101
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Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA. c-Myc regulates transcriptional pause release. Cell 2010; 141:432-45. [PMID: 20434984 PMCID: PMC2864022 DOI: 10.1016/j.cell.2010.03.030] [Citation(s) in RCA: 1033] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/14/2010] [Accepted: 02/21/2010] [Indexed: 12/30/2022]
Abstract
Recruitment of the RNA polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA-binding transcription factors is well recognized as a key regulatory step in gene expression. We report here that promoter-proximal pausing is a general feature of transcription by Pol II in mammalian cells and thus an additional step where regulation of gene expression occurs. This suggests that some transcription factors recruit the transcription apparatus to promoters, whereas others effect promoter-proximal pause release. Indeed, we find that the transcription factor c-Myc, a key regulator of cellular proliferation, plays a major role in Pol II pause release rather than Pol II recruitment at its target genes. We discuss the implications of these results for the role of c-Myc amplification in human cancer.
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Affiliation(s)
- Peter B. Rahl
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Charles Y. Lin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Amy C. Seila
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Ryan A. Flynn
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Scott McCuine
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Christopher B. Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Phillip A. Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
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102
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Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H. DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation. Genes Dev 2009; 23:2765-77. [PMID: 19952111 DOI: 10.1101/gad.1834709] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Transcription elongation factor DSIF/Spt4-Spt5 is capable of promoting and inhibiting RNA polymerase II elongation and is involved in the expression of various genes. While it has been known for many years that DSIF inhibits elongation in collaboration with the negative elongation factor NELF, how DSIF promotes elongation is largely unknown. Here, an activity-based biochemical approach was taken to understand the mechanism of elongation activation by DSIF. We show that the Paf1 complex (Paf1C) and Tat-SF1, two factors implicated previously in elongation control, collaborate with DSIF to facilitate efficient elongation. In human cells, these factors are recruited to the FOS gene in a temporally coordinated manner and contribute to its high-level expression. We also show that elongation activation by these factors depends on P-TEFb-mediated phosphorylation of the Spt5 C-terminal region. A clear conclusion emerging from this study is that a set of elongation factors plays nonredundant, cooperative roles in elongation. This study also shows unambiguously that Paf1C, which is generally thought to have chromatin-related functions, is involve directlyd in elongation control.
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Affiliation(s)
- Yexi Chen
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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103
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Zhou H, Liu Q, Gao Y, Teng M, Niu L. Crystal structure of NusG N-terminal (NGN) domain from Methanocaldococcus jannaschii and its interaction with rpoE''. Proteins 2009; 76:787-93. [PMID: 19475703 DOI: 10.1002/prot.22465] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcription in archaea employs a eukaryotic-type transcription apparatus but uses bacterial-type transcription factors. NusG is one of the few archaeal transcription factors whose orthologs are essential in both bacteria and eukaryotes. Archaeal NusG is composed of only an NusG N-terminal (NGN) domain and a KOW domain, which is similar to bacterial NusG but not to the eukaryotic ortholog, Spt5. However, archaeal NusG was confirmed recently to form a complex with rpoE'' that was similar to the Spt5-Spt4 complex. Thus, archaeal NusG presents hybrid features of Spt5 and bacterial NusG. Here we report the crystal structure of NGN from the archaea Methanocaldococcus jannaschii (MjNGN). MjNGN folds to an alpha-beta-alpha sandwich without the appendant domain of bacterial NGNs, and forms a unique homodimer in crystal and solution. MjNGN alone was found to be sufficient for rpoE'' binding and an MjNGN-rpoE'' model has been constructed by rigid docking.
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Affiliation(s)
- Huihao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
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104
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Hirtreiter A, Grohmann D, Werner F. Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro. Nucleic Acids Res 2009; 38:585-96. [PMID: 19906731 PMCID: PMC2811020 DOI: 10.1093/nar/gkp928] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Transcription elongation in vitro is affected by the interactions between RNA polymerase (RNAP) subunits and the nucleic acid scaffold of the ternary elongation complex (TEC, RNAP-DNA–RNA). We have investigated the role of the RNAP subunits F/E (homologous to eukaryotic RPB4/7) during transcription elongation and termination using a wholly recombinant archaeal RNAP and synthetic nucleic acid scaffolds. The F/E complex greatly stimulates the processivity of RNAP, it enhances the formation of full length products, reduces pausing, and increases transcription termination facilitated by weak termination signals. Mutant variants of F/E that are defective in RNA binding show that these activities correlate with the nucleic acid binding properties of F/E. However, a second RNA-binding independent component also contributes to the stimulatory activities of F/E. In summary, our results suggest that interactions between RNAP subunits F/E and the RNA transcript are pivotal to the molecular mechanisms of RNAP during transcription elongation and termination.
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Affiliation(s)
- Angela Hirtreiter
- Division of Biosciences, Institute for Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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105
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Brookes E, Pombo A. Modifications of RNA polymerase II are pivotal in regulating gene expression states. EMBO Rep 2009; 10:1213-9. [PMID: 19834511 DOI: 10.1038/embor.2009.221] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/14/2009] [Indexed: 01/15/2023] Open
Abstract
The regulation of gene expression programmes is essential for the generation of diverse cell types during development and for adaptation to environmental signals. RNA polymerase II (RNAPII) transcribes genetic information and coordinates the recruitment of accessory proteins that are responsible for the establishment of active chromatin states and transcript maturation. RNAPII is post-translationally modified at active genes during transcription initiation, elongation and termination, and thereby recruits specific histone and RNA modifiers. RNAPII complexes are also located at silent genes in promoter-proximal paused configurations that provide dynamic transcriptional regulation downstream from initiation. In embryonic stem cells, silent developmental regulator genes that are repressed by Polycomb are associated with a form of RNAPII that can elongate through coding regions but that lacks the post-translational modifications that are important for coupling RNA synthesis to co-transcriptional maturation. Here, we discuss the mechanisms through which the transcription of silent genes might be dissociated from productive expression, and the sophisticated interplay between the transcriptional machinery, Polycomb repression and RNA processing.
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Affiliation(s)
- Emily Brookes
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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106
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Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 2009; 16:1128-33. [PMID: 19820712 PMCID: PMC2783620 DOI: 10.1038/nsmb.1666] [Citation(s) in RCA: 355] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 08/11/2009] [Indexed: 12/26/2022]
Abstract
Transcription and splicing must proceed over genomic distances of hundreds of kilobases in many human genes. However, the rates and mechanisms of these processes are poorly understood. We have used the compound 5,6-Dichlorobenzimidazole 1-b-D-ribofuranoside (DRB) that reversibly blocks gene transcription in vivo combined with quantitative RT-PCR to analyze the transcription and RNA processing of several long human genes. We found that the rate of RNA polymerase II transcription over long genomic distances is about 3.8 kb per minute and is nearly the same whether transcribing long introns or exon rich regions. We also determined that co-transcriptional pre-mRNA splicing of U2-dependent introns occurs within 5–10 minutes of synthesis irrespective of intron length between 1 kb and 240 kb. Similarly, U12-dependent introns were co-transcriptionally spliced within 10 minutes of synthesis confirming that these introns are spliced within the nuclear compartment. These results show that the expression of large genes is surprisingly rapid and efficient.
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107
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Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc Natl Acad Sci U S A 2009; 106:18207-12. [PMID: 19820169 DOI: 10.1073/pnas.0910177106] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The kinetics and magnitude of cytokine gene expression are tightly regulated to elicit a balanced response to pathogens and result from integrated changes in transcription and mRNA stability. Yet, how a single microbial stimulus induces peak transcription of some genes (TNFalpha) within minutes whereas others (IP-10) require hours remains unclear. Here, we dissect activation of several lipopolysaccharide (LPS)-inducible genes in macrophages, an essential cell type mediating inflammatory response in mammals. We show that a key difference between the genes is the step of the transcription cycle at which they are regulated. Specifically, at TNFalpha, RNA Polymerase II initiates transcription in resting macrophages, but stalls near the promoter until LPS triggers rapid and transient release of the negative elongation factor (NELF) complex and productive elongation. In contrast, no NELF or polymerase is detectible near the IP-10 promoter before induction, and LPS-dependent polymerase recruitment is rate limiting for transcription. We further demonstrate that this strategy is shared by other immune mediators and is independent of the inducer and signaling pathway responsible for gene activation. Finally, as a striking example of evolutionary conservation, the Drosophila homolog of the TNFalpha gene, eiger, displayed all of the hallmarks of NELF-dependent polymerase stalling. We propose that polymerase stalling ensures the coordinated, timely activation the inflammatory gene expression program from Drosophila to mammals.
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108
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Chen H, Contreras X, Yamaguchi Y, Handa H, Peterlin BM, Guo S. Repression of RNA polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5. PLoS One 2009; 4:e6918. [PMID: 19742326 PMCID: PMC2735033 DOI: 10.1371/journal.pone.0006918] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 07/22/2009] [Indexed: 11/19/2022] Open
Abstract
The stalling of RNA polymerase II (RNAPII) at the promoters of many genes, including developmental regulators, stress-responsive genes, and HIVLTR, suggests transcription elongation as a critical regulatory step in addition to initiation. Spt5, the large subunit of the DRB sensitivity-inducing factor (DSIF), represses or activates RNAPII elongation in vitro. How RNAPII elongation is repressed in vivo is not well understood. Here we report that CTR1 and CTR2CT, the two repeat-containing regions constituting the C-terminus of Spt5, play a redundant role in repressing RNAPII elongation in vivo. First, mis-expression of Spt5 lacking CTR1 or CTR2CT is inconsequential, but mis-expression of Spt5 lacking the entire C-terminus (termed NSpt5) dominantly impairs embryogenesis in zebrafish. Second, NSpt5 de-represses the transcription of hsp70-4 in zebrafish embryos and HIVLTR in cultured human cells, which are repressed at the RNAPII elongation step under non-inducible conditions. Third, NSpt5 directly associates with hsp70-4 chromatin in vivo and increases the occupancy of RNAPII, positive transcription elongation factor b (P-TEFb), histone H3 Lys 4 trimethylation (H3K4Me3), and surprisingly, the negative elongation factor A (NELF-A) at the locus, indicating a direct action of NSpt5 on the elongation repressed locus. Together, these results reveal a dominant activity of NSpt5 to de-repress RNAPII elongation, and suggest that the C-terminus of Spt5 is critical for repressing RNAPII elongation in vivo.
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Affiliation(s)
- Hui Chen
- Department of Biopharmaceutical Sciences, and Programs in Biological Sciences and Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Xavier Contreras
- Departments of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Yuki Yamaguchi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - B. Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Su Guo
- Department of Biopharmaceutical Sciences, and Programs in Biological Sciences and Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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109
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Price DH. Guest Editor's Introduction. Controlling which genes are transcriptionally expressed is key to the generation and maintenance of the repertoire of cell types needed to support the mammalian lifestyle. Methods 2009; 48:321-2. [PMID: 19654069 DOI: 10.1016/j.ymeth.2009.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 07/21/2009] [Indexed: 11/24/2022] Open
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110
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Gilchrist DA, Fargo D, Adelman K. Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods 2009; 48:398-408. [PMID: 19275938 PMCID: PMC3431615 DOI: 10.1016/j.ymeth.2009.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/25/2009] [Accepted: 02/27/2009] [Indexed: 10/21/2022] Open
Abstract
Transcription is a sophisticated multi-step process in which RNA polymerase II (Pol II) transcribes a DNA template into RNA in concert with a broad array of transcription initiation, elongation, capping, termination, and histone modifying factors. Recent global analyses of Pol II distribution have indicated that many genes are regulated during the elongation phase, shedding light on a previously underappreciated mechanism for controlling gene expression. Understanding how various factors regulate transcription elongation in living cells has been greatly aided by chromatin immunoprecipitation (ChIP) studies, which can provide spatial and temporal resolution of protein-DNA binding events. The coupling of ChIP with DNA microarray and high-throughput sequencing technologies (ChIP-chip and ChIP-seq) has significantly increased the scope of ChIP studies and genome-wide maps of Pol II or elongation factor binding sites can now be readily produced. However, while ChIP-chip/ChIP-seq data allow for high-resolution localization of protein-DNA binding sites, they are not sufficient to dissect protein function. Here we describe techniques for coupling ChIP-chip/ChIP-seq with genetic, chemical, and experimental manipulation to obtain mechanistic insight from genome-wide protein-DNA binding studies. We have employed these techniques to discern immature promoter-proximal Pol II from productively elongating Pol II, and infer a critical role for the transition between initiation and full elongation competence in regulating development and gene induction in response to environmental signals.
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Affiliation(s)
- Daniel A. Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - David Fargo
- Library and Information Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Karen Adelman
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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111
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Kireeva M, Nedialkov YA, Gong XQ, Zhang C, Xiong Y, Moon W, Burton ZF, Kashlev M. Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase. Methods 2009; 48:333-45. [PMID: 19398005 PMCID: PMC2721912 DOI: 10.1016/j.ymeth.2009.04.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 04/05/2009] [Accepted: 04/06/2009] [Indexed: 11/16/2022] Open
Abstract
Strategies for assembly and analysis of human, yeast, and bacterial RNA polymerase elongation complexes are described, and methods are shown for millisecond phase kinetic analyses of elongation using rapid chemical quench flow. Human, yeast, and bacterial RNA polymerases function very similarly in NTP-Mg2+ commitment and phosphodiester bond formation. A "running start, two-bond, double-quench" protocol is described and its advantages discussed. These studies provide information about stable NTP-Mg2+ loading, phosphodiester bond synthesis, the processive transition between bonds, and sequence-specific effects on transcription elongation dynamics.
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Affiliation(s)
- Maria Kireeva
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute-Frederick, Bldg. 539, Room 222, Frederick, MD 21702-1201, USA
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112
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Cheng B, Price DH. Isolation and functional analysis of RNA polymerase II elongation complexes. Methods 2009; 48:346-52. [PMID: 19409997 PMCID: PMC2754188 DOI: 10.1016/j.ymeth.2009.02.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 01/23/2009] [Accepted: 02/26/2009] [Indexed: 10/20/2022] Open
Abstract
The elongation phase of transcription by RNA polymerase II (RNAP II) is tightly controlled by a large number of transcription elongation factors. Here we describe experimental approaches for the isolation of RNAPII elongation complexes in vitro and the use of these complexes in the examination of the function of a variety of factors. The methods start with formation of elongation complexes on DNA templates immobilized to paramagnetic beads. Elongation is halted by removing the nucleotides and the ternary elongation complexes are then stripped of factors by a high salt wash. The effect of any factor or mixture of factors on elongation is determined by adding the factor(s) along with nucleotides and observing the change in the pattern of RNAs generated. Association of a factor with elongation complexes can be examined using an elongation complex-electrophoretic mobility shift assay (EC-EMSA) in which elongation complexes that have been liberated from the beads are analyzed on a native gel. Besides being used to dissect the mechanisms of elongation control, these experimental systems are useful for analyzing the function of termination factors and mRNA processing factors. Together these experimental systems permit detailed characterization of the molecular mechanisms of elongation, termination, and mRNA processing factors by providing information concerning both physical interactions with and functional consequences of the factors on RNAPII elongation complexes.
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Affiliation(s)
- Bo Cheng
- Molecular and Cellular Biology Program, University of Iowa, Iowa City IA 52242
| | - David H. Price
- Molecular and Cellular Biology Program, University of Iowa, Iowa City IA 52242
- Department of Biochemistry University of Iowa, Iowa City IA 52242
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113
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Beckerman R, Donner AJ, Mattia M, Peart MJ, Manley JL, Espinosa JM, Prives C. A role for Chk1 in blocking transcriptional elongation of p21 RNA during the S-phase checkpoint. Genes Dev 2009; 23:1364-77. [PMID: 19487575 DOI: 10.1101/gad.1795709] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We reported previously that when cells are arrested in S phase, a subset of p53 target genes fails to be strongly induced despite the presence of high levels of p53. When DNA replication is inhibited, reduced p21 mRNA accumulation is correlated with a marked reduction in transcription elongation. Here we show that ablation of the protein kinase Chk1 rescues the p21 transcription elongation defect when cells are blocked in S phase, as measured by increases in both p21 mRNA levels and the presence of the elongating form of RNA polymerase II (RNAPII) toward the 3' end of the p21 gene. Recruitment of specific elongation and 3' processing factors (DSIF, CstF-64, and CPSF-100) is also restored. While additional components of the RNAPII transcriptional machinery, such as TFIIB and CDK7, are recruited more extensively to the p21 locus after DNA damage than after replication stress, their recruitment is not enhanced by ablation of Chk1. Significantly, ablating Chk2, a kinase closely related in substrate specificity to Chk1, does not rescue p21 mRNA levels during S-phase arrest. Thus, Chk1 has a direct and selective role in the elongation block to p21 observed during S-phase arrest. These findings demonstrate for the first time a link between the replication checkpoint mediated by ATR/Chk1 and the transcription elongation/3' processing machinery.
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Affiliation(s)
- Rachel Beckerman
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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114
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Komori T, Inukai N, Yamada T, Yamaguchi Y, Handa H. Role of human transcription elongation factor DSIF in the suppression of senescence and apoptosis. Genes Cells 2009; 14:343-54. [PMID: 19210550 DOI: 10.1111/j.1365-2443.2008.01273.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DSIF is an evolutionarily conserved, ubiquitously expressed, heterodimeric transcription elongation factor composed of two subunits, Spt4 and Spt5. Previous biochemical studies have shown that DSIF positively and negatively regulates RNA polymerase II elongation in collaboration with other protein factors. While several data suggest that DSIF is a 'general' elongation factor, there is also evidence that DSIF exerts a tissue- and gene-specific function. Here we sought to address the question of whether physiological functions of DSIF are general or specific, by using a sophisticated knockdown approach and gene expression microarray analysis. We found that Spt5 is essential for cell growth of various human cell lines and that Spt5 knockdown causes senescence and apoptosis. However, Spt5 knockdown affects a surprisingly small number of genes. In Spt5 knockdown cells, the p53 signaling pathway is activated and mediates part of the knockdown-induced transcriptional change, but apoptotic cell death occurs in the absence of p53. Structure-function analysis of Spt5 shows that the C-terminal approximately 300 amino acid residues are not required to support cell proliferation. These results suggest that one of the functions of Spt5 is to suppress senescence and apoptosis, and that this function is exerted through its association with Spt4 and Pol II.
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Affiliation(s)
- Toshiharu Komori
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
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115
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Guo M, Xu F, Yamada J, Egelhofer T, Gao Y, Hartzog GA, Teng M, Niu L. Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation. Structure 2008; 16:1649-58. [PMID: 19000817 PMCID: PMC2743916 DOI: 10.1016/j.str.2008.08.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Revised: 08/20/2008] [Accepted: 08/20/2008] [Indexed: 11/30/2022]
Abstract
The Spt4-Spt5 complex is an essential RNA polymerase II elongation factor found in all eukaryotes and important for gene regulation. We report here the crystal structure of Saccharomyces cerevisiae Spt4 bound to the NGN domain of Spt5. This structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4. Mutations that disrupt this interaction disrupt the complex. Residues forming this pivotal interaction are conserved in the archaeal homologs of Spt4 and Spt5, which we show also form a complex. Even though bacteria lack a Spt4 homolog, the NGN domains of Spt5 and its bacterial homologs are structurally similar. Spt4 is located at a position that may help to maintain the functional conformation of the following KOW domains in Spt5. This structural and evolutionary perspective of the Spt4-Spt5 complex and its homologs suggest that it is an ancient, core component of the transcription elongation machinery.
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Affiliation(s)
- Min Guo
- Hefei National Laboratory for Physical Sciences at Microscale and Key Laboratory of Structural Biology, School of Life Sciences, University of Science & Technology of China, 96 Jinzhai Rd, Hefei, Anhui 230027, China
| | - Fei Xu
- Hefei National Laboratory for Physical Sciences at Microscale and Key Laboratory of Structural Biology, School of Life Sciences, University of Science & Technology of China, 96 Jinzhai Rd, Hefei, Anhui 230027, China
| | - Jena Yamada
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz California, 95064, USA
| | - Thea Egelhofer
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz California, 95064, USA
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale and Key Laboratory of Structural Biology, School of Life Sciences, University of Science & Technology of China, 96 Jinzhai Rd, Hefei, Anhui 230027, China
| | - Grant A. Hartzog
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz California, 95064, USA
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and Key Laboratory of Structural Biology, School of Life Sciences, University of Science & Technology of China, 96 Jinzhai Rd, Hefei, Anhui 230027, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and Key Laboratory of Structural Biology, School of Life Sciences, University of Science & Technology of China, 96 Jinzhai Rd, Hefei, Anhui 230027, China
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116
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Cheng B, Price DH. Analysis of factor interactions with RNA polymerase II elongation complexes using a new electrophoretic mobility shift assay. Nucleic Acids Res 2008; 36:e135. [PMID: 18832375 PMCID: PMC2582608 DOI: 10.1093/nar/gkn630] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/09/2008] [Accepted: 09/12/2008] [Indexed: 11/19/2022] Open
Abstract
The elongation phase of transcription by RNA polymerase II (RNAP II) is controlled by a carefully orchestrated series of interactions with both negative and positive factors. However, due to the limitations of current methods and techniques, not much is known about whether and how these proteins physically associate with the engaged polymerases. To gain insight into the detailed mechanisms involved, we established an experimental system for analyzing direct factor interactions to RNAP II elongation complexes on native gels, namely elongation complex electrophoretic mobility shift assay (EC-EMSA). This new assay effectively allowed detection of interactions of TFIIF, TTF2, TFIIS, DSIF and P-TEFb with elongation complexes generated from a natural promoter using an immobilized template. As an application of this assay system, we characterized the association of transcription elongation factor DSIF with RNAP II elongation complexes and discovered that the nascent transcript facilitated recruitment of DSIF. Examples of how the system can be manipulated to address different questions are provided. EC-EMSA should be useful for further investigation of factor interactions with RNAP II elongation complexes.
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Affiliation(s)
- Bo Cheng
- Molecular and Cellular Biology Program and Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - David H. Price
- Molecular and Cellular Biology Program and Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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117
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Gilmour DS. Promoter proximal pausing on genes in metazoans. Chromosoma 2008; 118:1-10. [PMID: 18830703 DOI: 10.1007/s00412-008-0182-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/14/2008] [Accepted: 09/14/2008] [Indexed: 10/21/2022]
Abstract
The past two decades of research into transcriptional control of protein-encoding genes in eukaryotes have focused on regulatory mechanisms that act by controlling the recruitment of Pol II to a gene's promoter. Recent genome-wide analyses of the distribution of Pol II indicates that Pol II is concentrated in the promoter regions of thousands of genes in human and Drosophila cells. In many cases, Pol II may have initiated transcription but paused in the promoter proximal region. Hence, release of Pol II from the promoter region into the body of a gene is now recognized as a common rate-limiting step in the control of gene expression. Notably, most genes with paused Pol II are expressed indicating that the pause can be transient. What causes Pol II to concentrate in the promoter region and how it is released to transcribe a gene are the focus of this review.
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Affiliation(s)
- David S Gilmour
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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118
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Gilchrist DA, Nechaev S, Lee C, Ghosh SKB, Collins JB, Li L, Gilmour DS, Adelman K. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev 2008; 22:1921-33. [PMID: 18628398 PMCID: PMC2492738 DOI: 10.1101/gad.1643208] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 05/21/2008] [Indexed: 11/24/2022]
Abstract
The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including Drosophila Hsp70, mammalian proto-oncogene junB, and HIV RNA. To determine the full spectrum of NELF target genes in Drosophila, we performed a microarray analysis of S2 cells depleted of NELF and discovered that NELF RNAi affects many rapidly inducible genes involved in cellular responses to stimuli. Surprisingly, only one-third of NELF target genes were, like Hsp70, up-regulated by NELF-depletion, whereas the majority of target genes showed decreased expression levels upon NELF RNAi. Our data reveal that the presence of stalled Pol II at this latter group of genes enhances gene expression by maintaining a permissive chromatin architecture around the promoter-proximal region, and that loss of Pol II stalling at these promoters is accompanied by a significant increase in nucleosome occupancy and a decrease in histone H3 Lys 4 trimethylation. These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure.
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Affiliation(s)
- Daniel A. Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Sergei Nechaev
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Chanhyo Lee
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Saikat Kumar B. Ghosh
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jennifer B. Collins
- Microarray Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Leping Li
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - David S. Gilmour
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Karen Adelman
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Microarray Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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119
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Abstract
Recent global analyses have determined that many Drosophila and human genes have engaged polymerase molecules trapped immediately downstream of promoters. These results strongly implicate RNA polymerase II elongation control as a major regulator of differentiation and development.
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Affiliation(s)
- David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52240, USA.
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120
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NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol 2008; 28:3290-300. [PMID: 18332113 DOI: 10.1128/mcb.02224-07] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent analyses of RNA polymerase II (Pol II) revealed that Pol II is concentrated at the promoters of many active and inactive genes. NELF causes Pol II to pause in the promoter-proximal region of the hsp70 gene in Drosophila melanogaster. In this study, genome-wide location analysis (chromatin immunoprecipitation-microarray chip [ChIP-chip] analysis) revealed that NELF is concentrated at the 5' ends of 2,111 genes in Drosophila cells. Permanganate genomic footprinting was used to determine if paused Pol II colocalized with NELF. Forty-six of 56 genes with NELF were found to have paused Pol II. Pol II pauses 30 to 50 nucleotides downstream from transcription start sites. Analysis of DNA sequences in the vicinity of paused Pol II identified a conserved DNA sequence that probably associates with TFIID but detected no evidence of RNA secondary structures or other conserved sequences that might directly control elongation. ChIP-chip experiments indicate that GAGA factor associates with 39% of the genes that have NELF. Surprisingly, NELF associates with almost one-half of the most highly expressed genes, indicating that NELF is not necessarily a repressor of gene expression. NELF-associated pausing of Pol II might be an obligatory but sometimes transient checkpoint during the transcription cycle.
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121
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Cojocaru M, Jeronimo C, Forget D, Bouchard A, Bergeron D, Côte P, Poirier GG, Greenblatt J, Coulombe B. Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J 2008; 409:139-47. [PMID: 17848138 PMCID: PMC4498901 DOI: 10.1042/bj20070751] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The functions ascribed to the mammalian GTFs (general transcription factors) during the various stages of the RNAPII (RNA polymerase II) transcription reaction are based largely on in vitro studies. To gain insight as to the functions of the GTFs in living cells, we have analysed the genomic location of several human GTF and RNAPII subunits carrying a TAP (tandem-affinity purification) tag. ChIP (chromatin immunoprecipitation) experiments using anti-tag beads (TAP-ChIP) allowed the systematic localization of the tagged factors. Enrichment of regions located close to the TIS (transcriptional initiation site) versus further downstream TRs (transcribed regions) of nine human genes, selected for the minimal divergence of their alternative TIS, were analysed by QPCR (quantitative PCR). We show that, in contrast with reports using the yeast system, human TFIIF (transcription factor IIF) associates both with regions proximal to the TIS and with further downstream TRs, indicating an in vivo function in elongation for this GTF. Unexpectedly, we found that the Rpb7 subunit of RNAPII, known to be required only for the initiation phase of transcription, remains associated with the polymerase during early elongation. Moreover, ChIP experiments conducted under stress conditions suggest that Rpb7 is involved in the stabilization of transcribing polymerase molecules, from initiation to late elongation stages. Together, our results provide for the first time a general picture of GTF function during the RNAPII transcription reaction in live mammalian cells and show that TFIIF and Rpb7 are involved in both early and late transcriptional stages.
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Affiliation(s)
- Marilena Cojocaru
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Célia Jeronimo
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Diane Forget
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Dominique Bergeron
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Pierre Côte
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
| | - Guy G. Poirier
- Centre Hospitalier Universitaire de QC, Université Laval, Québec, QC, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, Canada H2W 1R7
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122
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Inhibition of the cyclin-dependent kinases at the beginning of human cytomegalovirus infection specifically alters the levels and localization of the RNA polymerase II carboxyl-terminal domain kinases cdk9 and cdk7 at the viral transcriptosome. J Virol 2007; 82:394-407. [PMID: 17942543 DOI: 10.1128/jvi.01681-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We previously reported that defined components of the host transcription machinery are recruited to human cytomegalovirus immediate-early (IE) transcription sites, including cdk9 and cdk7 (S. Tamrakar, A. J. Kapasi, and D. H. Spector, J. Virol. 79:15477-15493, 2005). In this report, we further document the complexity of this site, referred to as the transcriptosome, through identification of additional resident proteins, including viral UL69 and cellular cyclin T1, Brd4, histone deacetylase 1 (HDAC1), and HDAC2. To examine the role of cyclin-dependent kinases (cdks) in the establishment of this site, we used roscovitine, a specific inhibitor of cdk1, cdk2, cdk7, and cdk9, that alters processing of viral IE transcripts and inhibits expression of viral early genes. In the presence of roscovitine, IE2, cyclin T1, Brd4, HDAC1, and HDAC2 accumulate at the transcriptosome. However, accumulation of cdk9 and cdk7 was specifically inhibited. Roscovitine treatment also resulted in decreased levels of cdk9 and cdk7 RNA. There was a corresponding reduction in cdk9 protein but only a modest decrease in cdk7 protein. However, overexpression of cdk9 does not compensate for the effects of roscovitine on cdk9 localization or viral gene expression. Delaying the addition of roscovitine until 8 h postinfection prevented all of the observed effects of the cdk inhibitor. These data suggest that IE2 and multiple cellular factors needed for viral RNA synthesis accumulate within the first 8 h at the viral transcriptosome and that functional cdk activity is required for the specific recruitment of cdk7 and cdk9 during this time interval.
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