently, two CBP/p300 inhibitors are under clinical evaluation in patients with advanced and drug-resistant solid tumors or hematological malignancies. In summary, CBP/p300 have recently been identified as critical tumorigenic drivers, and CBP/p300 inhibitors and protein degraders are emerging as promising novel anticancer agents for clinical translation.
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Affiliation(s)
- Qingjuan Chen
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Binhui Yang
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Xiaochen Liu
- Department of Oncology, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong, Shaanxi 723000, China
| | - Xu D. Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia.,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
| | - Tao Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,Children's Cancer Institute Australia, Randwick, Sydney, NSW 2031, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.,✉ Corresponding authors: E-mail: (Xu D. Zhang), (Lirong Zhang); (Tao Liu)
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3
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Moon HM, Park JS, Lee IB, Kang YI, Jung HJ, An D, Shin Y, Kim MJ, Kim HI, Song JJ, Kim J, Lee NK, Hong SC. Cisplatin fastens chromatin irreversibly even at a high chloride concentration. Nucleic Acids Res 2021; 49:12035-12047. [PMID: 34865121 PMCID: PMC8643659 DOI: 10.1093/nar/gkab922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/12/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
Cisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.
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Affiliation(s)
- Hyeon-Min Moon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Jin-Sung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | - Il-Buem Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Young-Im Kang
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Hae Jun Jung
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Dongju An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yumi Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Min Ji Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul 05006, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
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4
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Leonen CJA, Shimada M, Weller CE, Nakadai T, Hsu PL, Tyson EL, Mishra A, Shelton PM, Sadilek M, Hawkins RD, Zheng N, Roeder RG, Chatterjee C. Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts. eLife 2021; 10:67952. [PMID: 34747692 PMCID: PMC8626089 DOI: 10.7554/elife.67952] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 11/06/2021] [Indexed: 01/22/2023] Open
Abstract
The post-translational modification of histones by the small ubiquitin-like modifier (SUMO) protein has been associated with gene regulation, centromeric localization, and double-strand break repair in eukaryotes. Although sumoylation of histone H4 was specifically associated with gene repression, this could not be proven due to the challenge of site-specifically sumoylating H4 in cells. Biochemical crosstalk between SUMO and other histone modifications, such as H4 acetylation and H3 methylation, that are associated with active genes also remains unclear. We addressed these challenges in mechanistic studies using an H4 chemically modified at Lys12 by SUMO-3 (H4K12su) and incorporated into mononucleosomes and chromatinized plasmids for functional studies. Mononucleosome-based assays revealed that H4K12su inhibits transcription-activating H4 tail acetylation by the histone acetyltransferase p300, as well as transcription-associated H3K4 methylation by the extended catalytic module of the Set1/COMPASS (complex of proteins associated with Set1) histone methyltransferase complex. Activator- and p300-dependent in vitro transcription assays with chromatinized plasmids revealed that H4K12su inhibits both H4 tail acetylation and RNA polymerase II-mediated transcription. Finally, cell-based assays with a SUMO-H4 fusion that mimics H4 tail sumoylation confirmed the negative crosstalk between histone sumoylation and acetylation/methylation. Thus, our studies establish the key role for histone sumoylation in gene silencing and its negative biochemical crosstalk with active transcription-associated marks in human cells.
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Affiliation(s)
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Caroline E Weller
- Department of Chemistry, University of Washington, Seattle, United States
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States.,Project for Cancer Epigenomics, Cancer Institute of JFCR, Tokyo, Japan
| | - Peter L Hsu
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Elizabeth L Tyson
- Department of Chemistry, University of Washington, Seattle, United States
| | - Arpit Mishra
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Patrick Mm Shelton
- Department of Chemistry, University of Washington, Seattle, United States
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, United States
| | - R David Hawkins
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, United States
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5
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Huang H, Zhang D, Weng Y, Delaney K, Tang Z, Yan C, Qi S, Peng C, Cole PA, Roeder RG, Zhao Y. The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway. SCIENCE ADVANCES 2021; 7:7/9/eabe2771. [PMID: 33627428 PMCID: PMC7904266 DOI: 10.1126/sciadv.abe2771] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/12/2021] [Indexed: 05/07/2023]
Abstract
Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyrate to lysine (Kbhb), while histone deacetylase 1 (HDAC1) and HDAC2 enzymatically remove Kbhb. We demonstrate that p300-dependent histone Kbhb can directly mediate in vitro transcription. Moreover, a comprehensive analysis of Kbhb substrates in mammalian cells has identified 3248 Kbhb sites on 1397 substrate proteins. The dependence of histone Kbhb on p300 argues that enzyme-catalyzed acylation is the major mechanism for nuclear Kbhb. Our study thus reveals key regulatory elements for the Kbhb pathway, laying a foundation for studying its roles in diverse cellular processes.
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Affiliation(s)
- He Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yejing Weng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kyle Delaney
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Cong Yan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shankang Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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6
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Vaid R, Wen J, Mannervik M. Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition. Nucleic Acids Res 2020; 48:4877-4890. [PMID: 32297950 PMCID: PMC7229826 DOI: 10.1093/nar/gkaa234] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022] Open
Abstract
A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter–proximal paused RNA polymerase II (Pol II) into elongation is stimulated, whereas initiation is not. Although histone acetylation is elevated globally by HDAC inhibition, less than 100 genes respond within 10 min. These genes are highly paused, are strongly associated with the chromatin regulators NURF and Trithorax, display a greater increase in acetylation of the first nucleosomes than other genes, and become transcriptionally activated by HDAC inhibition. Among these rapidly up-regulated genes are HDAC1 (Rpd3) and subunits of HDAC-containing co-repressor complexes, demonstrating feedback regulation upon HDAC inhibition. Our results suggest that histone acetylation stimulates transcription of paused genes by release of Pol II into elongation, and that increased acetylation is not a consequence of their enhanced expression. We propose that HDACs are major regulators of Pol II pausing and that this partly explains the presence of HDACs at active genes.
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Affiliation(s)
- Roshan Vaid
- Dept. Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Jiayu Wen
- Dept. Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Mattias Mannervik
- Dept. Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
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7
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Cramer P. Eukaryotic Transcription Turns 50. Cell 2020; 179:808-812. [PMID: 31675494 DOI: 10.1016/j.cell.2019.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/15/2022]
Abstract
This year we celebrate the 50th anniversary of the discovery of the three eukaryotic RNA polymerases. Ever since this seminal event in 1969, researchers have investigated the intricate mechanisms of gene transcription with great dedication. The transcription field continues to influence developmental, stem cell, and cancer biology.
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Affiliation(s)
- Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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8
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Perillo B, Di Santi A, Cernera G, Galasso G, Pocsfalvi G, Castoria G, Migliaccio A. Acetylation/methylation at lysine 9 in histone H3 as a mark of nucleosome asymmetry in human somatic breast cells. Cell Death Discov 2020; 6:39. [PMID: 32528728 PMCID: PMC7251094 DOI: 10.1038/s41420-020-0278-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/01/2023] Open
Affiliation(s)
- Bruno Perillo
- Istituto per l’Endocrinologia e l’Oncologia Sperimentale “G. Salvatore”, C.N.R, 80131 Naples, Italy
| | | | - Gustavo Cernera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli “Federico II”, 80131 Naples, Italy
| | - Giovanni Galasso
- Dipartimento di Medicina di Precisione, Università della Campania “L. Vanvitelli”, 80138 Naples, Italy
| | | | - Gabriella Castoria
- Dipartimento di Medicina di Precisione, Università della Campania “L. Vanvitelli”, 80138 Naples, Italy
| | - Antimo Migliaccio
- Dipartimento di Medicina di Precisione, Università della Campania “L. Vanvitelli”, 80138 Naples, Italy
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9
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Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 350] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
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10
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The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat Struct Mol Biol 2019; 26:766-770. [PMID: 31439939 DOI: 10.1038/s41594-019-0278-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/10/2019] [Indexed: 11/08/2022]
Abstract
The discovery of RNA polymerases I, II, and III opened up a new era in gene expression. Here I provide a personal retrospective account of the transformation of the DNA template, as it evolved from naked DNA to chromatin, in the biochemical analysis of transcription by RNA polymerase II. These studies have revealed new insights into the mechanisms by which transcription factors function with chromatin to regulate gene expression.
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11
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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12
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Shimada M, Chen WY, Nakadai T, Onikubo T, Guermah M, Rhodes D, Roeder RG. Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway. Mol Cell 2019; 74:268-283.e5. [PMID: 30902546 DOI: 10.1016/j.molcel.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/07/2019] [Accepted: 02/12/2019] [Indexed: 02/03/2023]
Abstract
Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by the H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A-H2B. An analysis in B cells confirms the strong dependency on NAP1-mediated H1 eviction for induction of the silent CD40 gene and further demonstrates that H1 eviction, seeded by activator-p300-NAP1-H1 interactions, is propagated over a CCCTC-binding factor (CTCF)-demarcated region through a distinct mechanism that also involves NAP1. Our results confirm direct transcriptional inhibition by H1 and establish a gene-specific H1 eviction mechanism through an activator→p300→NAP1→H1 pathway.
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Affiliation(s)
- Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wei-Yi Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan; Cancer Progression Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Takashi Onikubo
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Mohamed Guermah
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Daniela Rhodes
- NTU Institute of Structural Biology and School of Biological Sciences, Nanyang Technological University, Singapore 636921, Singapore
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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13
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Oncogenic N-Ras Stimulates SRF-Mediated Transactivation via H3 Acetylation at Lysine 9. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5473725. [PMID: 29511684 PMCID: PMC5817314 DOI: 10.1155/2018/5473725] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 01/10/2023]
Abstract
Signal transduction pathways regulate the gene expression by altering chromatin dynamics in response to mitogens. Ras proteins are key regulators linking extracellular stimuli to a diverse range of biological responses associated with gene regulation. In mammals, the three ras genes encode four Ras protein isoforms: H-Ras, K-Ras4A, K-Ras4B, and N-Ras. Although emerging evidence suggests that Ras isoforms differentially regulate gene expressions and are functionally nonredundant, the mechanisms underlying Ras specificity and Ras signaling effects on gene expression remain unclear. Here, we show that oncogenic N-Ras acts as the most potent regulator of SRF-, NF-κB-, and AP-1-dependent transcription. N-Ras-RGL2 axis is a distinct signaling pathway for SRF target gene expression such as Egr1 and JunB, as RGL2 Ras binding domain (RBD) significantly impaired oncogenic N-Ras-induced SRE activation. By monitoring the effect of Ras isoforms upon the change of global histone modifications in oncogenic Ras-overexpressed cells, we discovered that oncogenic N-Ras elevates H3K9ac/H3K23ac levels globally in the chromatin context. Importantly, chromatin immunoprecipitation (ChIP) assays revealed that H3K9ac is significantly enriched at the promoter and coding regions of Egr1 and JunB. Collectively, our findings define an undocumented role of N-Ras in modulating of H3 acetylation and in gene regulation.
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14
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Kebede AF, Nieborak A, Shahidian LZ, Le Gras S, Richter F, Gómez DA, Baltissen MP, Meszaros G, Magliarelli HDF, Taudt A, Margueron R, Colomé-Tatché M, Ricci R, Daujat S, Vermeulen M, Mittler G, Schneider R. Histone propionylation is a mark of active chromatin. Nat Struct Mol Biol 2017; 24:1048-1056. [PMID: 29058708 DOI: 10.1038/nsmb.3490] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/22/2017] [Indexed: 12/17/2022]
Abstract
Histones are highly covalently modified, but the functions of many of these modifications remain unknown. In particular, it is unclear how histone marks are coupled to cellular metabolism and how this coupling affects chromatin architecture. We identified histone H3 Lys14 (H3K14) as a site of propionylation and butyrylation in vivo and carried out the first systematic characterization of histone propionylation. We found that H3K14pr and H3K14bu are deposited by histone acetyltransferases, are preferentially enriched at promoters of active genes and are recognized by acylation-state-specific reader proteins. In agreement with these findings, propionyl-CoA was able to stimulate transcription in an in vitro transcription system. Notably, genome-wide H3 acylation profiles were redefined following changes to the metabolic state, and deletion of the metabolic enzyme propionyl-CoA carboxylase altered global histone propionylation levels. We propose that histone propionylation, acetylation and butyrylation may act in combination to promote high transcriptional output and to couple cellular metabolism with chromatin structure and function.
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Affiliation(s)
- Adam F Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Anna Nieborak
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Florian Richter
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Goethe-Universität Fachbereich Medizin, Frankfurt, Germany
| | - Diana Aguilar Gómez
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Undergraduate Program in Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Marijke P Baltissen
- Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Gergo Meszaros
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Université de Strasbourg, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | | | - Aaron Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Technical University Munich, Freising, Germany
| | - Romeo Ricci
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Université de Strasbourg, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Michiel Vermeulen
- Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Ludwig-Maximilains-Universität München, Faculty of Biology, Munich, Germany
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15
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Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing. Proc Natl Acad Sci U S A 2017; 114:E7949-E7958. [PMID: 28855339 PMCID: PMC5617306 DOI: 10.1073/pnas.1711158114] [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] [Indexed: 01/25/2023] Open
Abstract
Posttranslational histone modifications play important roles in regulating chromatin-based nuclear processes. Histone H2AK119 ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing. However, the underlying mechanism remains largely obscure. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF complex, as a H2Aub binding protein, which mediates the gene-silencing function of this histone modification. RSF1 associates specifically with H2Aub, but not H2Bub nucleosomes, through a previously uncharacterized and obligatory region designated as ubiquitinated H2A binding domain. In human and mouse cells, genes regulated by RSF1 overlap significantly with those controlled by RNF2/Ring1B, the subunit of Polycomb repressive complex 1 (PRC1) which catalyzes the ubiquitination of H2AK119. About 82% of H2Aub-enriched genes, including the classic PRC1 target Hox genes, are bound by RSF1 around their transcription start sites. Depletion of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. In contrast, RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but leads to derepression of H2Aub target genes, accompanied by changes in H2Aub chromatin organization and release of linker histone H1. The action of RSF1 in H2Aub-mediated gene silencing is further demonstrated by chromatin-based in vitro transcription. Finally, RSF1 and Ring1 act cooperatively to regulate mesodermal cell specification and gastrulation during Xenopus early embryonic development. Taken together, these data identify RSF1 as a H2Aub reader that contributes to H2Aub-mediated gene silencing by maintaining a stable nucleosome pattern at promoter regions.
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16
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Goudarzi A, Zhang D, Huang H, Barral S, Kwon OK, Qi S, Tang Z, Buchou T, Vitte AL, He T, Cheng Z, Montellier E, Gaucher J, Curtet S, Debernardi A, Charbonnier G, Puthier D, Petosa C, Panne D, Rousseaux S, Roeder RG, Zhao Y, Khochbin S. Dynamic Competing Histone H4 K5K8 Acetylation and Butyrylation Are Hallmarks of Highly Active Gene Promoters. Mol Cell 2017; 62:169-180. [PMID: 27105113 PMCID: PMC4850424 DOI: 10.1016/j.molcel.2016.03.014] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/05/2016] [Accepted: 03/10/2016] [Indexed: 12/01/2022]
Abstract
Recently discovered histone lysine acylation marks increase the functional diversity of nucleosomes well beyond acetylation. Here, we focus on histone butyrylation in the context of sperm cell differentiation. Specifically, we investigate the butyrylation of histone H4 lysine 5 and 8 at gene promoters where acetylation guides the binding of Brdt, a bromodomain-containing protein, thereby mediating stage-specific gene expression programs and post-meiotic chromatin reorganization. Genome-wide mapping data show that highly active Brdt-bound gene promoters systematically harbor competing histone acetylation and butyrylation marks at H4 K5 and H4 K8. Despite acting as a direct stimulator of transcription, histone butyrylation competes with acetylation, especially at H4 K5, to prevent Brdt binding. Additionally, H4 K5K8 butyrylation also marks retarded histone removal during late spermatogenesis. Hence, alternating H4 acetylation and butyrylation, while sustaining direct gene activation and dynamic bromodomain binding, could impact the final male epigenome features. Active gene TSSs are marked by competing H4 K5K8 acetylation and butyrylation Histone butyrylation directly stimulates transcription H4K5 butyrylation prevents binding of the testis specific gene expression-driver Brdt H4K5K8 butyrylation is associated with delayed histone removal in spermatogenic cells
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Affiliation(s)
- Afsaneh Goudarzi
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Di Zhang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Sophie Barral
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Oh Kwang Kwon
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Shankang Qi
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Thierry Buchou
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Anne-Laure Vitte
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Tieming He
- Jingjie PTM Biolab (Hangzhou) Co., Ltd., Hangzhou 310018, China
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou) Co., Ltd., Hangzhou 310018, China
| | - Emilie Montellier
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Jonathan Gaucher
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France; EMBL Grenoble, BP 181, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Sandrine Curtet
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Alexandra Debernardi
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Guillaume Charbonnier
- TAGC, UMR, S 1090 INSERM Aix-Marseille Université, U928 Parc Scientifique de Luminy case 928 163, Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Denis Puthier
- TAGC, UMR, S 1090 INSERM Aix-Marseille Université, U928 Parc Scientifique de Luminy case 928 163, Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Carlo Petosa
- Université Grenoble Alpes/CEA/CNRS, Institut de Biologie Structurale, 38027 Grenoble, France
| | - Daniel Panne
- EMBL Grenoble, BP 181, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Sophie Rousseaux
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
| | - Saadi Khochbin
- CNRS UMR 5309, INSERM, U1209, Université Grenoble Alpes, Institut Albert Bonniot, 38700 Grenoble, France.
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17
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Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas. Nat Med 2017; 23:493-500. [PMID: 28263307 DOI: 10.1038/nm.4296] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/30/2017] [Indexed: 12/14/2022]
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brainstem tumor characterized by rapid and uniform patient demise. A heterozygous point mutation of histone H3 occurs in more than 80% of these tumors and results in a lysine-to-methionine substitution (H3K27M). Expression of this histone mutant is accompanied by a reduction in the levels of polycomb repressive complex 2 (PRC2)-mediated H3K27 trimethylation (H3K27me3), and this is hypothesized to be a driving event of DIPG oncogenesis. Despite a major loss of H3K27me3, PRC2 activity is still detected in DIPG cells positive for H3K27M. To investigate the functional roles of H3K27M and PRC2 in DIPG pathogenesis, we profiled the epigenome of H3K27M-mutant DIPG cells and found that H3K27M associates with increased H3K27 acetylation (H3K27ac). In accordance with previous biochemical data, the majority of the heterotypic H3K27M-K27ac nucleosomes colocalize with bromodomain proteins at the loci of actively transcribed genes, whereas PRC2 is excluded from these regions; this suggests that H3K27M does not sequester PRC2 on chromatin. Residual PRC2 activity is required to maintain DIPG proliferative potential, by repressing neuronal differentiation and function. Finally, to examine the therapeutic potential of blocking the recruitment of bromodomain proteins by heterotypic H3K27M-K27ac nucleosomes in DIPG cells, we performed treatments in vivo with BET bromodomain inhibitors and demonstrate that they efficiently inhibit tumor progression, thus identifying this class of compounds as potential therapeutics in DIPG.
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18
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Li N, Yuan Q, Cao XL, Zhang Y, Min ZL, Xu SQ, Yu ZJ, Cheng J, Zhang C, Hu XM. Opposite effects of HDAC5 and p300 on MRTF-A-related neuronal apoptosis during ischemia/reperfusion injury in rats. Cell Death Dis 2017; 8:e2624. [PMID: 28230854 PMCID: PMC5386465 DOI: 10.1038/cddis.2017.16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/23/2016] [Accepted: 12/28/2016] [Indexed: 01/22/2023]
Abstract
Our recent study has revealed that the myocardin-related transcription factor-A (MRTF-A) is involved in the apoptosis of cortical neurons induced by ischemia/reperfusion (I/R). Histone deacetylase 5 (HDAC5) and histone acetyltransferase p300 (P300) are two well-known regulators for transcription factors; however, their roles in MRTF-A-related effect on neuronal injuries during I/R are still unclear. In this study, in a model rat cerebral I/R injury via middle cerebral artery occlusion and reperfusion, we found that the expression and activity of HDAC5 was upregulated, whereas p300 and MRTF-A were downregulated both in expression and activity during I/R. Their expression changes and the interaction of the MRTF-A with HDAC5 or p300 were further verified by double immunofluorescence and co-immunoprecipitation. In cultured neuronal apoptosis model induced by H2O2, MRTF-A exhibited an anti-apoptotic effect by enhancing the transcription of Bcl-2 and Mcl-1 via CArG box binding. MRTF-A-induced anti-apoptotic effect was effectively inhibited by HDAC5, but was significantly enhanced by p300. The results suggest that both HDAC5 and p300 are involved in MRTF-A-mediated effect on neuronal apoptosis during ischemia/reperfusion injury, but with opposite effects.
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Affiliation(s)
- Na Li
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Qiong Yuan
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Xiao-Lu Cao
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Ying Zhang
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Zhen-Li Min
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Shi-Qiang Xu
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Zhi-Jun Yu
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Jing Cheng
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
| | - Chunxiang Zhang
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xia-Min Hu
- Department of Pharmacy, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China.,Drug Research Base of Cardiovascular and Cerebral Vascular, College of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China
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19
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Metabolic regulation of gene expression through histone acylations. Nat Rev Mol Cell Biol 2016; 18:90-101. [PMID: 27924077 DOI: 10.1038/nrm.2016.140] [Citation(s) in RCA: 640] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Eight types of short-chain Lys acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggests that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this Review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, the acylation 'reader' proteins that mediate the effects of different acylations and their physiological functions, which include signal-dependent gene activation, spermatogenesis, tissue injury and metabolic stress. We propose a model to explain our present understanding of how differential histone acylation is regulated by the metabolism of the different acyl-CoA forms, which in turn modulates the regulation of gene expression.
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20
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Sabari BR, Tang Z, Huang H, Yong-Gonzalez V, Molina H, Kong HE, Dai L, Shimada M, Cross JR, Zhao Y, Roeder RG, Allis CD. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol Cell 2015; 58:203-15. [PMID: 25818647 PMCID: PMC4501262 DOI: 10.1016/j.molcel.2015.02.029] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 12/29/2014] [Accepted: 02/20/2015] [Indexed: 01/30/2023]
Abstract
Acetylation of histones at DNA regulatory elements plays a critical role in transcriptional activation. Histones are also modified by other acyl moieties, including crotonyl, yet the mechanisms that govern acetylation versus crotonylation and the functional consequences of this "choice" remain unclear. We show that the coactivator p300 has both crotonyltransferase and acetyltransferase activities, and that p300-catalyzed histone crotonylation directly stimulates transcription to a greater degree than histone acetylation. Levels of histone crotonylation are regulated by the cellular concentration of crotonyl-CoA, which can be altered through genetic and environmental perturbations. In a cell-based model of transcriptional activation, increasing or decreasing the cellular concentration of crotonyl-CoA leads to enhanced or diminished gene expression, respectively, which correlates with the levels of histone crotonylation flanking the regulatory elements of activated genes. Our findings support a general principle wherein differential histone acylation (i.e., acetylation versus crotonylation) couples cellular metabolism to the regulation of gene expression.
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Affiliation(s)
- Benjamin R Sabari
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Ha Eun Kong
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Lunzhi Dai
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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21
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Ghare SS, Joshi-Barve S, Moghe A, Patil M, Barker DF, Gobejishvili L, Brock GN, Cave M, McClain CJ, Barve SS. Coordinated histone H3 methylation and acetylation regulate physiologic and pathologic fas ligand gene expression in human CD4+ T cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:412-21. [PMID: 24899502 PMCID: PMC5096587 DOI: 10.4049/jimmunol.1400055] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activation-induced Fas ligand (FasL) mRNA expression in CD4+ T cells is mainly controlled at transcriptional initiation. To elucidate the epigenetic mechanisms regulating physiologic and pathologic FasL transcription, TCR stimulation-responsive promoter histone modifications in normal and alcohol-exposed primary human CD4+ T cells were examined. TCR stimulation of normal and alcohol-exposed cells led to discernible changes in promoter histone H3 lysine trimethylation, as documented by an increase in the levels of transcriptionally permissive histone 3 lysine 4 trimethylation and a concomitant decrease in the repressive histone 3 lysine 9 trimethylation. Moreover, acetylation of histone 3 lysine 9 (H3K9), a critical feature of the active promoter state that is opposed by histone 3 lysine 9 trimethylation, was significantly increased and was essentially mediated by the p300-histone acetyltransferase. Notably, the degree of these coordinated histone modifications and subsequent recruitment of transcription factors and RNA polymerase II were significantly enhanced in alcohol-exposed CD4+ T cells and were commensurate with the pathologic increase in the levels of FasL mRNA. The clinical relevance of these findings is further supported by CD4+ T cells obtained from individuals with a history of heavy alcohol consumption, which demonstrate significantly greater p300-dependent H3K9 acetylation and FasL expression. Overall, these data show that, in human CD4+ T cells, TCR stimulation induces a distinct promoter histone profile involving a coordinated cross-talk between histone 3 lysine 4 and H3K9 methylation and acetylation that dictates the transcriptional activation of FasL under physiologic, as well as pathologic, conditions of alcohol exposure.
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Affiliation(s)
- Smita S Ghare
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202
| | - Swati Joshi-Barve
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
| | - Akshata Moghe
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
| | - Madhuvanti Patil
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
| | - David F Barker
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202
| | - Leila Gobejishvili
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202
| | - Guy N Brock
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202
| | - Matthew Cave
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
| | - Craig J McClain
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
| | - Shirish S Barve
- Department of Medicine, University of Louisville, Louisville, KY 40202; University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40202; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202; and
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22
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Jiang H, Lu X, Shimada M, Dou Y, Tang Z, Roeder RG. Regulation of transcription by the MLL2 complex and MLL complex-associated AKAP95. Nat Struct Mol Biol 2013; 20:1156-63. [PMID: 23995757 PMCID: PMC3813012 DOI: 10.1038/nsmb.2656] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/24/2013] [Indexed: 01/18/2023]
Abstract
Although histone H3 lysine 4 (H3K4) methylation is widely associated with gene activation, direct evidence for its causal role in transcription, through specific MLL family members, is scarce. Here we have purified a human MLL2 (Kmt2b) complex that is highly active in H3K4 methylation and chromatin transcription in a cell-free system. This effect requires SAM and intact H3K4, establishing a direct and causal role for MLL2-mediated H3K4 methylation in transcription. We then show that human AKAP95, a chromatin-associated protein, is physically and functionally associated with the DPY30–MLL complexes and directly enhances their methyltransferase activity. Ectopic AKAP95 stimulates expression of a chromosomal reporter in synergy with MLL1 or MLL2, whereas AKAP95 depletion impairs retinoic acid-mediated gene induction in embryonic stem cells. These results demonstrate an important role for AKAP95 in regulating histone methylation and gene expression, particularly during cell fate transitions.
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Affiliation(s)
- Hao Jiang
- 1] Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York, USA. [2] Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA. [3] UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA. [4]
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Mocquard-Bucher E, Galvani A, Thiriet C. Histone H4 acetylation links nucleosome turnover and nucleosome assembly: lessons from the slime moldPhysarum polycephalum. FRONTIERS IN LIFE SCIENCE 2013. [DOI: 10.1080/21553769.2013.848241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 2013; 152:859-72. [PMID: 23415232 DOI: 10.1016/j.cell.2013.01.032] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 11/25/2012] [Accepted: 01/22/2013] [Indexed: 12/11/2022]
Abstract
Histone modifications are key regulators of chromatin function. However, little is known to what extent histone modifications can directly impact on chromatin. Here, we address how a modification within the globular domain of histones regulates chromatin function. We demonstrate that H3K122ac can be sufficient to stimulate transcription and that mutation of H3K122 impairs transcriptional activation, which we attribute to a direct effect of H3K122ac on histone-DNA binding. In line with this, we find that H3K122ac defines genome-wide genetic elements and chromatin features associated with active transcription. Furthermore, H3K122ac is catalyzed by the coactivators p300/CBP and can be induced by nuclear hormone receptor signaling. Collectively, this suggests that transcriptional regulators elicit their effects not only via signaling to histone tails but also via direct structural perturbation of nucleosomes by directing acetylation to their lateral surface.
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25
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Abstract
The reversible acetylation of specific lysine residues on core histones regulates gene transcription in eukaryotes. Since the discovery of GCN5 as the first transcription-regulating histone acetyltransferase (HAT), a variety of HATs have now been identified and shown to acetylate different sites on histones as well as on non-histone proteins, including transcription regulators. In general, purified recombinant HATs expressed in bacteria or in insect cells are able to acetylate free histones and sometimes other substrates in vitro. However, such activity is often restricted to certain substrates and/or is very weak on physiological substrates, such as nucleosomes. Moreover, it does not reflect the actual scenario inside the cell, where HATs generally associate with other proteins to form stable multisubunit complexes. Importantly, these peripheral proteins significantly influence the functions of the catalytic HAT subunit by regulating its intrinsic catalytic activity and/or by modulating its target substrate selectivity. In this chapter, we describe detailed methods for the rapid (two step) and efficient purification of large, multiprotein HAT complexes from nuclear extracts of mammalian epitope-tagged cell lines, including protocols for the generation and large-scale suspension culture of these cell lines. These methods have been used to purify and characterize different human GCN5 HAT complexes that retain activity toward their physiological substrates in vitro.
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Zhang Y, Qiu J, Wang X, Zhang Y, Xia M. AMP-Activated Protein Kinase Suppresses Endothelial Cell Inflammation Through Phosphorylation of Transcriptional Coactivator p300. Arterioscler Thromb Vasc Biol 2011; 31:2897-908. [DOI: 10.1161/atvbaha.111.237453] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective—
Considerable evidence supports the early involvement of monocyte/macrophage recruitment to activated endothelial cells by leukocyte adhesion molecules during atherogenesis. AMP-activated protein kinase (AMPK) is highly expressed in vascular endothelial cells, but its impact on monocyte adhesion and the related mechanisms are not fully understood. The present study was designed to evaluate the impact of and gain mechanistic insight into the signaling coupling AMPK function to the antiinflammatory response.
Methods and Results—
5-Aminoimidazole-4-carboxamide-1-β-
d
-ribonucleotide (AICAR) treatment or overexpression of constitutively active AMPK markedly reduced human monocytic human acute monocytic leukemia cell line-1 cell adhesion and the expression of vascular cell adhesion molecule-1 in tumor necrosis factor-α–activated human aortic endothelial cells. Furthermore, AICAR or constitutively active AMPK overexpression strongly inhibited the histone acetyltransferase activity of the transcriptional coactivator p300 by phosphorylation of Ser89, which in turn decreased tumor necrosis factor-α-activated p300-mediated acetylation of nuclear factor-κB p65 on Lys221 and reduced the DNA binding activity of nuclear factor-κB by inhibiting its recruitment to its target gene promoters. AMPK phosphorylates the transcriptional coactivator p300 via the atypical protein kinase Cι/λ.
Conclusion—
Our findings demonstrate that transcriptional coactivator p300 phosphorylation at Ser89 by AMPK is critical for the therapeutic effect of AMPK and may be a potential target for pharmaceutical intervention in inflammatory diseases such as atherosclerosis.
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Affiliation(s)
- Yuan Zhang
- From the Department of Cardiovascular Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China (Yuan Zhang, J.Q., X.W., Yuhua Zhang, M.X.); Guangdong Provincial Key Laboratory of Food, Nutrition and Health (X.W., Yuhua Zhang, M.X.); Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China (X.W., Yuhua Zhang, M.X.)
| | - Jian Qiu
- From the Department of Cardiovascular Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China (Yuan Zhang, J.Q., X.W., Yuhua Zhang, M.X.); Guangdong Provincial Key Laboratory of Food, Nutrition and Health (X.W., Yuhua Zhang, M.X.); Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China (X.W., Yuhua Zhang, M.X.)
| | - Xiaoming Wang
- From the Department of Cardiovascular Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China (Yuan Zhang, J.Q., X.W., Yuhua Zhang, M.X.); Guangdong Provincial Key Laboratory of Food, Nutrition and Health (X.W., Yuhua Zhang, M.X.); Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China (X.W., Yuhua Zhang, M.X.)
| | - Yuhua Zhang
- From the Department of Cardiovascular Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China (Yuan Zhang, J.Q., X.W., Yuhua Zhang, M.X.); Guangdong Provincial Key Laboratory of Food, Nutrition and Health (X.W., Yuhua Zhang, M.X.); Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China (X.W., Yuhua Zhang, M.X.)
| | - Min Xia
- From the Department of Cardiovascular Medicine, General Hospital of Guangzhou Military Command, Guangzhou, China (Yuan Zhang, J.Q., X.W., Yuhua Zhang, M.X.); Guangdong Provincial Key Laboratory of Food, Nutrition and Health (X.W., Yuhua Zhang, M.X.); Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, China (X.W., Yuhua Zhang, M.X.)
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Park JH, Magan N. Reverse transcriptase-coupled quantitative real time PCR analysis of cell-free transcription on the chromatin-assembled p21 promoter. PLoS One 2011; 6:e23617. [PMID: 21886803 PMCID: PMC3160311 DOI: 10.1371/journal.pone.0023617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/21/2011] [Indexed: 11/28/2022] Open
Abstract
Background Cell-free eukaryotic transcription assays have contributed tremendously to the current understanding of the molecular mechanisms that govern transcription at eukaryotic promoters. Currently, the conventional G-less cassette transcription assay is one of the simplest and fastest methods for measuring transcription in vitro. This method requires several components, including the radioisotope labelling of RNA product during the transcription reaction followed by visualization of transcripts using autoradiography. Methodology/Principal Findings To further simplify and expedite the conventional G-less cassette transcription assay, we have developed a method to incorporate a reverse transcriptase-coupled quantitative real time PCR (RT-qPCR). By using DNA template depletion steps that include DNA template immobilization, Trizol extraction and DNase I treatment, we have successfully enriched p21 promoter-driven transcripts over DNA templates. The quantification results of RNA transcripts using the RT-qPCR assay were comparable to the results of the conventional G-less cassette transcription assay both in naked DNA and chromatin-assembled templates. Conclusions We first report a proof-of-concept demonstration that incorporating RT-qPCR in cell-free transcription assays can be a simpler and faster alternative method to the conventional radioisotope-mediated transcription assays. This method will be useful for developing high throughput in vitro transcription assays and provide quantitative data for RNA transcripts generated in a defined cell-free transcription reaction.
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Affiliation(s)
- Jeong Hyeon Park
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.
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Choi J, Kim H, Kim K, Lee B, Lu W, An W. Selective requirement of H2B N-Terminal tail for p14ARF-induced chromatin silencing. Nucleic Acids Res 2011; 39:9167-80. [PMID: 21846774 PMCID: PMC3241654 DOI: 10.1093/nar/gkr642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The N-terminal tail of histone H2B is believed to be involved in gene silencing, but how it exerts its function remains elusive. Here, we report the biochemical characterization of p14ARF tumor suppressor as a transcriptional repressor that selectively recognizes the unacetylated H2B tails on nucleosomes. The p14ARF–H2B tail interaction is functional, as the antagonistic effect of p14ARF on chromatin transcription is lost upon deletion or acetylation of H2B tails. Gene expression profiling and chromatin immunoprecipitation studies emphasize the significance of H2B deacetylation and p14ARF recruitment in establishing a repressive environment over the cell cycle regulatory genes. Moreover, HDAC1-mediated H2B deacetylation, especially at K20, constitutes an essential step in tethering p14ARF near target promoters. Our results thus reveal a hitherto unknown role of p14ARF in the regulation of chromatin transcription, as well as molecular mechanisms governing the repressive action of p14ARF.
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Affiliation(s)
- Jongkyu Choi
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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29
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Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14. Proc Natl Acad Sci U S A 2010; 107:19254-9. [PMID: 20974913 DOI: 10.1073/pnas.1009650107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone posttranslational modifications and chromatin dynamics are inextricably linked to eukaryotic gene expression. Among the many modifications that have been characterized, histone tail acetylation is most strongly correlated with transcriptional activation. In Metazoa, promoters of transcriptionally active genes are generally devoid of physically repressive nucleosomes, consistent with the contemporaneous binding of the large RNA polymerase II transcription machinery. The histone acetyltransferase p300 is also detected at active gene promoters, flanked by regions of histone hyperacetylation. Although the correlation between histone tail acetylation and gene activation is firmly established, the mechanisms by which acetylation facilitates this fundamental biological process remain poorly understood. To explore the role of acetylation in nucleosome dynamics, we utilized an immobilized template carrying a natural promoter reconstituted with various combinations of wild-type and mutant histones. We find that the histone H3 N-terminal tail is indispensable for activator, p300, and acetyl-CoA-dependent nucleosome eviction mediated by the histone chaperone Nap1. Significantly, we identify H3 lysine 14 as the essential p300 acetylation substrate required for dissociation of the histone octamer from the promoter DNA. Together, a total of 11 unique mutant octamer sets corroborated these observations and revealed a striking correlation between nucleosome eviction and strong activator and acetyl-CoA-dependent transcriptional activation. These novel findings uncover an exclusive role for H3 lysine 14 acetylation in facilitating the ATP-independent and transcription-independent disassembly of promoter nucleosomes by Nap1. Furthermore, these studies directly couple nucleosome disassembly with strong, activator-dependent transcription.
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30
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Hansen JC, Nyborg JK, Luger K, Stargell LA. Histone chaperones, histone acetylation, and the fluidity of the chromogenome. J Cell Physiol 2010; 224:289-99. [PMID: 20432449 DOI: 10.1002/jcp.22150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The "chromogenome" is defined as the structural and functional status of the genome at any given moment within a eukaryotic cell. This article focuses on recently uncovered relationships between histone chaperones, post-translational acetylation of histones, and modulation of the chromogenome. We emphasize those chaperones that function in a replication-independent manner, and for which three-dimensional structural information has been obtained. The emerging links between histone acetylation and chaperone function in both yeast and higher metazoans are discussed, including the importance of nucleosome-free regions. We close by posing many questions pertaining to how the coupled action of histone chaperones and acetylation influences chromogenome structure and function.
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Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
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31
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Shimada M, Nakadai T, Fukuda A, Hisatake K. cAMP-response element-binding protein (CREB) controls MSK1-mediated phosphorylation of histone H3 at the c-fos promoter in vitro. J Biol Chem 2010; 285:9390-9401. [PMID: 20089855 DOI: 10.1074/jbc.m109.057745] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rapid induction of the c-fos gene correlates with phosphorylations of histone H3 and HMGN1 by mitogen- and stress-activated protein kinases. We have used a cell-free system to dissect the mechanism by which MSK1 phosphorylates histone H3 within the c-fos chromatin. Here, we show that the reconstituted c-fos chromatin presents a strong barrier to histone H3 phosphorylation by MSK1; however, the activators (serum response factor, Elk-1, cAMP-response element-binding protein (CREB), and ATF1) bound on their cognate sites recruit MSK1 to phosphorylate histone H3 at Ser-10 within the chromatin. This activator-dependent phosphorylation of histone H3 is enhanced by HMGN1 and occurs preferentially near the promoter region. Among the four activators, CREB plays a predominant role in MSK1-mediated phosphorylation of histone H3, and the phosphorylation of Ser-133 in CREB is essential for this process. Mutational analyses of MSK1 show that its N-terminal inhibition domain is critical for the kinase to phosphorylate chromatin-embedded histone H3 in a CREB-dependent manner, indicating the presence of an intricate regulatory network for MSK1-mediated phosphorylation of histone H3.
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Affiliation(s)
- Miho Shimada
- Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495
| | - Tomoyoshi Nakadai
- Department of Molecular Biology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495
| | - Aya Fukuda
- Department of Biochemistry, Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Koji Hisatake
- Department of Biochemistry, Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki 305-8575, Japan.
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32
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Transcription of in vitro assembled chromatin templates in a highly purified RNA polymerase II system. Methods 2009; 48:353-60. [PMID: 19272450 DOI: 10.1016/j.ymeth.2009.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 02/25/2009] [Indexed: 11/20/2022] Open
Abstract
In mammalian cells RNA polymerase II efficiently transcribes nucleosome-packaged DNA. In this regard, a fundamental question concerns the nature and mechanism of action of the accessory factors that are necessary and sufficient for, or enhance, transcription through nucleosomal arrays by RNA polymerase II. Here we describe a highly purified system that allows for efficient activator-dependent transcription by RNA polymerase II from the promoter through several contiguous nucleosomes on defined chromatin templates. The system contains natural or recombinant histones, chromatin assembly factors, the histone-acetyltransferase p300, all components of the general transcription machinery, general coactivators and the elongation factor SII (TFIIS). As examples of the applicability of this system for mechanistic analyses of these and other factors, representative experiments show (i) that activated transcription from chromatin templates is concomitantly dependent on the activator, p300-mediated histone acetylation and elongation factor SII/TFIIS. (ii) that SII/TFIIS acts in a highly synergistic manner with p300 (and histone acetylation) at a step subsequent to preinitiation complex (PIC) formation and (iii) that SII/TFIIS works directly at the elongation step of chromatin transcription. Here we describe purification methods for the different factors employed and the specific transcriptional assays that led to the above-mentioned conclusions. This purified system will be very useful as an assay system for the discovery of new factors or the mechanistic analysis of known or candidate factors involved in transcription initiation or elongation on chromatin templates, including factors that effect specific histone modifications or nucleosomal remodeling.
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33
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Boutros T, Chevet E, Metrakos P. Mitogen-activated protein (MAP) kinase/MAP kinase phosphatase regulation: roles in cell growth, death, and cancer. Pharmacol Rev 2009; 60:261-310. [PMID: 18922965 DOI: 10.1124/pr.107.00106] [Citation(s) in RCA: 438] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mitogen-activated protein kinase dual-specificity phosphatase-1 (also called MKP-1, DUSP1, ERP, CL100, HVH1, PTPN10, and 3CH134) is a member of the threonine-tyrosine dual-specificity phosphatases, one of more than 100 protein tyrosine phosphatases. It was first identified approximately 20 years ago, and since that time extensive investigations into both mkp-1 mRNA and protein regulation and function in different cells, tissues, and organs have been conducted. However, no general review on the topic of MKP-1 exists. As the subject matter pertaining to MKP-1 encompasses many branches of the biomedical field, we focus on the role of this protein in cancer development and progression, highlighting the potential role of the mitogen-activated protein kinase (MAPK) family. Section II of this article elucidates the MAPK family cross-talk. Section III reviews the structure of the mkp-1 encoding gene, and the known mechanisms regulating the expression and activity of the protein. Section IV is an overview of the MAPK-specific dual-specificity phosphatases and their role in cancer. In sections V and VI, mkp-1 mRNA and protein are examined in relation to cancer biology, therapeutics, and clinical studies, including a discussion of the potential role of the MAPK family. We conclude by proposing an integrated scheme for MKP-1 and MAPK in cancer.
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Affiliation(s)
- Tarek Boutros
- Department of Surgery, Royal Victoria Hospital, McGill University, 687 Pine Ave. W., Montreal, QC H3A1A1, Canada.
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34
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Different functional modes of p300 in activation of RNA polymerase III transcription from chromatin templates. Mol Cell Biol 2008; 28:5764-76. [PMID: 18644873 DOI: 10.1128/mcb.01262-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional coactivators that regulate the activity of human RNA polymerase III (Pol III) in the context of chromatin have not been reported. Here, we describe a completely defined in vitro system for transcription of a human tRNA gene assembled into a chromatin template. Transcriptional activation and histone acetylation in this system depend on recruitment of p300 by general initiation factor TFIIIC, thus providing a new paradigm for recruitment of histone-modifying coactivators. Beyond its role as a chromatin-modifying factor, p300 displays an acetyltransferase-independent function at the level of preinitiation complex assembly. Thus, direct interaction of p300 with TFIIIC stabilizes binding of TFIIIC to core promoter elements and results in enhanced transcriptional activity on histone-free templates. Additional studies show that p300 is recruited to the promoters of actively transcribed tRNA and U6 snRNA genes in vivo. These studies identify TFIIIC as a recruitment factor for p300 and thus may have important implications for the emerging concept that tRNA genes or TFIIIC binding sites act as chromatin barriers to prohibit spreading of silenced heterochromatin domains.
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35
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Robinson PJJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D. 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol 2008; 381:816-25. [PMID: 18653199 DOI: 10.1016/j.jmb.2008.04.050] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 04/20/2008] [Accepted: 04/22/2008] [Indexed: 01/03/2023]
Abstract
The mechanism by which chromatin is decondensed to permit access to DNA is largely unknown. Here, using a model nucleosome array reconstituted from recombinant histone octamers, we have defined the relative contribution of the individual histone octamer N-terminal tails as well as the effect of a targeted histone tail acetylation on the compaction state of the 30 nm chromatin fiber. This study goes beyond previous studies as it is based on a nucleosome array that is very long (61 nucleosomes) and contains a stoichiometric concentration of bound linker histone, which is essential for the formation of the 30 nm chromatin fiber. We find that compaction is regulated in two steps: Introduction of H4 acetylated to 30% on K16 inhibits compaction to a greater degree than deletion of the H4 N-terminal tail. Further decompaction is achieved by removal of the linker histone.
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36
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González-Romero R, Méndez J, Ausió J, Eirín-López JM. Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd. Gene 2008; 413:1-7. [PMID: 18329190 DOI: 10.1016/j.gene.2008.02.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 02/04/2008] [Accepted: 02/07/2008] [Indexed: 11/19/2022]
Abstract
Histone H2A.Bbd (Barr body-deficient) is a novel histone variant which is largely excluded from the inactive X chromosome of mammals. Discovered only 6 years ago, H2A.Bbd displays very unusual structural and functional properties, for instance, it is relatively shorter and only 48% identical compared to H2A, lacking both the typical C-terminal tail of the H2A family and the very last sequence of the docking domain, making it the most specialized among all histone variants known to date. Indeed, molecular evolutionary analyses have shown that H2A.Bbd is a highly hypervariable and quickly evolving protein exclusive to mammalian lineages, in striking contrast to all other histones. Different studies have described a deposition pattern of H2A.Bbd in the chromatin that overlaps with regions of histone H4 acetylation suggesting its association with transcriptionally active euchromatic regions of the genome. In this regard, it is believed that this histone variant plays an important role in determining such regions by destabilizing the nucleosome and locally unfolding the chromatin fiber. This review provides a concise, comprehensive and timely summary of the work published on H2A.Bbd structure and function. Special emphasis is placed on its chromatin deposition patterns in relation to gene expression profiles and its evolutionary history, as well as on the dynamics of H2A.Bbd-containing nucleosomes.
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Affiliation(s)
- Rodrigo González-Romero
- Departamento de Biología Celular y Molecular, Universidade da Coruña, A Coruña - E15071, Spain
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37
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Kim K, Choi J, Heo K, Kim H, Levens D, Kohno K, Johnson EM, Brock HW, An W. Isolation and characterization of a novel H1.2 complex that acts as a repressor of p53-mediated transcription. J Biol Chem 2008; 283:9113-26. [PMID: 18258596 DOI: 10.1074/jbc.m708205200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Linker histone H1 has been generally viewed as a global repressor of transcription by preventing the access of transcription factors to sites in chromatin. However, recent studies suggest that H1 can interact with other regulatory factors for its action as a negative modulator of specific genes. To investigate these aspects, we established a human cell line expressing H1.2, one of the H1 subtypes, for the purification of H1-interacting proteins. Our results showed that H1.2 can stably associate with sets of cofactors and ribosomal proteins that can significantly repress p53-dependent, p300-mediated chromatin transcription. This repressive action of H1.2 complex involves direct interaction of H1.2 with p53, which in turn blocks p300-mediated acetylation of chromatin. YB1 and PURalpha, two factors present in the H1.2 complex, together with H1.2 can closely recapitulate the repressive action of the entire H1.2 complex in transcription. Chromatin immunoprecipitation and RNA interference analyses further confirmed that the recruitment of YB1, PURalpha, and H1.2 to the p53 target gene Bax is required for repression of p53-induced transcription. Therefore, these results reveal a previously unrecognized function of H1 as a transcriptional repressor as well as the underlying mechanism involving specific sets of factors in this repression process.
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Affiliation(s)
- Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
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38
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Ishiguro K, Sartorelli AC. Relationship between the induction of leukemia cell differentiation and the enhancement of reporter gene expression in 3T3 Swiss cells. Leuk Res 2007; 32:89-96. [PMID: 17617452 PMCID: PMC2778346 DOI: 10.1016/j.leukres.2007.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/10/2007] [Accepted: 05/17/2007] [Indexed: 11/18/2022]
Abstract
The histone deacetylase (HDAC) inhibitor trichostatin A (TSA) and hexamethylene bisacetamide (HMBA), which lacks HDAC inhibitory activity, both possess the capacity to induce leukemia cell differentiation and to enhance the expression of a wide range of transiently transfected reporter genes in 3T3 Swiss cells. In addition, known inducers of leukemia cell differentiation, including hypoxanthine, diazepam, 6-thioguanine and phorbol 12-myristate 13-acetate, also exhibited the ability to enhance reporter gene expression, while randomly chosen compounds that did not induce leukemia cell differentiation did not enhance reporter gene expression. The activity of TSA in the transfection system was modified by co-expression of histone acetyltransferase p300 and HDAC1; whereas, that of HMBA was enhanced by co-expression of the TATA-binding protein TBP. The stimulatory effects of diverse chemical inducers on transiently transfected genes suggest the existence of multiple exploitable targets for the selection of novel inducers of differentiation that function as modulators of gene activity.
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Affiliation(s)
| | - Alan C. Sartorelli
- Corresponding author. Tel.: +1 203 785 4533; fax: +1 203 737 2045. (A.C. Sartorelli)
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39
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Saint Just Ribeiro M, Hansson M, Wallberg A. A proline repeat domain in the Notch co-activator MAML1 is important for the p300-mediated acetylation of MAML1. Biochem J 2007; 404:289-98. [PMID: 17300219 PMCID: PMC1868802 DOI: 10.1042/bj20061900] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ligand activation of Notch leads to the release of Notch IC (the intracellular receptor domain), which translocates to the nucleus and interacts with the DNA-binding protein CSL to control expression of specific target genes. In addition to ligand-mediated activation, Notch signalling can be further modulated by interactions of Notch IC with a number of other proteins. MAML1 has previously been shown to act co-operatively with the histone acetyltransferase p300 in Notch IC-mediated transcription. In the present study we show that the N-terminal domain of MAML1 directly interacts with both p300 and histones, and the p300-MAML1 complex specifically acetylates histone H3 and H4 tails in chromatin. Furthermore, p300 acetylates MAML1 and evolutionarily conserved lysine residues in the MAML1 N-terminus are direct substrates for p300-mediated acetylation. The N-terminal domain of MAML1 contains a proline repeat motif (PXPAAPAP) that was previously shown to be present in p53 and important for the p300-p53 interaction. We show that the MAML1 proline repeat motif interacts with p300 and enhances the activity of the MAML1 N-terminus in vivo. These findings suggest that the N-terminal domain of MAML1 plays an important role in Notch-regulated transcription, by direct interactions with Notch, p300 and histones.
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Affiliation(s)
| | - Magnus L. Hansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Annika E. Wallberg
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 86 Stockholm, Sweden
- To whom correspondence should be addressed (email )
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40
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Choi J, Kim B, Heo K, Kim K, Kim H, Zhan Y, Ranish JA, An W. Purification and characterization of cellular proteins associated with histone H4 tails. J Biol Chem 2007; 282:21024-31. [PMID: 17548343 DOI: 10.1074/jbc.m703883200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The histone H4 N-terminal tail has long been regarded as a major regulator in chromatin structure and function. Although the underlying mechanism has not been unraveled, an emerging body of evidence supports that H4 tail and its post-translational modification function as a recruitment motif for key factors required for proper regulation of chromatin transcription. To investigate these aspects, we have generated HeLa cell lines that constitutively express ectopic H4 tail domain for biochemical purification of proteins associated with H4 tail. We found that expressed H4 tails stably associate with sets of transcription regulatory factors and histone methyltransferases distinct from those that associate with histone H3 tails. Importantly, point mutations of four major lysine substrates to block cellular acetylation of ectopic H4 tail significantly inhibited the association of histone methyltransferases and sets of transcription-activating factors, supporting a major role of acetylation on recruitmentbased action of H4 tail during transcription. Further, our transcription analysis revealed that the proteins associated with wild-type/acetylated H4 tail, but not with mutant/unacetylated H4 tail, can enhance p300-dependent chromatin transcription. Taken together, these findings demonstrate novel roles for H4 tail and its acetylation in mediating recruitment of multiple regulatory factors that can change chromatin states for transcription regulation.
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Affiliation(s)
- Jongkyu Choi
- Department of Biochemistry and Molecular Biology, University of Southern California (USC)/Norris Comprehensive Cancer Center, USC Keck School of Medicine, Los Angeles, California 90033, USA
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41
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An W. Histone acetylation and methylation: combinatorial players for transcriptional regulation. Subcell Biochem 2007. [PMID: 17484136 DOI: 10.1007/1-4020-5466-1_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Post-synthetic modification of histone proteins in chromatin architecture plays a central role in the epigenetic regulation of transcription. Histone acetylation and methylation are the two major modifications that function as a specific transcription regulator in response to various cellular signals. Albeit the mechanism of action of these modifications in transcription is not well understood, recent discovery of histone acetyltransferase (HAT) and methyltransferase (HMT) activities within transcriptional regulators has an important implication for histone modification to be a key player for the precise regulation of transcription processes. Here, we discuss recent advances made on histone acetylation and methylation as a fundamental process to modulate gene transcription, with a particular emphasis on their combinatorial effects in transcriptional control.
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Affiliation(s)
- Woojin An
- Department of Biochemistry & Molecular Biology, USC/Norris Comprehensive Cancer Center, 1501 San Pablo Street, ZNI 241, MC 2821, Los Angeles, California 90089-2821, USA.
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Heo K, Kim B, Kim K, Choi J, Kim H, Zhan Y, Ranish JA, An W. Isolation and characterization of proteins associated with histone H3 tails in vivo. J Biol Chem 2007; 282:15476-83. [PMID: 17403666 DOI: 10.1074/jbc.m610270200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The histone H3 amino-terminal tails play an important role in regulating chromatin transcription. Although the mechanisms by which the H3 tail modulates transcription are not well understood, recent discoveries of specific interactions of regulatory factors with H3 tails suggest that H3 tails are a key player in the precise regulation of transcription activity. To investigate the recruitment-based action of H3 tails in chromatin transcription, we purified H3 tail-associated proteins from HeLa cells that stably express epitope-tagged H3 tails. This approach resulted in the identification of multiple histone methyltransferase activities and transcription regulatory factors that are specifically associated with expressed H3 tail domains. Point mutations of Lys-9 and Lys-27 to block cellular modifications of the tail domains completely abolished the association of specific factors, including HP1 and several repressors. Importantly, our transcription analysis revealed that the purified factors can significantly stimulate p300-mediated transcription from chromatin templates. These results implicate that the H3 tail, when accessible in relaxed chromatin, acts as a transcriptional regulator by mediating recruitment of specific sets of cofactors.
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Affiliation(s)
- Kyu Heo
- Department of Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
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Shen B, Harrison-Bernard LM, Fuller AJ, Vanderpool V, Saifudeen Z, El-Dahr SS. The Bradykinin B2 receptor gene is a target of angiotensin II type 1 receptor signaling. J Am Soc Nephrol 2007; 18:1140-9. [PMID: 17344422 DOI: 10.1681/asn.2006101127] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Cross-talk between G protein-coupled receptors (GPCR) is known to occur at multiple levels, including receptor heterodimerization and intracellular signaling. This study tested the hypothesis that GPCR cross-talk occurs at the transcriptional level. It was demonstrated that the bradykinin B2 receptor gene (BdkrB2) is a direct transcriptional target of the angiotensin II (AngII) type 1 receptor (AT(1)R) in collecting duct cells. AngII induced BdkrB2 mRNA expression in mouse inner medullary collecting duct cells, and this effect was abrogated by AT(1)R blockade; in contrast, AT(2)R blockade was ineffective. Actinomycin D, an inhibitor of gene transcription, abrogated AngII-stimulated BdkrB2 expression. In addition, AngII produced dosage- and time-dependent increases in B2 receptor protein levels (2.9 +/- 0.4 fold; P < 0.05). AngII stimulated phosphorylation of cAMP response element binding protein (CREB) on Ser-133 and assembly of p-CREB on the BdkrB2 promoter in vivo. Moreover, AngII induced hyperacetylation of BdkrB2 promoter-associated H4 histones, a chromatin modification that is associated with gene activation. Mutations of the CRE abrogated AngII-induced activation of the BdkrB2 promoter. AngII-treated inner medullary collecting duct cells exhibited augmented intracellular calcium signaling in response to bradykinin, confirming the functional relevance of AT(1)-B2 receptor signaling. Finally, studies that were conducted in angiotensin type 1 receptor (Agtr1)-null mice revealed that BdkrB2 mRNA levels were significantly lower in the renal medulla of Agtr1(A)(-/-) and Agtr1(A/B)(-/-) than in Agtr1(+/+) and Agtr1(B)(-/-) mice. It is concluded that BdkrB2 is a downstream target of the AT(1)R-CREB signaling pathway. Transcriptional regulation represents a novel form of cross-talk between GPCR that link the renin-angiotensin and kallikrein-kinin systems.
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Affiliation(s)
- Bing Shen
- Department of Pediatrics, SL-37, Tulane University Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
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Zlatanova J, Seebart C, Tomschik M. Nap1: taking a closer look at a juggler protein of extraordinary skills. FASEB J 2007; 21:1294-310. [PMID: 17317729 DOI: 10.1096/fj.06-7199rev] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The nucleosome assembly protein Nap1 is used extensively in the chromatin field to reconstitute nucleosomal templates for structural and functional studies. Beyond its role in facilitating experimental investigation of nucleosomes, the highly conserved Nap1 is one of the best-studied members of the histone chaperone group. Here we review its numerous functions, focusing mainly on its roles in assembly and disassembly of the nucleosome particle, and its interactions with chromatin remodeling factors. Its presumed role in transcription through chromatin is also reviewed in detail. An attempt is made to clearly discriminate between fact and fiction, and to formulate the unresolved questions that need further attention. It is beyond doubt that the numerous, seemingly unrelated functions of this juggler protein have to be precisely channeled, coordinated, and regulated. Why nature endowed this specific protein with so many functions may remain a mystery. We are aware of the enormous challenge to the scientific community that understanding the mechanisms underlying these activities presents.
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Affiliation(s)
- Jordanka Zlatanova
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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Pavri R, Zhu B, Li G, Trojer P, Mandal S, Shilatifard A, Reinberg D. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 2006; 125:703-17. [PMID: 16713563 DOI: 10.1016/j.cell.2006.04.029] [Citation(s) in RCA: 558] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 03/23/2006] [Accepted: 04/20/2006] [Indexed: 12/31/2022]
Abstract
Over the past years, a large number of histone posttranslational modifications have been described, some of which function to attain a repressed chromatin structure, while others facilitate activation by allowing access of regulators to DNA. Histone H2B monoubiquitination is a mark associated with transcriptional activity. Using a highly reconstituted chromatin-transcription system incorporating the inducible RARbeta2 promoter, we find that the establishment of H2B monoubiquitination by RNF20/40 and UbcH6 is dependent on the transcription elongation regulator complex PAF, the histone chaperone FACT, and transcription. H2B monoubiquitination facilitates FACT function, thereby stimulating transcript elongation and the generation of longer transcripts. These in vitro analyses and corroborating in vivo experiments demonstrate that elongation by RNA polymerase II through the nucleosomal barrier is minimally dependent upon (1) FACT and (2) the recruitment of PAF and the H2B monoubiquitination machinery.
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Affiliation(s)
- Rushad Pavri
- Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 683 Hoes Lane, Piscataway, NJ 08854, USA
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Guermah M, Palhan VB, Tackett AJ, Chait BT, Roeder RG. Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates. Cell 2006; 125:275-86. [PMID: 16630816 DOI: 10.1016/j.cell.2006.01.055] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Revised: 11/09/2005] [Accepted: 01/22/2006] [Indexed: 11/22/2022]
Abstract
We have reconstituted a highly purified RNA polymerase II transcription system containing chromatin templates assembled with purified histones and assembly factors, the histone acetyltransferase p300, and components of the general transcription machinery that, by themselves, suffice for activated transcription (initiation and elongation) on DNA templates. We show that this system mediates activator-dependent initiation, but not productive elongation, on chromatin templates. We further report the purification of a chromatin transcription-enabling activity (CTEA) that, in a manner dependent upon p300 and acetyl-CoA, strongly potentiates transcription elongation through several contiguous nucleosomes as must occur in vivo. The transcription elongation factor SII is a major component of CTEA and strongly synergizes with p300 (histone acetylation) at a step subsequent to preinitiation complex formation. The purification of CTEA also identified HMGB2 as a coactivator that, while inactive on its own, enhances SII and p300 functions.
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Affiliation(s)
- Mohamed Guermah
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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Boulard M, Gautier T, Mbele GO, Gerson V, Hamiche A, Angelov D, Bouvet P, Dimitrov S. The NH2 tail of the novel histone variant H2BFWT exhibits properties distinct from conventional H2B with respect to the assembly of mitotic chromosomes. Mol Cell Biol 2006; 26:1518-26. [PMID: 16449661 PMCID: PMC1367197 DOI: 10.1128/mcb.26.4.1518-1526.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have studied the functional and structural properties of nucleosomes reconstituted with H2BFWT, a recently identified putative histone variant of the H2B family with totally unknown function. We show that H2BFWT can replace the conventional histone H2B in the nucleosome. The presence of H2BFWT did not affect the overall structure of the nucleosome, and the H2BFWT nucleosomes exhibited the same stability as conventional nucleosomes. SWI/SNF was able to efficiently remodel and mobilize the H2BFWT nucleosomes. Importantly, H2BFWT, in contrast to conventional H2B, was unable to recruit chromosome condensation factors and to participate in the assembly of mitotic chromosomes. This was determined by the highly divergent (compared to conventional H2B) NH2 tail of H2BFWT. These data, in combination with the observations that H2BFWT was found by others in the sperm nuclei and appeared to be associated with the telomeric chromatin, suggest that H2BFWT could act as a specific epigenetic marker.
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Affiliation(s)
- Mathieu Boulard
- Institut Albert Bonniot, INSERM U309, 38706 La Tronche Cedex, France
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Doyen CM, An W, Angelov D, Bondarenko V, Mietton F, Studitsky VM, Hamiche A, Roeder RG, Bouvet P, Dimitrov S. Mechanism of polymerase II transcription repression by the histone variant macroH2A. Mol Cell Biol 2006; 26:1156-64. [PMID: 16428466 PMCID: PMC1347033 DOI: 10.1128/mcb.26.3.1156-1164.2006] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
macroH2A (mH2A) is an unusual histone variant consisting of a histone H2A-like domain fused to a large nonhistone region. In this work, we show that histone mH2A represses p300- and Gal4-VP16-dependent polymerase II transcription, and we have dissected the mechanism by which this repression is realized. The repressive effect of mH2A is observed at the level of initiation but not at elongation of transcription, and mH2A interferes with p300-dependent histone acetylation. The nonhistone region of mH2A is responsible for both the repression of initiation of transcription and the inhibition of histone acetylation. In addition, the presence of this domain of mH2A within the nucleosome is able to block nucleosome remodeling and sliding of the histone octamer to neighboring DNA segments by the remodelers SWI/SNF and ACF. These data unambiguously identify mH2A as a strong transcriptional repressor and show that the repressive effect of mH2A is realized on at least two different transcription activation chromatin-dependent pathways: histone acetylation and nucleosome remodeling.
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Santoso B, Kadonaga JT. Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300. Nat Struct Mol Biol 2006; 13:131-9. [PMID: 16415879 DOI: 10.1038/nsmb1048] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 12/08/2005] [Indexed: 11/09/2022]
Abstract
Here we describe an in vitro chromatin transcription system in which chromatin assembly and transcription are carried out with purified and defined factors. With basal (also known as general) transcription factors and sequence-specific DNA-binding activators, we observed chromatin-specific, activation domain-dependent transcription. We then examined the biochemical function of purified p300 in the absence of the endogenous factor and other related activities and found, unexpectedly, that p300 has a chromatin-specific, transcriptional repression activity that can be relieved by the addition of acetyl-CoA. This p300-mediated repression is reversible, requires the p300 bromodomain but not the acetyltransferase region, and does not involve the formation of a stable, nuclease-resistant nucleoprotein complex. Hence, the mechanism of transcriptional repression by p300 is distinct from that of histone H1, PARP-1 or Sir2. These findings reveal a novel chromatin-specific repressive function of p300.
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Affiliation(s)
- Buyung Santoso
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0347, USA
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50
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Hizume K, Yoshimura SH, Takeyasu K. Linker histone H1 per se can induce three-dimensional folding of chromatin fiber. Biochemistry 2005; 44:12978-89. [PMID: 16185066 DOI: 10.1021/bi050623v] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Higher-order architectures of chromosomes play important roles in the regulation of genome functions. To understand the molecular mechanism of genome packing, an in vitro chromatin reconstitution method and a single-molecule imaging technique (atomic force microscopy) were combined. In 50 mM NaCl, well-stretched beads-on-a-string chromatin fiber was observed. However, in 100 mM NaCl, salt-induced interaction between nucleosomes caused partial aggregation. Addition of histone H1 promoted a further folding of the fiber into thicker fibers 20-30 nm in width. Micrococcal nuclease digestion of these thicker fibers produced an approximately 170 bp fragment of nucleosomal DNA, which was approximately 20 bp longer than in the absence of histone H1 ( approximately 150 bp), indicating that H1 is correctly placed at the linker region. The width of the fiber depended on the ionic strength. Widths of 20 nm in 50 mM NaCl became 30 nm as the ionic strength was changed to 100 mM. On the basis of these results, a flexible model of chromatin fiber formation was proposed, where the mode of the fiber compaction changes depending both on salt environment and linker histone H1. The biological significance of this property of the chromatin architecture will be apparent in the closed segments ( approximately 100 kb) between SAR/MAR regions.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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