51
|
Iyer VR. Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol 2012; 22:250-6. [PMID: 22421062 DOI: 10.1016/j.tcb.2012.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/07/2012] [Accepted: 02/10/2012] [Indexed: 11/18/2022]
Abstract
Nucleosomes are an essential component of eukaryotic chromosomes. The impact of nucleosomes is seen not just on processes that directly access the genome, such as transcription, but also on an evolutionary timescale. Recent studies in various organisms have provided high-resolution maps of nucleosomes throughout the genome. Computational analysis, in conjunction with many other kinds of data, has shed light on several aspects of nucleosome biology. Nucleosomes are positioned by several means, including intrinsic sequence biases, by stacking against a fixed barrier, by DNA-binding proteins and by chromatin remodelers. These studies underscore the important organizational role of nucleosomes in all eukaryotic genomes. This paper reviews recent genomic studies that have shed light on the determinants of nucleosome positioning and their impact on the genome.
Collapse
Affiliation(s)
- Vishwanath R Iyer
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA.
| |
Collapse
|
52
|
Crisucci EM, Arndt KM. The Roles of the Paf1 Complex and Associated Histone Modifications in Regulating Gene Expression. GENETICS RESEARCH INTERNATIONAL 2011; 2011. [PMID: 22408743 PMCID: PMC3296560 DOI: 10.4061/2011/707641] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The conserved Paf1 complex (Paf1C) carries out multiple functions during transcription by RNA polymerase (pol) II, and these functions are required for the proper expression of numerous genes in yeast and metazoans. In the elongation stage of the transcription cycle, the Paf1C associates with RNA pol II, interacts with other transcription elongation factors, and facilitates modifications to the chromatin template. At the end of elongation, the Paf1C plays an important role in the termination of RNA pol II transcripts and the recruitment of proteins required for proper RNA 3′ end formation. Significantly, defects in the Paf1C are associated with several human diseases. In this paper, we summarize current knowledge on the roles of the Paf1C in RNA pol II transcription.
Collapse
Affiliation(s)
- Elia M Crisucci
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | |
Collapse
|
53
|
Abstract
It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by "opening" or "closing" chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts.
Collapse
Affiliation(s)
- Magdalena Murawska
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | | |
Collapse
|
54
|
Stevens JR, O'Donnell AF, Perry TE, Benjamin JJR, Barnes CA, Johnston GC, Singer RA. FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation. PLoS One 2011; 6:e25644. [PMID: 22022426 PMCID: PMC3192111 DOI: 10.1371/journal.pone.0025644] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/06/2011] [Indexed: 02/03/2023] Open
Abstract
Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer. FACT mediates transcription-linked nucleosome disassembly and also nucleosome reassembly in the wake of the RNA polymerase II transcription complex, and in this way maintains the repression of ‘cryptic’ promoters found within some genes. Here we focus on a novel mutant version of the yeast FACT subunit Spt16 that supplies essential Spt16 activities but impairs transcription-linked nucleosome reassembly in dominant fashion. This Spt16 mutant protein also has genetic effects that are recessive, which we used to show that certain Spt16 activities collaborate with histone acetylation and the activities of a Bur-kinase/Spt4–Spt5/Paf1C pathway that facilitate transcription elongation. These collaborating activities were opposed by the actions of Rpd3S, a histone deacetylase that restores a repressive chromatin environment in a transcription-linked manner. Spt16 activity paralleling that of HirC, a co-repressor of histone gene expression, was also found to be opposed by Rpd3S. Our findings suggest that Spt16, the Bur/Spt4–Spt5/Paf1C pathway, and normal histone abundance and/or stoichiometry, in mutually cooperative fashion, facilitate nucleosome disassembly during transcription elongation. The recessive nature of these effects of the mutant Spt16 protein on transcription-linked nucleosome disassembly, contrasted to its dominant negative effect on transcription-linked nucleosome reassembly, indicate that mutant FACT harbouring the mutant Spt16 protein competes poorly with normal FACT at the stage of transcription-linked nucleosome disassembly, but effectively with normal FACT for transcription-linked nucleosome reassembly. This functional difference is consistent with the idea that FACT association with the transcription elongation complex depends on nucleosome disassembly, and that the same FACT molecule that associates with an elongation complex through nucleosome disassembly is retained for reassembly of the same nucleosome.
Collapse
Affiliation(s)
- Jennifer R. Stevens
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Allyson F. O'Donnell
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Troy E. Perry
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jeremy J. R. Benjamin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christine A. Barnes
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gerald C. Johnston
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Richard A. Singer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
| |
Collapse
|
55
|
Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton G, Owen-Hughes T. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011; 333:1758-60. [PMID: 21940898 PMCID: PMC3428865 DOI: 10.1126/science.1206097] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here, we show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicate that adenosine triphosphate-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.
Collapse
Affiliation(s)
- Triantaffyllos Gkikopoulos
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Pieta Schofield
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marina Pinskaya
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Jane Mellor
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Michaela Smolle
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Jerry L. Workman
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Geoffrey Barton
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| |
Collapse
|
56
|
Buratowski S, Kim T. The role of cotranscriptional histone methylations. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2011; 75:95-102. [PMID: 21447819 DOI: 10.1101/sqb.2010.75.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The carboxy-terminal domain (CTD) of the RNA polymerase II subunit Rpb1 undergoes dynamic phosphorylation, with different phosphorylation sites predominating at different stages of transcription. Our laboratory studies show how various mRNA-processing and chromatin-modifying enzymes interact with the phosphorylated CTD to efficiently produce mRNAs. The H3K36 methyltransferase Set2 interacts with CTD carrying phosphorylations characteristic of downstream elongation complexes, and the resulting cotranscriptional H3K36 methylation targets the Rpd3S histone deacetylase to downstream transcribed regions. Although positively correlated with gene activity, this pathway actually inhibits transcription elongation as well as initiation from cryptic promoters within genes. During early elongation, CTD serine 5 phosphorylation helps recruit the H3K4 methyltransferase complex containing Set1. Within 5' transcribed regions, cotranscriptional H3K4 dimethylation (H3K4me2) by Set1 recruits the deacetylase complex Set3C. Finally, H3K4 trimethylation at the most promoter-proximal nucleosomes is thought to stimulate transcription by promoting histone acetylation by complexes containing the ING/Yng PHD finger proteins. Surprisingly, the Rpd3L histone deacetylase complex, normally a transcription repressor, may also recognize H3K4me3. Together, the cotranscriptional histone methylations appear to function primarily to distinguish active promoter regions, which are marked by high levels of acetylation and nucleosome turnover, from the deacetylated, downstream transcribed regions of genes.
Collapse
Affiliation(s)
- S Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | |
Collapse
|
57
|
Yap KL, Zhou MM. Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription. Biochemistry 2011; 50:1966-80. [PMID: 21288002 DOI: 10.1021/bi101885m] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone methylation recognition is accomplished by a number of evolutionarily conserved protein domains, including those belonging to the methylated lysine-binding Royal family of structural folds. One well-known member of the Royal family, the chromodomain, is found in the HP1/chromobox and CHD subfamilies of proteins, in addition to a small number of other proteins that are involved in chromatin remodeling and gene transcriptional silencing. Here we discuss the structure and function of the chromodomain within these proteins as methylated histone lysine binders and how the functions of these chromodomains can be modulated by additional post-translational modifications or binding to nucleic acids.
Collapse
Affiliation(s)
- Kyoko L Yap
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1677, New York, New York 10065, United States
| | | |
Collapse
|
58
|
Morettini S, Tribus M, Zeilner A, Sebald J, Campo-Fernandez B, Scheran G, Wörle H, Podhraski V, Fyodorov DV, Lusser A. The chromodomains of CHD1 are critical for enzymatic activity but less important for chromatin localization. Nucleic Acids Res 2010; 39:3103-15. [PMID: 21177652 PMCID: PMC3082874 DOI: 10.1093/nar/gkq1298] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular motor protein CHD1 has been implicated in the regulation of transcription and in the transcription-independent genome-wide incorporation of H3.3 into paternal chromatin in Drosophila melanogaster. A key feature of CHD1 is the presence of two chromodomains, which can bind to histone H3 methylated at lysine 4 and thus might serve to recruit and/or maintain CHD1 at the chromatin. Here, we describe genetic and biochemical approaches to the study of the Drosophila CHD1 chromodomains. We found that overall localization of CHD1 on polytene chromosomes does not appreciably change in chromodomain-mutant flies. In contrast, the chromodomains are important for transcription-independent activities of CHD1 during early embryonic development as well as for transcriptional regulation of several heat shock genes. However, neither CHD1 nor its chromodomains are needed for RNA polymerase II localization and H3K4 methylation but loss of CHD1 decreases transcription-induced histone eviction at the Hsp70 gene in vivo. Chromodomain mutations negatively affect the chromatin assembly activities of CHD1 in vitro, and they appear to be involved in linking the ATP-dependent motor to the chromatin assembly function of CHD1.
Collapse
Affiliation(s)
- Stefano Morettini
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Fritz-Pregl Strasse 3, 6020 Innsbruck, Austria
| | | | | | | | | | | | | | | | | | | |
Collapse
|
59
|
DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS Genet 2010; 6:e1001173. [PMID: 21060864 PMCID: PMC2965751 DOI: 10.1371/journal.pgen.1001173] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/21/2010] [Indexed: 01/17/2023] Open
Abstract
Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP–Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain. Acetylation of histone N-terminal tails occurs on nucleosomes as a gene is being transcribed, therefore helping the RNA polymerase II traveling through nucleosomes. Histone acetylation, however, has to be reversed in the wake of the polymerase in order to prevent transcription from initiating at the wrong place. Rpd3S is a histone deacetylase complex recruited to transcribed genes to fulfill this function. The Rpd3S complex contains a chromodomain that is thought to be responsible for the association of Rpd3S with genes since it interacts with methylated histones, a feature found on transcribed genes. Here, we show that the recruitment of Rpd3S to transcribed genes does not require histone methylation. We found that Rpd3S is actually recruited by a mechanism implicating the phosphorylation of the RNA polymerase II C-terminal domain and that this mechanism is regulated by a transcriptional elongation complex called DSIF. We propose that the interaction between the Rpd3S chromodomain and methylated histones helps anchoring the deacetylase to its substrate only after it has been recruited to the elongating RNA polymerase.
Collapse
|
60
|
Tirosh I, Sigal N, Barkai N. Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol 2010; 11:R49. [PMID: 20459718 PMCID: PMC2898075 DOI: 10.1186/gb-2010-11-5-r49] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/24/2010] [Accepted: 05/10/2010] [Indexed: 12/02/2022] Open
Abstract
In yeast, the chromatin remodeler Isw1 shifts nucleosomes from mid-coding, to more 5’ regions of genes and may regulate transcriptional elongation. Background The positions of nucleosomes along eukaryotic DNA are defined by the local DNA sequence and are further tuned by the activity of chromatin remodelers. While the genome-wide effect of most remodelers has not been described, recent studies in Saccharomyces cerevisiae have shown that Isw2 prevents ectopic expression of anti-sense and suppressed transcripts at gene ends. Results We examined the genome-wide function of the Isw2 homologue, Isw1, by mapping nucleosome positioning in S. cerevisiae and Saccharomyces paradoxus strains deleted of ISW1. We found that Isw1 functions primarily within coding regions of genes, consistent with its putative role in transcription elongation. Upon deletion of ISW1, mid-coding nucleosomes were shifted upstream (towards the 5' ends) in about half of the genes. Isw1-dependent shifts were correlated with trimethylation of H3K79 and were enriched at genes with internal cryptic initiation sites. Conclusions Our results suggest a division of labor between Isw1 and Isw2, whereby Isw2 maintains repressive chromatin structure at gene ends while Isw1 has a similar function at mid-coding regions. The differential specificity of the two remodelers may be specified through interactions with particular histone marks.
Collapse
Affiliation(s)
- Itay Tirosh
- Department of Molecular genetics, Weizmann Institute of Science, Herzl street, Rehovot 76100, Israel.
| | | | | |
Collapse
|