201
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An W, Kim J, Roeder RG. Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 2004; 117:735-48. [PMID: 15186775 DOI: 10.1016/j.cell.2004.05.009] [Citation(s) in RCA: 402] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Revised: 04/19/2004] [Accepted: 04/20/2004] [Indexed: 12/31/2022]
Abstract
Transcriptional coactivators that modify histones represent an increasingly important group of regulatory factors, although their ability to modify other factors as well precludes common assumptions that they necessarily act by histone modification. In an extension of previous studies showing a role for acetyltransferase p300/CBP in p53 function, we have used systems reconstituted with recombinant chromatin templates and (co)activators to demonstrate (1) the additional involvement of protein arginine methyltransferases PRMT1 and CARM1 in p53 function; (2) both independent and ordered cooperative functions of p300, PRMT1, and CARM1; and (3) mechanisms that involve direct interactions with p53 and, most importantly, obligatory modifications of corresponding histone substrates. ChIP analyses have confirmed the ordered accumulation of these (and other) coactivators and cognate histone modifications on the GADD45 gene following ectopic p53 expression and/or UV irradiation. These studies thus define diverse cofactor functions, as well as underlying mechanisms involving distinct histone modifications, in p53-dependent gene activation.
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Affiliation(s)
- Woojin An
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10021, USA
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202
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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203
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Abstract
Nuclear receptors (also known as nuclear hormone receptors) are hormone-regulated transcription factors that control many important physiological and developmental processes in animals and humans. Defects in receptor function result in disease. The diverse biological roles of these receptors reflect their surprisingly versatile transcriptional properties, with many receptors possessing the ability to both repress and activate target gene expression. These bipolar transcriptional properties are mediated through the interactions of the receptors with two distinct classes of auxiliary proteins: corepressors and coactivators. This review focuses on how corepressors work together with nuclear receptors to repress gene transcription in the normal organism and on the aberrations in this process that lead to neoplasia and endocrine disorders. The actions of coactivators and the contributions of the same corepressors to the functions of nonreceptor transcription factors are also touched on.
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Affiliation(s)
- Martin L Privalsky
- Section of Microbiology, Division of Biological Sciences, University of California, Davis, California 95616, USA.
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204
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Kinyamu HK, Archer TK. Modifying chromatin to permit steroid hormone receptor-dependent transcription. ACTA ACUST UNITED AC 2004; 1677:30-45. [PMID: 15020043 DOI: 10.1016/j.bbaexp.2003.09.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Revised: 09/24/2003] [Accepted: 09/24/2003] [Indexed: 02/07/2023]
Abstract
Lipophilic hormones, including steroids, exert their physiological effects through binding to high-affinity superfamily of steroid hormone receptor (SR) proteins that function as ligand-dependent DNA binding transcription factors. To date, SR proteins are among a few transcription factors shown to directly interact with higher order chromatin structures to regulate gene expression. To perturb chromatin, SRs employ enzymatic multicomplexes that can either remodel or modify chromatin. Here we examine the current state of knowledge concerning multicomplex chromatin remodeling/modification machines and SR-dependent transcription. We will focus on the role of these protein-protein and chromatin-protein interactions in vivo with the MMTV promoter as a primary model. In addition, we discuss emerging evidence implicating chaperone proteins and proteasome degradation machinery in SR-mediated gene regulation within chromatin.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, PO Box 12233 (MD E4-06), Research Triangle Park, NC 27709, USA
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205
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Schneider R, Bannister AJ, Weise C, Kouzarides T. Direct binding of INHAT to H3 tails disrupted by modifications. J Biol Chem 2004; 279:23859-62. [PMID: 15100215 DOI: 10.1074/jbc.c400151200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N-terminal tails of histones are central to the regulation of chromatin structure. They form a binding platform for multiple protein complexes, which in turn regulate DNA processes such as transcription. Using peptide mass fingerprinting we identified INHAT (inhibitor of acetyltransferases) as a specific histone H3 N-terminal tail-binding complex. INHAT comprises two essential subunits, SET and pp32. We demonstrate that both SET and pp32 bind directly to the N terminus of H3. The binding is differentially affected by various modifications within the H3 N terminus. In particular, single phosphorylations within the H3 tail abrogates binding of INHAT, as does the simultaneous acetylation of multiple lysine residues. The histone modifications that affect INHAT binding are therefore compatible with its known role in transcriptional repression. We suggest that the charge of the histone tail is a major determinant in allowing INHAT to bind chromatin and coordinate the activity of multiple histone acetyltransferases.
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Affiliation(s)
- Robert Schneider
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, United Kingdom
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206
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Métivier R, Penot G, Hübner MR, Reid G, Brand H, Kos M, Gannon F. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 2004; 115:751-63. [PMID: 14675539 DOI: 10.1016/s0092-8674(03)00934-6] [Citation(s) in RCA: 1143] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transcriptional activation of a gene involves an orchestrated recruitment of components of the basal transcription machinery and intermediate factors, concomitant with an alteration in local chromatin structure generated by posttranslational modifications of histone tails and nucleosome remodeling. We provide here a comprehensive picture of events resulting in transcriptional activation of a gene, through evaluating the estrogen receptor-alpha (NR3A1) target pS2 gene promoter in MCF-7 cells. This description integrates chromatin remodeling with a kinetic evaluation of cyclical networks of association of 46 transcription factors with the promoter, as determined by chromatin immunoprecipitation assays. We define the concept of a "transcriptional clock" that directs and achieves the sequential and combinatorial assembly of a transcriptionally productive complex on a promoter. Furthermore, the unanticipated findings of key roles for histone deacetylases and nucleosome-remodeling complexes in limiting transcription implies that transcriptional activation is a cyclical process that requires both activating and repressive epigenetic processes.
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Affiliation(s)
- Raphaël Métivier
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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207
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Xu W, Cho H, Kadam S, Banayo EM, Anderson S, Yates JR, Emerson BM, Evans RM. A methylation-mediator complex in hormone signaling. Genes Dev 2004; 18:144-56. [PMID: 14729568 PMCID: PMC324421 DOI: 10.1101/gad.1141704] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recruitment of coactivators by nuclear hormone receptors (NRs) promotes transcription by subverting chromatin-mediated repression. Although the histone methylation enzyme CARM1 and an ATP-remodeling complex have been individually implicated in nuclear receptor-dependent transcription, neither a functional nor mechanistic linkage between these systems has been identified. In the process of purifying endogenous CARM1-interacting proteins, we identified an associated complex, nucleosomal methylation activator complex (NUMAC), which includes at least eight components of SWI/SNF, including the ATPase BRG1. In the NUMAC complex, the methylase, CARM1, acquires the ability to covalently modify nucleosomal histones, and the directed nucleosome versus free core histone methylation-specificity change is increased dramatically. Reciprocally, CARM1 stimulates the ATPase activity of BRG1, a key component in nucleosome remodeling. In vivo, CARM1 and BRG1 coassemble on an estrogen receptor (ER)-target gene to cooperatively activate ER-dependent transcription. This association of ATP-remodeling factors with HMT CARM1 defines a new component of regulation in the nuclear hormone-signaling pathway.
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Affiliation(s)
- Wei Xu
- Howard Hughes Medical Institute, Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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208
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Histone modifications. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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209
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Tsai CC, Fondell JD. Nuclear Receptor Recruitment of Histone-Modifying Enzymes to Target Gene Promoters. NUCLEAR RECEPTOR COREGULATORS 2004; 68:93-122. [PMID: 15193452 DOI: 10.1016/s0083-6729(04)68003-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nuclear receptors (NRs) compose one of the largest known families of eukaryotic transcription factors and, as such, serve as a paradigm for understanding the fundamental molecular mechanisms of eukaryotic transcriptional regulation. The packaging of eukaryotic genomic DNA into a higher ordered chromatin structure, which generally acts as a barrier to transcription by inhibiting transcription factor accessibility, has a major influence on the mechanisms by which NRs activate or repress gene expression. A major breakthrough in the field's understanding of these mechanisms comes from the recent identification of NR-associated coregulatory factors (i.e., coactivators and corepressors). Although several of these NR cofactors are involved in chromatin remodeling and facilitating the recruitment of the basal transcription machinery, the focus of this chapter is on NR coactivators and corepressors that act to covalently modify the amino-terminal tails of core histones. These modifications (acetylation, methylation, and phosphorylation) are thought to directly affect chromatin structure and?or serve as binding surfaces for other coregulatory proteins. This chapter presents the most current models for NR recruitment of histone-modifying enzymes and then summarizes their functional importance in NR-associated gene expression.
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Affiliation(s)
- Chih-Cheng Tsai
- Department of Physiology and Biophysics, UMDNJ, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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210
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Gilbert N, Gilchrist S, Bickmore WA. Chromatin organization in the mammalian nucleus. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 242:283-336. [PMID: 15598472 DOI: 10.1016/s0074-7696(04)42007-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian cells package their DNA into chromatin and arrange it in the nucleus as chromosomes. In interphase cells chromosomes are organized in a radial distribution with the most gene-dense chromosomes toward the center of the nucleus. Gene transcription, replication, and repair are influenced by the underlying chromatin architecture, which in turn is affected by the formation of chromosome territories. This arrangement in the nucleus presumably facilitates cellular functions to occur in an efficient and ordered fashion and exploring the link between transcription and nuclear organization will be an exciting area of further research.
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Affiliation(s)
- Nick Gilbert
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
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211
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Lachner M, O'Sullivan RJ, Jenuwein T. An epigenetic road map for histone lysine methylation. J Cell Sci 2003; 116:2117-24. [PMID: 12730288 DOI: 10.1242/jcs.00493] [Citation(s) in RCA: 468] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Monika Lachner
- Research Institute of Molecular Pathology, The Vienna Biocenter, Dr Bohrgasse7, A-1030 Vienna, Austria
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212
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Yadav N, Lee J, Kim J, Shen J, Hu MCT, Aldaz CM, Bedford MT. Specific protein methylation defects and gene expression perturbations in coactivator-associated arginine methyltransferase 1-deficient mice. Proc Natl Acad Sci U S A 2003; 100:6464-8. [PMID: 12756295 PMCID: PMC164469 DOI: 10.1073/pnas.1232272100] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Arginine methylation has been implicated in the regulation of gene expression. The coactivator-associated arginine methyltransferase 1 (CARM1/PRMT4) binds the p160 family of steroid receptor coactivators (SRCs). This association enhances transcriptional activation by nuclear receptors. Here, we show that embryos with a targeted disruption of CARM1 are small in size and die perinatally. The methylation of two known CARM1 substrates, poly(A)-binding protein (PABP1) and the transcriptional cofactor p300, was abolished in knockout embryos and cells. However, CARM1-dependent methylation of histone H3 was not observed. Furthermore, estrogen-responsive gene expression was aberrant in Carm1-/- fibroblasts and embryos, thus emphasizing the role of arginine methylation as a transcription activation tag. These findings provide genetic evidence for the essential role of CARM1 in estrogen-mediated transcriptional activation.
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Affiliation(s)
- Neelu Yadav
- Department of Carcinogenesis, University of Texas M. D. Anderson Cancer Center, P.O. Box 389, Smithville 78957, USA
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213
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Affiliation(s)
- Andrew J Bannister
- Wellcome Trust/Cancer Research, United Kingdom Institute, Department of Pathology, University of Cambridge, United Kingdom
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214
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Imhof A. Histone modifications--marks for gene expression? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 544:169-80. [PMID: 14713227 DOI: 10.1007/978-1-4419-9072-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Axel Imhof
- Adolf-Butenandt Institut, University of Munich, Schillerstr. 44, 80336 Muenchen, Germany.
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215
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Lo WS, Henry KW, Schwartz MF, Berger SL. Histone Modification Patterns During Gene Activation. Methods Enzymol 2003; 377:130-53. [PMID: 14979022 DOI: 10.1016/s0076-6879(03)77007-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Affiliation(s)
- Wan-Sheng Lo
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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