951
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LeRoy G, Rickards B, Flint S. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell 2008; 30:51-60. [PMID: 18406326 PMCID: PMC2387119 DOI: 10.1016/j.molcel.2008.01.018] [Citation(s) in RCA: 295] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 10/18/2007] [Accepted: 01/25/2008] [Indexed: 12/18/2022]
Abstract
Posttranslational histone modifications are crucial for the modulation of chromatin structure and regulation of transcription. Bromodomains present in many chromatin-associated proteins recognize acetylated lysines in the unstructured N-terminal regions of histones. Here, we report that the double bromodomain proteins Brd2 and Brd3 associate preferentially in vivo with hyperacetylated chromatin along the entire lengths of transcribed genes. Brd2- and Brd3-associated chromatin is significantly enriched in H4K5, H4K12, and H3K14 acetylation and contains relatively little dimethylated H3K9. Both Brd2 and Brd3 allowed RNA polymerase II to transcribe through nucleosomes in a defined transcription system. Such activity depended on specific histone H4 modifications known to be recognized by the Brd proteins. We also demonstrate that Brd2 has intrinsic histone chaperone activity and is required for transcription of the cyclin D1 gene in vivo. These data identify proteins that render nucleosomes marked by acetylation permissive to the passage of elongating RNA polymerase II.
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Affiliation(s)
| | | | - S.J. Flint
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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952
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Krueger BJ, Jeronimo C, Roy BB, Bouchard A, Barrandon C, Byers SA, Searcey CE, Cooper JJ, Bensaude O, Cohen ÉA, Coulombe B, Price DH. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res 2008; 36:2219-29. [PMID: 18281698 PMCID: PMC2367717 DOI: 10.1093/nar/gkn061] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/30/2008] [Accepted: 01/30/2008] [Indexed: 02/02/2023] Open
Abstract
Regulation of the elongation phase of RNA polymerase II transcription by P-TEFb is a critical control point for gene expression. The activity of P-TEFb is regulated, in part, by reversible association with one of two HEXIMs and the 7SK snRNP. A recent proteomics survey revealed that P-TEFb and the HEXIMs are tightly connected to two previously-uncharacterized proteins, the methyphosphate capping enzyme, MEPCE, and a La-related protein, LARP7. Glycerol gradient sedimentation analysis of lysates from cells treated with P-TEFb inhibitors, suggested that the 7SK snRNP reorganized such that LARP7 and 7SK remained associated after P-TEFb and HEXIM1 were released. Immunodepletion of LARP7 also depleted most of the 7SK regardless of the presence of P-TEFb, HEXIM or hnRNP A1 in the complex. Small interfering RNA knockdown of LARP7 in human cells decreased the steady-state level of 7SK, led to an initial increase in free P-TEFb and increased Tat transactivation of the HIV-1 LTR. Knockdown of LARP7 or 7SK ultimately caused a decrease in total P-TEFb protein levels. Our studies have identified LARP7 as a 7SK-binding protein and suggest that free P-TEFb levels are determined by a balance between release from the large form and reduction of total P-TEFb.
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Affiliation(s)
- Brian J. Krueger
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Célia Jeronimo
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Bibhuti Bhusan Roy
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Annie Bouchard
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Charlotte Barrandon
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Sarah A. Byers
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Courtney E. Searcey
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Jeffrey J. Cooper
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Olivier Bensaude
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Éric A. Cohen
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - Benoit Coulombe
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
| | - David H. Price
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, Iowa, USA, Gene Transcription and Proteomics Laboratory, Institut de recherches cliniques de Montréal, Human Retrovirology Laboratory, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada H2W 1R7, UMR 8541 CNRS, Ecole Normale Supérieure, 75230 Paris Cedex 05, France and Biochemistry Department, University of Iowa, Iowa City, Iowa, USA
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953
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Thompson M, Chandrasekaran R. Thermodynamic analysis of acetylation-dependent Pb1 bromodomain-histone H3 interactions. Anal Biochem 2008; 374:304-12. [PMID: 18191465 PMCID: PMC2693409 DOI: 10.1016/j.ab.2007.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 12/23/2022]
Abstract
An acetyl-histone peptide library was used to determine the thermodynamic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains interact with histones by binding acetylated lysines. The bromodomain used in this study, BrD3, is derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin remodeling complex. Steady-state fluorescence anisotropy was used to examine the variations in specificity and affinity that drive molecular recognition. Temperature and salt concentration dependence studies demonstrate that the hydrophobic effect is the primary driving force, consistent with lysine acetylation being required for binding. An electrostatic effect was observed in only two complexes where the acetyl-lysine was adjacent to an arginine. The large change in heat capacity determined for the specific complex suggests that the dehydrated BrD3-histone interface forms a tightly bound, high-affinity complex with the target site. These explorations into the thermodynamic driving forces that confer acetylation site-dependent BrD3-histone interactions improve our understanding of how individual bromodomains work in isolation. Furthermore, this work will permit the development of hypotheses regarding how the native Pb1, and the broader class of bromodomain proteins, directs multisubunit chromatin remodeling complexes to specific acetyl-nucleosome sites in vivo.
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Affiliation(s)
- Martin Thompson
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA.
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954
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He N, Jahchan NS, Hong E, Li Q, Bayfield MA, Maraia RJ, Luo K, Zhou Q. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol Cell 2008; 29:588-99. [PMID: 18249148 PMCID: PMC6239424 DOI: 10.1016/j.molcel.2008.01.003] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 10/03/2007] [Accepted: 01/02/2008] [Indexed: 11/18/2022]
Abstract
The general transcription factor P-TEFb stimulates RNA polymerase II elongation and cotranscriptional processing of pre-mRNA. Contributing to a functional equilibrium important for growth control, a reservoir of P-TEFb is maintained in an inactive snRNP where 7SK snRNA is a central scaffold. Here, we identify PIP7S as a La-related protein stably associated with and required for 7SK snRNP integrity. PIP7S binds and stabilizes nearly all the nuclear 7SK via 3' -UUU-OH, leading to the sequestration and inactivation of P-TEFb. This function requires its La domain and intact C terminus. The latter is frequently deleted in human tumors due to microsatellite instability-associated mutations. Consistent with the tumor suppressor role of a Drosophila homolog of PIP7S, loss of PIP7S function shifts the P-TEFb equilibrium toward the active state, disrupts epithelial differentiation, and causes P-TEFb-dependent malignant transformation. Through PIP7S modulation of P-TEFb, our data thus link a general elongation factor to growth control and tumorigenesis.
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Affiliation(s)
- Nanhai He
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nadine S. Jahchan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Eunmee Hong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qiang Li
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Mark A. Bayfield
- Intramural Research Program, Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Intramural Research Program, Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kunxin Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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955
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Suzuki T, Mochizuki K, Goda T. Histone H3 modifications and Cdx-2 binding to the sucrase-isomaltase (SI) gene is involved in induction of the gene in the transition from the crypt to villus in the small intestine of rats. Biochem Biophys Res Commun 2008; 369:788-93. [PMID: 18313392 DOI: 10.1016/j.bbrc.2008.02.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 02/22/2008] [Indexed: 10/22/2022]
Abstract
Expression of the sucrase-isomaltase (SI) gene is induced in cells transitioning from the crypt to the villus of rat jejunum. In the present study, we revealed by ChIP assay using a cryostat sectioning technique that binding of the di-acetylated histone H3 at lysine 9/14 and the transcriptional factor Cdx-2 to the promoter region on the SI gene, as well as mRNA, increased in the transient process. Additionally, di-/tri-methylation of histone H3 at lysine 9/14 on the promoter region of the SI gene rapidly decreased with increasing mRNA. These results suggest that induction of the SI gene during the transition from the crypt to the villi is associated with changes in histone H3 modifications from methylation at lysine 9 to di-acetylation at lysine 9/14, as well as increased binding of Cdx-2 to the SI promoter region.
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Affiliation(s)
- Takuji Suzuki
- Laboratory of Nutritional Physiology, The University of Shizuoka, Graduate School of Nutritional and Environmental Sciences and Global COE, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan
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956
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Crawford NPS, Walker RC, Lukes L, Officewala JS, Williams RW, Hunter KW. The Diasporin Pathway: a tumor progression-related transcriptional network that predicts breast cancer survival. Clin Exp Metastasis 2008; 25:357-69. [PMID: 18301994 PMCID: PMC2410042 DOI: 10.1007/s10585-008-9146-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 02/06/2008] [Indexed: 12/21/2022]
Abstract
Microarray expression signature analyses have suggested that extracellular matrix (ECM) gene dysregulation is predictive of metastasis in both mouse mammary tumorigenesis and human breast cancer. We have previously demonstrated that such ECM dysregulation is influenced by hereditary germline-encoded variation. To identify novel metastasis efficiency modifiers, we performed expression QTL (eQTL) mapping in recombinant inbred mice by characterizing genetic loci modulating metastasis-predictive ECM gene expression. Three reproducible eQTLs were observed on chromosomes 7, 17 and 18. Candidate genes were identified by correlation analyses and known associations with metastasis. Seven candidates were identified (Ndn, Pi16, Luc7l, Rrp1b, Brd4, Centd3 and Csf1r). Stable transfection of the highly metastatic Mvt-1 mouse mammary tumor cell line with expression vectors encoding each candidate modulated metastasis-predictive ECM gene expression. Implantation of these cells into mice demonstrated that candidate gene ectopic expression impacts tumor progression. Gene expression analyses facilitated the construction of a transcriptional network that we have termed the 'Diasporin Pathway'. This pathway contains the seven candidates, as well as metastasis-predictive ECM genes and metastasis suppressors. Brd4 and Rrp1b appear to form a central node within this network, which likely is a consequence of their physical interaction with the metastasis efficiency modifier Sipa1. Furthermore, we demonstrate that the microarray gene expression signatures induced by activation of ECM eQTL genes in the Mvt-1 cell line can be used to accurately predict survival in a human breast cancer cohort. These data imply that the Diasporin Pathway may be an important nexus in tumor progression in both mice and humans.
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Affiliation(s)
- Nigel P S Crawford
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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957
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Mochizuki K, Nishiyama A, Jang MK, Dey A, Ghosh A, Tamura T, Natsume H, Yao H, Ozato K. The bromodomain protein Brd4 stimulates G1 gene transcription and promotes progression to S phase. J Biol Chem 2008; 283:9040-8. [PMID: 18223296 DOI: 10.1074/jbc.m707603200] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Brd4 is a bromodomain protein that binds to acetylated chromatin. It regulates cell growth, although the underlying mechanism has remained elusive. Brd4 has also been shown to control transcription of viral genes, whereas its role in transcription of cellular genes has not been fully elucidated. Here we addressed the role of Brd4 in cell growth and transcription using a small hairpin (sh) RNA approach. The Brd4 shRNA vector stably knocked down Brd4 protein expression by approximately 90% in NIH3T3 cells and mouse embryonic fibroblasts. Brd4 knockdown cells were growth impaired and grew more slowly than control cells. When synchronized by serum starvation and released, Brd4 knockdown cells were arrested at G(1), whereas control cells progressed to S phase. In microarray analysis, although numerous genes were up-regulated during G(1) in control cells, many of these G(1) genes were not up-regulated in Brd4 knockdown cells. Reintroduction of Brd4 rescued expression of these G(1) genes in Brd4 knockdown cells, allowing cells to progress toward S phase. Chromatin immunoprecipitation analysis showed that Brd4 was recruited to the promoters of these G(1) genes during G(0)-G(1) progression. Furthermore, Brd4 recruitment coincided with increased binding of Cdk9, a component of P-TEFb and RNA polymerase II to these genes. Brd4 recruitment was low to absent at genes not affected by Brd4 shRNA. The results indicate that Brd4 stimulates G(1) gene expression by binding to multiple G(1) gene promoters in a cell cycle-dependent manner.
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Affiliation(s)
- Kazuki Mochizuki
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892, USA
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958
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Toda K, Yamamoto D, Fumoto M, Ikeshita N, Herningtyas EH, Iida K, Takahashi Y, Kaji H, Chihara K, Okimura Y. Involvement of mPOU (Brn-5), a class VI POU protein, in the gene expression of Pit-1 as well as PRL. Mol Cell Endocrinol 2008; 280:20-9. [PMID: 17933456 DOI: 10.1016/j.mce.2007.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2006] [Revised: 09/01/2007] [Accepted: 09/05/2007] [Indexed: 11/27/2022]
Abstract
PRL is mainly expressed in the pituitary and its gene expression is regulated by a variety of transcription factors including Pit-1. Brn-5 is a transcription factor that binds to Pit-1 binding elements and stimulates PRL reporter gene expression. In this study, the role of Brn-5 was examined. RNA interference (RNAi) against Brn-5 leaded to reduction in PRL content of GH3 cells, indicating endogenous Brn-5 may play a role in PRL gene expression. Furthermore Brn-5 RNAi decreased Pit-1 mRNA. Transfection of expression vectors for mPOU (human ortholog of Brn-5) modestly but significantly stimulated activities of PRL-Luc and Pit-1-Luc reporter genes in GH3 and HEK 293 cells. In addition, mPOU showed synergistic action with Pit-1 and CBP on PRL-Luc expression. mPOU-FL, a splicing variant of mPOU, showed weaker activity than mPOU. Chip assay suggested binding of mPOU to PRL and Pit-1 promoters of genomic DNA. Taken together, these results suggest that mPOU (Brn-5) enhances PRL gene expression directly in association with Pit-1 and CBP, and indirectly via the activation of Pit-1 gene expression.
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Affiliation(s)
- Keizo Toda
- Department of Basic Allied Medicine, Kobe University School of Medicine, 7-10-2, Tomogaoka, Suma-ku, Kobe 654-0142, Japan
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959
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Abstract
Protein interactions are a fundamental mechanism for the generation of biological regulatory specificity. The study of protein interactions in living cells is of particular significance because the interactions that occur in a particular cell depend on the full complement of proteins present in the cell and the external stimuli that influence the cell. Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the association between two nonfluorescent fragments of a fluorescent protein when they are brought in proximity to each other by an interaction between proteins fused to the fragments. Numerous protein interactions have been visualized using the BiFC assay in many different cell types and organisms. The BiFC assay is technically straightforward and can be performed using standard molecular biology and cell culture reagents and a regular fluorescence microscope or flow cytometer.
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Affiliation(s)
- Tom K Kerppola
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0650, USA.
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960
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Abstract
Papillomaviruses establish persistent infection in the dividing, basal epithelial cells of the host. The viral genome is maintained as a circular, double-stranded DNA, extrachromosomal element within these cells. Viral genome amplification occurs only when the epithelial cells differentiate and viral particles are shed in squames that are sloughed from the surface of the epithelium. There are three modes of replication in the papillomavirus life cycle. Upon entry, in the establishment phase, the viral genome is amplified to a low copy number. In the second maintenance phase, the genome replicates in dividing cells at a constant copy number, in synchrony with the cellular DNA. And finally, in the vegetative or productive phase, the viral DNA is amplified to a high copy number in differentiated cells and is destined to be packaged in viral capsids. This review discusses the cis elements and protein factors required for each stage of papillomavirus replication.
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Affiliation(s)
- Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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961
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Abstract
A variety of experimental methods have been developed for the analysis of protein interactions. The majority of these methods either require disruption of the cells to detect molecular interactions or rely on indirect detection of the protein interaction. The bimolecular fluorescence complementation (BiFC) assay provides a direct approach for the visualization of molecular interactions in living cells and organisms. The BiFC approach is based on the facilitated association between two fragments of a fluorescent protein when the fragments are brought together by an interaction between proteins fused to the fragments. The BiFC approach has been used for visualization of interactions among a variety of structurally diverse interaction partners in many different cell types. It enables detection of transient complexes as well as complexes formed by a subpopulation of the interaction partners. It is essential to include negative controls in each experiment in which the interface between the interaction partners has been mutated or deleted. The BiFC assay has been adapted for simultaneous visualization of multiple protein complexes in the same cell and the competition for shared interaction partners. A ubiquitin-mediated fluorescence complementation assay has also been developed for visualization of the covalent modification of proteins by ubiquitin family peptides. These fluorescence complementation assays have a great potential to illuminate a variety of biological interactions in the future.
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Affiliation(s)
- Tom K Kerppola
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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962
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Hartzog GA, Tamkun JW. A new role for histone tail modifications in transcription elongation. Genes Dev 2007; 21:3209-13. [DOI: 10.1101/gad.1628707] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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963
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Brd4 recruits P-TEFb to chromosomes at late mitosis to promote G1 gene expression and cell cycle progression. Mol Cell Biol 2007; 28:967-76. [PMID: 18039861 DOI: 10.1128/mcb.01020-07] [Citation(s) in RCA: 303] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brd4, a bromodomain protein capable of interacting with acetylated histones, is implicated in transmitting epigenetic memory through mitosis. It also functions as an associated factor and positive regulator of P-TEFb, a Cdk9-cyclin T1 heterodimer that stimulates transcriptional elongation by phosphorylating RNA polymerase II. In the present study, experiments were performed to determine whether these two functions of Brd4 are interrelated and, if so, how they may impact cell cycle progression. Our data demonstrate that while the P-TEFb level remains constant, the Brd4-P-TEFb interaction increases dramatically in cells progressing from late mitosis to early G(1). Concurrently, P-TEFb is recruited to chromosomes, beginning around mid- to late anaphase and before nuclear envelope/lamina formation and nuclear import of other general transcription factors. Importantly, the recruitment of P-TEFb depends on Brd4. Abrogation of this process through Brd4 knockdown reduces the binding of P-TEFb to and expression of key G(1) and growth-associated genes, leading to G(1) cell cycle arrest and apoptosis. Because P-TEFb is synonymous with productive elongation, its recruitment by Brd4 to chromosomes at late mitosis may indicate those genes whose active transcription status must be preserved across cell division.
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964
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Differential chromatin looping regulates CD4 expression in immature thymocytes. Mol Cell Biol 2007; 28:907-12. [PMID: 18039856 DOI: 10.1128/mcb.00909-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Runx1 binds the silencer and represses CD4 transcription in immature thymocytes. In this study, using looping chromatin immunoprecipitation and chromatin conformation capture assays, we demonstrated that interactions between Runx1 and positive elongation factor b (P-TEFb) appose the silencer and enhancer in CD4-negative thymoma cells and double-negative immature thymocytes. This chromatin loop decoys P-TEFb away from the promoter, thus preventing RNA polymerase II from elongating on the CD4 gene. In the absence of Runx1 on the silencer, P-TEFb interacts with the transcription complex, forming a different chromatin loop between the enhancer and the promoter, which leads to the expression of the CD4 gene in CD4-positive hybridoma cells and double-positive thymocytes. Moreover, the knockdown of CycT1 from P-TEFb abolishes both of these chromatin loops. Finally, the selective removal and restoration of Runx1 causes rapid interchanges between these chromatin loops, which reveals the plasticity of this regulatory circuit. Thus, differential looping and decoying of P-TEFb away from the promoter mediate active repression of the CD4 gene during thymocyte development.
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965
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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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966
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Ivaldi MS, Karam CS, Corces VG. Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in Drosophila. Genes Dev 2007; 21:2818-31. [PMID: 17942706 DOI: 10.1101/gad.1604007] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Drosophila JIL-1 kinase is known to phosphorylate histone H3 at Ser10 (H3S10) during interphase. This modification is associated with transcriptional activation, but its function is not well understood. Here we present evidence suggesting that JIl-1-mediated H3S10 phosphorylation is dependent on chromatin remodeling by the brahma complex and is required during early transcription elongation to release RNA polymerase II (Pol II) from promoter-proximal pausing. JIL-1 localizes to transcriptionally active regions and is required for activation of the E75A ecdysone-responsive and hsp70 heat-shock genes. The heat-shock transcription factor, the promoter-paused form of Pol II (Pol IIo(ser5)), and the pausing factor DSIF (DRB sensitivity-inducing factor) are still present at the hsp70 loci in JIL-1-null mutants, whereas levels of the elongating form of Pol II (Pol IIo(ser2)) and the P-TEFb kinase are dramatically reduced. These observations suggest that phosphorylation of H3S10 takes place after transcription initiation but prior to recruitment of P-TEFb and productive elongation. Western analyses of global levels of both forms of Pol II further suggest that JIL-1 plays a general role in early elongation of a broad range of genes. Taken together, the results introduce H3S10 phosphorylation by JIL-1 as a hallmark of early transcription elongation in Drosophila.
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Affiliation(s)
- M Soledad Ivaldi
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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967
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BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells. Oncogene 2007; 27:2237-42. [PMID: 17934517 DOI: 10.1038/sj.onc.1210852] [Citation(s) in RCA: 331] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An unusual group of carcinomas, here termed nuclear protein in testis (NUT) midline carcinomas (NMC), are characterized by translocations that involve NUT, a novel gene on chromosome 15. In about 2/3rds of cases, NUT is fused to BRD4 on chromosome 19. Using a candidate gene approach, we identified two NMCs harboring novel rearrangements that result in the fusion of NUT to BRD3 on chromosome 9. The BRD3-NUT fusion gene encodes a protein composed of two tandem chromatin-binding bromodomains, an extra-terminal domain, a bipartite nuclear localization sequence, and almost the entirety of NUT that is highly homologous to BRD4-NUT. The function of NUT is unknown, but here we show that NUT contains nuclear localization and export sequences that promote nuclear-cytoplasmic shuttling via a leptomycin-sensitive pathway. In contrast, BRD3-NUT and BRD4-NUT are strictly nuclear, implying that the BRD moiety retains NUT in the nucleus via interactions with chromatin. Consistent with this idea, FRAP studies show that BRD4, BRD4-NUT and BRD3-NUT have significantly slower rates of lateral nuclear diffusion than that of NUT. To investigate the functional role of BRD-NUT fusion proteins in NMCs, we investigated the effects of siRNA-induced BRD3-NUT and BRD4-NUT withdrawal. Silencing of these proteins in NMC cell lines resulted in squamous differentiation and cell cycle arrest. Together, these data suggest that BRD-NUT fusion proteins contribute to carcinogenesis by associating with chromatin and interfering with epithelial differentiation.
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968
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Contreras X, Barboric M, Lenasi T, Peterlin BM. HMBA releases P-TEFb from HEXIM1 and 7SK snRNA via PI3K/Akt and activates HIV transcription. PLoS Pathog 2007; 3:1459-69. [PMID: 17937499 PMCID: PMC2014796 DOI: 10.1371/journal.ppat.0030146] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 08/21/2007] [Indexed: 01/27/2023] Open
Abstract
Hexamethylene bisacetamide (HMBA) is a potent inducer of cell differentiation and HIV production in chronically infected cells. However, its mechanism of action remains poorly defined. In this study, we demonstrate that HMBA activates transiently the PI3K/Akt pathway, which leads to the phosphorylation of HEXIM1 and the subsequent release of active positive transcription elongation factor b (P-TEFb) from its transcriptionally inactive complex with HEXIM1 and 7SK small nuclear RNA (snRNA). As a result, P-TEFb is recruited to the HIV promoter to stimulate transcription elongation and viral production. Despite the continuous presence of HMBA, the released P-TEFb reassembles rapidly with 7SK snRNA and HEXIM1. In contrast, a mutant HEXIM1 protein that cannot be phosphorylated and released from P-TEFb and 7SK snRNA via the PI3K/Akt pathway antagonizes this HMBA-mediated induction of viral production. Thus, our studies reveal how HIV transcription is induced by HMBA and suggest how modifications in the equilibrium between active and inactive P-TEFb could contribute to cell differentiation.
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Affiliation(s)
- 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
| | - Matjaz Barboric
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Tina Lenasi
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - 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
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969
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Young TM, Tsai M, Tian B, Mathews MB, Pe'ery T. Cellular mRNA activates transcription elongation by displacing 7SK RNA. PLoS One 2007; 2:e1010. [PMID: 17925858 PMCID: PMC1995758 DOI: 10.1371/journal.pone.0001010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 09/11/2007] [Indexed: 11/24/2022] Open
Abstract
The positive transcription elongation factor P-TEFb is a pivotal regulator of gene expression in higher cells. Originally identified in Drosophila, attention was drawn to human P-TEFb by the discovery of its role as an essential cofactor for HIV-1 transcription. It is recruited to HIV transcription complexes by the viral transactivator Tat, and to cellular transcription complexes by a plethora of transcription factors. P-TEFb activity is negatively regulated by sequestration in a complex with the HEXIM proteins and 7SK RNA. The mechanism of P-TEFb release from the inhibitory complex is not known. We report that P-TEFb-dependent transcription from the HIV promoter can be stimulated by the mRNA encoding HIC, the human I-mfa domain-containing protein. The 3′-untranslated region of HIC mRNA is necessary and sufficient for this action. It forms complexes with P-TEFb and displaces 7SK RNA from the inhibitory complex in cells and cell extracts. A 314-nucleotide sequence near the 3′ end of HIC mRNA has full activity and contains a predicted structure resembling the 3′-terminal hairpin of 7SK that is critical for P-TEFb binding. This represents the first example of a cellular mRNA that can regulate transcription via P-TEFb. Our findings offer a rationale for 7SK being an RNA transcriptional regulator and suggest a practical means for enhancing gene expression.
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Affiliation(s)
- Tara M. Young
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Michael Tsai
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, Newark, New Jersey, United States of America
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Michael B. Mathews
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, Newark, New Jersey, United States of America
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- * To whom correspondence should be addressed. E-mail: (MM); (TP)
| | - Tsafi Pe'ery
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, Newark, New Jersey, United States of America
- Department of Medicine, New Jersey Medical School, Newark, New Jersey, United States of America
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- * To whom correspondence should be addressed. E-mail: (MM); (TP)
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970
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Abstract
Histone lysine acetylation is central to epigenetic control of gene transcription. The bromodomain, found in chromatin-associated proteins and histone acetyltranferases, functions as the sole protein module known to bind acetyl-lysine motifs. Recent structural and functional analyses of bromodomains' recognition of lysine-acetylated peptides derived from major acetylation sites in histones and cellular proteins provide new insights into differences in ligand binding selectivity as well as unifying features of histone recognition by the bromodomains. These new findings highlight the functional importance of bromodomain/acetyl-lysine binding as a pivotal mechanism for regulating protein-protein interactions in histone-directed chromatin remodeling and gene transcription. These new studies also support the notion that functional diversity of a conserved bromodomain structural fold is achieved by evolutionary changes of structurally flexible amino-acid sequences in the ligand binding site such as the ZA and BC loops.
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Affiliation(s)
- S Mujtaba
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
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971
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Huang H, Zhang J, Shen W, Wang X, Wu J, Wu J, Shi Y. Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC STRUCTURAL BIOLOGY 2007; 7:57. [PMID: 17848202 PMCID: PMC2065866 DOI: 10.1186/1472-6807-7-57] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 09/12/2007] [Indexed: 11/26/2022]
Abstract
Background Brd2 is a transcriptional regulator and belongs to BET family, a less characterized novel class of bromodomain-containing proteins. Brd2 contains two tandem bromodomains (BD1 and BD2, 46% sequence identity) in the N-terminus and a conserved motif named ET (extra C-terminal) domain at the C-terminus that is also present in some other bromodomain proteins. The two bromodomains have been shown to bind the acetylated histone H4 and to be responsible for mitotic retention on chromosomes, which is probably a distinctive feature of BET family proteins. Although the crystal structure of Brd2 BD1 is reported, no structure features have been characterized for Brd2 BD2 and its interaction with acetylated histones. Results Here we report the solution structure of human Brd2 BD2 determined by NMR. Although the overall fold resembles the bromodomains from other proteins, significant differences can be found in loop regions, especially in the ZA loop in which a two amino acids insertion is involved in an uncommon π-helix, termed πD. The helix πD forms a portion of the acetyl-lysine binding site, which could be a structural characteristic of Brd2 BD2 and other BET bromodomains. Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that the binding was with low affinity (2.9 mM) and in fast exchange. Using NMR and mutational analysis, we identified several residues important for the Brd2 BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the specific recognition of acetylated histone codes by Brd2 BD2. Conclusion Brd2 BD2 is monomeric in solution and dynamically interacts with H4-AcK12. The additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five aspartate residues form a negatively charged collar that serves as a secondary binding site for H4-AcK12. We suggest that Brd2 BD1 and BD2 may possess distinctive roles and cooperate to regulate Brd2 functions. The structure basis of Brd2 BD2 will help to further characterize the functions of Brd2 and its BET members.
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Affiliation(s)
- Hongda Huang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Weiqun Shen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xingsheng Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jiawen Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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972
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Ogura Y, Mochizuki K, Goda T. Induction of histone acetylation on the CRBPII gene in perinatal rat small intestine. Biochim Biophys Acta Gen Subj 2007; 1770:1289-96. [PMID: 17692466 DOI: 10.1016/j.bbagen.2007.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 06/03/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
The expression of genes associated with lipid and vitamin A metabolism is elevated when the small intestinal mucosa is maturing rapidly during the perinatal period. We have previously reported that cellular retinol-binding protein type II (CRBPII) mRNA levels rise abruptly in the rat small intestine during this period. In this study, we examined whether the acetylation of histones H3 and H4 is involved in the intestinal expression of CRBPII during the perinatal stage. The expression of cyclin D1 and cyclin B1 genes, which are markers of cell proliferation, decreased markedly during the perinatal period, whereas expression of CRBPII as well as villin, a marker of intestinal maturation, increased rapidly. Using a ChIP assay, we showed rapid induction of acetylation of the histones H3 and H4 which interacted with the promoter/enhancer region of the CRBPII gene at this time. The binding of CBP and p300, which have histone acetyltransferase activity, as well as binding of retinoid X receptor alpha (RXRalpha) increased on the CRBPII promoter/enhancer region during the perinatal period. These results suggest that CRBPII gene expression during the perinatal period is associated with abrupt acetylation of histones H3 and H4 followed by the binding of CBP/p300 and RXRalpha.
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Affiliation(s)
- Yuko Ogura
- Laboratory of Nutritional Physiology and COE Program in the 21st Century, University of Shizuoka School of Food and Nutritional Sciences, 52-1 Yada, Shizuoka 422-8526, Japan
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973
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Dames SA, Schönichen A, Schulte A, Barboric M, Peterlin BM, Grzesiek S, Geyer M. Structure of the Cyclin T binding domain of Hexim1 and molecular basis for its recognition of P-TEFb. Proc Natl Acad Sci U S A 2007; 104:14312-7. [PMID: 17724342 PMCID: PMC1955226 DOI: 10.1073/pnas.0701848104] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hexim1 is a cellular protein that associates with the positive transcription elongation factor b (P-TEFb) to regulate RNA polymerase II elongation of nascent mRNA transcripts. It directly binds to Cyclin T1 of P-TEFb and inhibits the kinase activity of Cdk9, leading to an arrest of transcription elongation. Here, we report the solution structure of the Cyclin T binding domain (TBD) of Hexim1 that forms a parallel coiled-coil homodimer composed of two segments and a preceding alpha helix that folds back onto the first coiled-coil unit. NMR titration, fluorescence, and immunoprecipitation experiments revealed the binding interface to Cyclin T1, which covers a large surface on the first coiled-coil segment. Electrostatic interactions between an acidic patch on Hexim1 and positively charged residues of Cyclin T1 drive the complex formation that is confirmed by mutagenesis data on Hexim1 mediated transcription regulation in cells. Thus, our studies provide structural insights how Hexim1 recognizes the Cyclin T1 subunit of P-TEFb, which is a key step toward the regulation of transcription elongation.
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Affiliation(s)
- Sonja A. Dames
- *Department of Structural Biology, Biozentrum Basel, University of Basel, 4003 Basel, Switzerland
- To whom correspondence may be addressed. E-mail: and
| | - André Schönichen
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, 44227 Dortmund, Germany; and
| | - Antje Schulte
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, 44227 Dortmund, Germany; and
| | - Matjaz Barboric
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California, San Francisco, CA 94143
| | - B. Matija Peterlin
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California, San Francisco, CA 94143
| | - Stephan Grzesiek
- *Department of Structural Biology, Biozentrum Basel, University of Basel, 4003 Basel, Switzerland
| | - Matthias Geyer
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, 44227 Dortmund, Germany; and
- To whom correspondence may be addressed. E-mail: and
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974
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Barrandon C, Bonnet F, Nguyen VT, Labas V, Bensaude O. The transcription-dependent dissociation of P-TEFb-HEXIM1-7SK RNA relies upon formation of hnRNP-7SK RNA complexes. Mol Cell Biol 2007; 27:6996-7006. [PMID: 17709395 PMCID: PMC2168891 DOI: 10.1128/mcb.00975-07] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The positive transcription elongation factor P-TEFb controls the elongation of transcription by RNA polymerase II. P-TEFb is inactivated upon binding to HEXIM1 or HEXIM2 proteins associated with a noncoding RNA, 7SK. In response to the inhibition of transcription, 7SK RNA, as well as HEXIM proteins, is released by an unknown mechanism and P-TEFb is activated. New partners of 7SK RNA were searched for as potential players in this feedback process. A subset of heterogeneous ribonuclear proteins, hnRNPs Q and R and hnRNPs A1 and A2, were thus identified as major 7SK RNA-associated proteins. The degree of association of 7SK RNA with these hnRNPs increased when P-TEFb-HEXIM1-7SK was dissociated following the inhibition of transcription or HEXIM1 knockdown. This finding suggested that 7SK RNA shuttles from HEXIM1-P-TEFb complexes to hnRNPs. The transcription-dependent dissociation of P-TEFb-HEXIM1-7SK complexes was attenuated when both hnRNPs A1 and A2 were knocked down by small interfering RNA. As hnRNPs are known to interact transiently with RNA while it is synthesized, hnRNPs released from nascent transcripts may trap 7SK RNA and thereby contribute to the activation of P-TEFb.
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Affiliation(s)
- Charlotte Barrandon
- UMR 8541 CNRS, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
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975
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Bisgrove DA, Mahmoudi T, Henklein P, Verdin E. Conserved P-TEFb-interacting domain of BRD4 inhibits HIV transcription. Proc Natl Acad Sci U S A 2007; 104:13690-5. [PMID: 17690245 PMCID: PMC1959443 DOI: 10.1073/pnas.0705053104] [Citation(s) in RCA: 314] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have identified a conserved region in the C-terminal domain of bromodomain-containing protein 4 (BRD4) that mediates its specific interaction with positive transcription elongation factor b (P-TEFb). This domain is highly conserved in testis-specific bromodomain protein (BRDT) and Drosophila fs(1)h. Both BRDT and fs(1)h specifically interact with P-TEFb in mammalian cells, and this interaction depends on their C-terminal domains. Overexpression of the BRD4 P-TEFb-interacting domain disrupts the interaction between the HIV transactivator Tat and P-TEFb and suppresses the ability of Tat to transactivate the HIV promoter. Incubation of cells with a synthetic peptide containing the C-terminal domain of BRD4 interferes with transactivation of the HIV promoter by the Tat protein.
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Affiliation(s)
- Dwayne A. Bisgrove
- *Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158; and
| | - Tokameh Mahmoudi
- *Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158; and
| | - Peter Henklein
- Institut für Biochemie, Charité-Universitaetsmedizin, D-10117 Berlin, Germany
| | - Eric Verdin
- *Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158; and
- To whom correspondence should be addressed at:
Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, CA 94158. E-mail:
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976
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Cho WK, Zhou M, Jang MK, Huang K, Jeong SJ, Ozato K, Brady JN. Modulation of the Brd4/P-TEFb interaction by the human T-lymphotropic virus type 1 tax protein. J Virol 2007; 81:11179-86. [PMID: 17686863 PMCID: PMC2045532 DOI: 10.1128/jvi.00408-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Positive transcription elongation factor (P-TEFb), which is composed of CDK9 and cyclin T1, plays an important role in cellular and viral gene expression. Our lab has recently demonstrated that P-TEFb is required for Tax transactivation of the viral long terminal repeat (LTR). P-TEFb is found in two major complexes: the inactive form, which is associated with inhibitory subunits 7SK snRNA and HEXIM1, and the active form, which is associated with, at least in part, Brd4. In this study, we analyzed the effect of Brd4 on human T-lymphotropic virus type 1 (HTLV-1) transcription. Overexpression of Brd4 repressed Tax transactivation of the HTLV-1 LTR in a dose-dependent manner. In vitro binding studies suggest that Tax and Brd4 compete for binding to P-TEFb through direct interaction with cyclin T1. Tax interacts with cyclin T1 amino acids 426 to 533, which overlaps the region responsible for Brd4 binding. In vivo, overexpression of Tax decreased the amount of 7SK snRNA associated with P-TEFb and stimulates serine 2 phosphorylation of the RNA polymerase II carboxyl-terminal domain, suggesting that Tax regulates the functionality of P-TEFb. Our results suggest the possibility that Tax may compete and functionally substitute for Brd4 in P-TEFb regulation.
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Affiliation(s)
- Won-Kyung Cho
- Virus Tumor Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Medlars Dr., Bldg. 41, Rm. B201, Bethesda, MD 20892, USA
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977
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Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Thérien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, Coulombe B. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell 2007; 27:262-274. [PMID: 17643375 PMCID: PMC4498903 DOI: 10.1016/j.molcel.2007.06.027] [Citation(s) in RCA: 361] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 05/16/2007] [Accepted: 06/22/2007] [Indexed: 01/20/2023]
Abstract
We have performed a survey of soluble human protein complexes containing components of the transcription and RNA processing machineries using protein affinity purification coupled to mass spectrometry. Thirty-two tagged polypeptides yielded a network of 805 high-confidence interactions. Remarkably, the network is significantly enriched in proteins that regulate the formation of protein complexes, including a number of previously uncharacterized proteins for which we have inferred functions. The RNA polymerase II (RNAP II)-associated proteins (RPAPs) are physically and functionally associated with RNAP II, forming an interface between the enzyme and chaperone/scaffolding proteins. BCDIN3 is the 7SK snRNA methylphosphate capping enzyme (MePCE) present in an snRNP complex containing both RNA processing and transcription factors, including the elongation factor P-TEFb. Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery.
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Affiliation(s)
- Célia Jeronimo
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diane Forget
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Annie Bouchard
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Qintong Li
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Gordon Chua
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Christian Poitras
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Cynthia Thérien
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Dominique Bergeron
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Sylvie Bourassa
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Benoit Chabot
- Département de microbiologie et infectiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guy G Poirier
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Timothy R Hughes
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 2B4, Canada
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Benoit Coulombe
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
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978
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Schweiger MR, Ottinger M, You J, Howley PM. Brd4-independent transcriptional repression function of the papillomavirus e2 proteins. J Virol 2007; 81:9612-22. [PMID: 17626100 PMCID: PMC2045424 DOI: 10.1128/jvi.00447-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The papillomavirus E2 protein is a critical viral regulatory protein with transcription, DNA replication, and genome maintenance functions. We have previously identified the cellular bromodomain protein Brd4 as a major E2-interacting protein and established that it participates in tethering bovine papillomavirus type 1 E2 and viral genomes to host cell mitotic chromosomes. We have also shown that Brd4 mediates E2-dependent transcriptional activation, which is strongly inhibited by the disruption of E2/Brd4 binding as well as by short hairpin RNA (shRNA) knockdown of Brd4 expression levels. Since several mutants harboring single amino acid substitutions within the E2 transactivation domain that are defective for both transcriptional transactivation and Brd4 binding are also defective for transcriptional repression, we examined the role of Brd4 in E2 repression of the human papillomavirus E6/E7 promoter. Surprisingly, in a variety of in vivo assays, including transcription reporter assays, HeLa cell proliferation and colony reduction assays, and Northern blot analyses, neither blocking of the binding of E2 to Brd4 nor shRNA knockdown of Brd4 affected the E2 repression function. Our study provides evidence for a Brd4-independent mechanism of E2-mediated repression and suggests that different cellular factors must be involved in E2-mediated transcriptional activation and repression functions.
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MESH Headings
- Amino Acid Substitution
- Cell Cycle Proteins
- Chromosomes, Human/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Regulation, Viral/physiology
- Genome, Viral/physiology
- HeLa Cells
- Humans
- Mitosis/physiology
- Mutation, Missense
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oncogene Proteins, Viral/biosynthesis
- Oncogene Proteins, Viral/genetics
- Promoter Regions, Genetic/physiology
- RNA, Small Interfering/genetics
- RNA, Small Interfering/pharmacology
- Repressor Proteins/antagonists & inhibitors
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic/physiology
- Transcriptional Activation/physiology
- Virus Replication/physiology
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Affiliation(s)
- Michal-Ruth Schweiger
- Harvard Medical School, Department of Pathology, 77 Avenue Louis Pasteur, Room 950, Boston, MA 02115, USA
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979
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Biglione S, Byers SA, Price JP, Nguyen VT, Bensaude O, Price DH, Maury W. Inhibition of HIV-1 replication by P-TEFb inhibitors DRB, seliciclib and flavopiridol correlates with release of free P-TEFb from the large, inactive form of the complex. Retrovirology 2007; 4:47. [PMID: 17625008 PMCID: PMC1948018 DOI: 10.1186/1742-4690-4-47] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 07/11/2007] [Indexed: 01/07/2023] Open
Abstract
Background The positive transcription elongation factor, P-TEFb, comprised of cyclin dependent kinase 9 (Cdk9) and cyclin T1, T2 or K regulates the productive elongation phase of RNA polymerase II (Pol II) dependent transcription of cellular and integrated viral genes. P-TEFb containing cyclin T1 is recruited to the HIV long terminal repeat (LTR) by binding to HIV Tat which in turn binds to the nascent HIV transcript. Within the cell, P-TEFb exists as a kinase-active, free form and a larger, kinase-inactive form that is believed to serve as a reservoir for the smaller form. Results We developed a method to rapidly quantitate the relative amounts of the two forms based on differential nuclear extraction. Using this technique, we found that titration of the P-TEFb inhibitors flavopiridol, DRB and seliciclib onto HeLa cells that support HIV replication led to a dose dependent loss of the large form of P-TEFb. Importantly, the reduction in the large form correlated with a reduction in HIV-1 replication such that when 50% of the large form was gone, HIV-1 replication was reduced by 50%. Some of the compounds were able to effectively block HIV replication without having a significant impact on cell viability. The most effective P-TEFb inhibitor flavopiridol was evaluated against HIV-1 in the physiologically relevant cell types, peripheral blood lymphocytes (PBLs) and monocyte derived macrophages (MDMs). Flavopiridol was found to have a smaller therapeutic index (LD50/IC50) in long term HIV-1 infectivity studies in primary cells due to greater cytotoxicity and reduced efficacy at blocking HIV-1 replication. Conclusion Initial short term studies with P-TEFb inhibitors demonstrated a dose dependent loss of the large form of P-TEFb within the cell and a concomitant reduction in HIV-1 infectivity without significant cytotoxicity. These findings suggested that inhibitors of P-TEFb may serve as effective anti-HIV-1 therapies. However, longer term HIV-1 replication studies indicated that these inhibitors were more cytotoxic and less efficacious against HIV-1 in the primary cell cultures.
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Affiliation(s)
- Sebastian Biglione
- Interdisciplinary Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA, USA
- CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Byers
- Interdisciplinary Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA, USA
- Oregon Health & Science University, Department of Molecular and Medical Genetics, Portland, OR 97239, USA
| | - Jason P Price
- Department of Microbiology, University of Iowa, Iowa City, IA, USA
| | - Van Trung Nguyen
- Laboratoire de Regulation de l'Expression Genetique, Ecole Normale Superieure, Paris, France
| | - Olivier Bensaude
- Laboratoire de Regulation de l'Expression Genetique, Ecole Normale Superieure, Paris, France
| | - David H Price
- Interdisciplinary Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - Wendy Maury
- Interdisciplinary Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA, USA
- Department of Microbiology, University of Iowa, Iowa City, IA, USA
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980
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Van Herreweghe E, Egloff S, Goiffon I, Jády BE, Froment C, Monsarrat B, Kiss T. Dynamic remodelling of human 7SK snRNP controls the nuclear level of active P-TEFb. EMBO J 2007; 26:3570-80. [PMID: 17611602 PMCID: PMC1949012 DOI: 10.1038/sj.emboj.7601783] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 06/11/2007] [Indexed: 11/08/2022] Open
Abstract
The 7SK small nuclear RNA (snRNA) regulates RNA polymerase II transcription elongation by controlling the protein kinase activity of the positive transcription elongation factor b (P-TEFb). In cooperation with HEXIM1, the 7SK snRNA sequesters P-TEFb into the kinase-inactive 7SK/HEXIM1/P-TEFb small nuclear ribonucleoprotein (snRNP), and thereby, controls the nuclear level of active P-TEFb. Here, we report that a fraction of HeLa 7SK snRNA that is not involved in 7SK/HEXIM1/P-TEFb formation, specifically interacts with RNA helicase A (RHA), heterogeneous nuclear ribonucleoprotein A1 (hnRNP), A2/B1, R and Q proteins. Inhibition of cellular transcription induces disassembly of 7SK/HEXIM1/P-TEFb and at the same time, increases the level of 7SK snRNPs containing RHA, hnRNP A1, A2/B1, R and Q. Removal of transcription inhibitors restores the original levels of the 7SK/HEXIM1/P-TEFb and '7SK/hnRNP' complexes. 7SK/HEXIM1/P-TEFb snRNPs containing mutant 7SK RNAs lacking the capacity for binding hnRNP A1, A2, R and Q are resistant to stress-induced disassembly, indicating that recruitment of the novel 7SK snRNP proteins is essential for disruption of 7SK/HEXIM1/P-TEFb. Thus, we propose that the nuclear level of active P-TEFb is controlled by dynamic and reversible remodelling of 7SK snRNP.
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Affiliation(s)
- Elodie Van Herreweghe
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, Toulouse, France
| | - Sylvain Egloff
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, Toulouse, France
| | - Isabelle Goiffon
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, Toulouse, France
| | - Beáta E Jády
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, Toulouse, France
| | - Carine Froment
- Plate-forme protéomique, Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse, France
| | - Bernard Monsarrat
- Plate-forme protéomique, Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, Toulouse, France
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, Toulouse, France
- Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
- Laboratoire de Biologie Moléculaire Eucaryote, UMR5099, CNRS-Université Paul Sabatier, IFR109, 118 route de Narbonne, Toulouse Cedex 9, 31062, France. Tel.: +33 561 335 907; Fax: +33 561 335 886; E-mail:
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981
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Williams SA, Greene WC. Regulation of HIV-1 latency by T-cell activation. Cytokine 2007; 39:63-74. [PMID: 17643313 PMCID: PMC2063506 DOI: 10.1016/j.cyto.2007.05.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 05/23/2007] [Accepted: 05/30/2007] [Indexed: 01/06/2023]
Abstract
HIV-infected patients harbor approximately 10(5)-10(6) memory CD4 T-cells that contain fully integrated but transcriptionally silent HIV proviruses. While small in number, these latently infected cells form a drug-insensitive reservoir that importantly contributes to the life-long persistence of HIV despite highly effective antiviral therapy. In tissue culture, latent HIV proviruses can be activated when their cellular hosts are exposed to select proinflammatory cytokines or their T-cell receptors are ligated. However, due to a lack of potency and/or dose-limiting toxicity, attempts to purge virus from this latent reservoir in vivo with immune-activating agents, such as anti-CD3 antibodies and IL-2, have failed. A deeper understanding of the molecular underpinnings of HIV latency is clearly required, including determining whether viral latency is actively reinforced by transcriptional repressors, defining which inducible host transcription factors most effectively antagonize latency, and elucidating the role of chromatin in viral latency. Only through such an improved understanding will it be possible to identify combination therapies that might allow complete purging of the latent reservoir and to realize the difficult and elusive goal of complete eradication of HIV in infected patients.
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Affiliation(s)
- Samuel A. Williams
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94141-1230
- Department of Physiology, University of California, San Francisco, CA, 94141-1230
- Department of Medicine, University of California, San Francisco, CA, 94141-1230
| | - Warner C. Greene
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, 94141-1230
- Department of Medicine, University of California, San Francisco, CA, 94141-1230
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94141-1230
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982
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Sharma M, George AA, Singh BN, Sahoo NC, Rao KVS. Regulation of Transcript Elongation through Cooperative and Ordered Recruitment of Cofactors. J Biol Chem 2007; 282:20887-96. [PMID: 17535807 DOI: 10.1074/jbc.m701420200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We studied the regulation of murine CD80, a gene whose basal transcriptional status was characterized by the presence of a stalled RNA polymerase II complex on the promoter-proximal region. Stimulus-induced activation of productive elongation involved a complex interplay of regulated events that included a synergy between ordered cofactor recruitment. This cascade of recruitments was initiated through the engagement of transcription factor NF-kappaB, leading to the temporal association of histone acetyltransferases and the consequent selective acetylation of a transcription start site downstream nucleosome. This in turn culminated into the nucleosomal association of Brd4-associated P-TEFb, a protein complex containing kinase specific for serine 2 of Rbp 1, the largest subunit of the carboxyl-terminal domain of RNA polymerase II. The consequent phosphorylation of serine 2 residues in CTD by CDK9 in the P-TEFb complex then facilitated escape of polymerase II into the productive elongation phase. Thus, the cooperative mechanisms that integrate between independent pathways characterize regulation of the elongation step of transcription, thereby providing another level at which specificity of gene regulation can be achieved.
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Affiliation(s)
- Manish Sharma
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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983
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He WJ, Chen R, Yang Z, Zhou Q. Regulation of two key nuclear enzymatic activities by the 7SK small nuclear RNA. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:301-11. [PMID: 17381310 DOI: 10.1101/sqb.2006.71.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
7SK is a highly conserved small nuclear RNA (snRNA) in vertebrates. Since its discovery in 1968, little had been known about its function until recently, when 7SK was found to associate with the general transcription elongation factor P-TEFb. Together with the HEXIM1 protein, 7SK sequesters P-TEFb into a kinase-inactive complex, where it mediates HEXIM1's inhibition of P-TEFb. This helps maintain P-TEFb in a functional equilibrium to control transcription, cell growth, and differentiation. Although highly abundant, only a small fraction of 7SK is P-TEFb-bound. Using affinity purification, we have identified APOBEC3C as another 7SK-associated protein. As a member of the APOBEC family that functions in diverse processes through deaminating cytosine in DNA, it is unclear how APOBEC3C's activity is controlled to prevent its mutations of genomic DNA. We show that most of APOBEC3C interact with about half of nuclear 7SK, which suppresses APOBEC3C's deaminase activity and sequesters APOBEC3C in the nucleolus where it could be at a safe distance from most genomic sequences. Because the DNA substrate-binding site in APOBEC3C differs from the region for 7SK binding, 7SK does not act as a substrate competitor in inhibiting APOBEC3C. The demonstration of 7SK's suppression of yet another enzyme besides P-TEFb suggests a general role for this RNA in regulating key nuclear functions.
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Affiliation(s)
- W-J He
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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984
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Sedore SC, Byers SA, Biglione S, Price JP, Maury WJ, Price DH. Manipulation of P-TEFb control machinery by HIV: recruitment of P-TEFb from the large form by Tat and binding of HEXIM1 to TAR. Nucleic Acids Res 2007; 35:4347-58. [PMID: 17576689 PMCID: PMC1935001 DOI: 10.1093/nar/gkm443] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Basal transcription of the HIV LTR is highly repressed and requires Tat to recruit the positive transcription elongation factor, P-TEFb, which functions to promote the transition of RNA polymerase II from abortive to productive elongation. P-TEFb is found in two forms in cells, a free, active form and a large, inactive complex that also contains 7SK RNA and HEXIM1 or HEXIM2. Here we show that HIV infection of cells led to the release of P-TEFb from the large form. Consistent with Tat being the cause of this effect, transfection of a FLAG-tagged Tat in 293T cells caused a dramatic shift of P-TEFb out of the large form to a smaller form containing Tat. In vitro, Tat competed with HEXIM1 for binding to 7SK, blocked the formation of the P-TEFb–HEXIM1–7SK complex, and caused the release P-TEFb from a pre-formed P-TEFb–HEXIM1–7SK complex. These findings indicate that Tat can acquire P-TEFb from the large form. In addition, we found that HEXIM1 binds tightly to the HIV 5′ UTR containing TAR and recruits and inhibits P-TEFb activity. This suggests that in the absence of Tat, HEXIM1 may bind to TAR and repress transcription elongation of the HIV LTR.
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Affiliation(s)
- Stanley C. Sedore
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
| | - Sarah A. Byers
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
| | - Sebastian Biglione
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
| | - Jason P. Price
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
| | - Wendy J. Maury
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
| | - David H. Price
- Department of Biochemistry, Department of Microbiology, Medical Scientist Training Program and Interdisciplinary Molecular Biology Program, University of Iowa, Iowa City, IA, USA
- *To whom correspondence should be addressed. +1 319 335 7910+1 319 384 4770
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985
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Zhu W, Wada T, Okabe S, Taneda T, Yamaguchi Y, Handa H. DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation. Nucleic Acids Res 2007; 35:4064-75. [PMID: 17567605 PMCID: PMC1919491 DOI: 10.1093/nar/gkm430] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The transcription elongation factor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF) regulates RNA polymerase II (RNAPII) processivity by promoting, in concert with negative elongation factor (NELF), promoter-proximal pausing of RNAPII. DSIF is also reportedly involved in transcriptional activation. However, the role of DSIF in transcriptional activation by DNA-binding activators is unclear. Here we show that DSIF acts cooperatively with a DNA-binding activator, Gal4-VP16, to promote transcriptional activation. In the absence of DSIF, Gal4-VP16-activated transcription resulted in frequent pausing of RNAPII during elongation in vitro. The presence of DSIF reduced pausing, thereby supporting Gal4-VP16-mediated activation. We found that DSIF exerts its positive effects within a short time-frame from initiation to elongation, and that NELF does not affect the positive regulatory function of DSIF. Knockdown of the gene encoding the large subunit of DSIF, human Spt5 (hSpt5), in HeLa cells reduced Gal4-VP16-mediated activation of a reporter gene, but had no effect on expression in the absence of activator. Together, these results provide evidence that higher-level transcription has a stronger requirement for DSIF, and that DSIF contributes to efficient transcriptional activation by preventing RNAPII pausing during transcription elongation.
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Affiliation(s)
- Wenyan Zhu
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tadashi Wada
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- *To whom correspondence should be addressed. +81-45-924-5798+81-45-924-5834,
| | - Sachiko Okabe
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Takuya Taneda
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Yuki Yamaguchi
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and Biotechnology and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- *To whom correspondence should be addressed. +81-45-924-5798+81-45-924-5834,
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986
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Cheng B, Price DH. Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J Biol Chem 2007; 282:21901-12. [PMID: 17548348 DOI: 10.1074/jbc.m702936200] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The positive transcription elongation factor, P-TEFb, controls the fraction of initiated RNA polymerase II molecules that enter into the productive mode of elongation necessary to generate mRNAs. To better understand the mechanism of this transition into productive elongation we optimized a defined in vitro transcription system and compared results obtained with it to those obtained with a crude system. We found that controlling the function of TFIIF is a key aspect of RNA polymerase II elongation control. Before P-TEFb function, early elongation complexes under the control of negative factors are completely unresponsive to the robust elongation stimulatory activity of TFIIF. P-TEFb-mediated phosphorylation events, targeting the elongation complex containing DSIF and NELF, reverse the negative effect of DSIF and NELF and simultaneously facilitate the action of TFIIF. We also found that productive elongation complexes are completely resistant to negative elongation factors. Our data suggest that an additional factor(s) is involved in establishing the unique resistance activities of the elongation complexes before and after P-TEFb function. Furthermore, we provide evidence for the existence of another positive activity required for efficient function of P-TEFb. A model of the mechanism of P-TEFb-mediated elongation control is proposed in which P-TEFb induces the transition into productive elongation by changing the accessibility of elongation factors to elongation complexes. Our results have uncovered important properties of elongation complexes that allow a more complete understanding of how P-TEFb controls the elongation phases of transcription by RNA polymerase II.
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Affiliation(s)
- Bo Cheng
- Department of Biochemistry, Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242, USA
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987
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Chang YL, King B, Lin SC, Kennison JA, Huang DH. A double-bromodomain protein, FSH-S, activates the homeotic gene ultrabithorax through a critical promoter-proximal region. Mol Cell Biol 2007; 27:5486-98. [PMID: 17526731 PMCID: PMC1952094 DOI: 10.1128/mcb.00692-07] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than a dozen trithorax group (trxG) proteins are involved in activation of Drosophila HOX genes. How they act coordinately to integrate signals from distantly located enhancers is not fully understood. The female sterile (1) homeotic (fs(1)h) gene is one of the trxG genes that is most critical for Ultrabithorax (Ubx) activation. We show that one of the two double-bromodomain proteins encoded by fs(1)h acts as an essential factor in the Ubx proximal promoter. First, overexpression of the small isoform FSH-S, but not the larger one, can induce ectopic expression of HOX genes and cause body malformation. Second, FSH-S can stimulate Ubx promoter in cultured cells through a critical proximal region in a bromodomain-dependent manner. Third, purified FSH-S can bind specifically to a motif within this region that was previously known as the ZESTE site. The physiological relevance of FSH-S is ascertained using transgenic embryos containing a modified Ubx proximal promoter and chromatin immunoprecipitation. In addition, we show that FSH-S is involved in phosphorylation of itself and other regulatory factors. We suggest that FSH-S acts as a critical component of a regulatory circuitry mediating long-range effects of distant enhancers.
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Affiliation(s)
- Yuh-Long Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
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988
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Fu J, Yoon HG, Qin J, Wong J. Regulation of P-TEFb elongation complex activity by CDK9 acetylation. Mol Cell Biol 2007; 27:4641-51. [PMID: 17452463 PMCID: PMC1951478 DOI: 10.1128/mcb.00857-06] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P-TEFb, comprised of CDK9 and a cyclin T subunit, is a global transcriptional elongation factor important for most RNA polymerase II (pol II) transcription. P-TEFb facilitates transcription elongation in part by phosphorylating Ser2 of the heptapeptide repeat of the carboxy-terminal domain (CTD) of the largest subunit of pol II. Previous studies have shown that P-TEFb is subjected to negative regulation by forming an inactive complex with 7SK small RNA and HEXIM1. In an effort to investigate the molecular mechanism by which corepressor N-CoR mediates transcription repression, we identified HEXIM1 as an N-CoR-interacting protein. This finding led us to test whether the P-TEFb complex is regulated by acetylation. We demonstrate that CDK9 is an acetylated protein in cells and can be acetylated by p300 in vitro. Through both in vitro and in vivo assays, we identified lysine 44 of CDK9 as a major acetylation site. We present evidence that CDK9 is regulated by N-CoR and its associated HDAC3 and that acetylation of CDK9 affects its ability to phosphorylate the CTD of pol II. These results suggest that acetylation of CDK9 is an important posttranslational modification that is involved in regulating P-TEFb transcriptional elongation function.
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Affiliation(s)
- Junjiang Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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989
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Honma K, Mochizuki K, Goda T. Carbohydrate/fat ratio in the diet alters histone acetylation on the sucrase-isomaltase gene and its expression in mouse small intestine. Biochem Biophys Res Commun 2007; 357:1124-9. [PMID: 17466947 DOI: 10.1016/j.bbrc.2007.04.070] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 04/12/2007] [Indexed: 11/22/2022]
Abstract
A diet with a high carbohydrate/fat ratio enhances jejunal SI gene expression. Using ChIP assay, we revealed that the acetylation of histone H3 on transcriptional region and H4 on promoter region, respectively, of mouse SI gene are high. The acetylation of histone H3 and H4 as well as binding of HNF-1 and Cdx-2 on SI gene, was enhanced by increase in carbohydrate/fat ratio in the diet. These suggest that induction of SI gene by the diet rich in carbohydrate is associated with acetylation of histone H3 and H4 as well as binding of HNF-1 and Cdx-2 on SI gene.
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Affiliation(s)
- Kazue Honma
- Laboratory of Nutritional Physiology, The University of Shizuoka, Graduate School of Nutritional and Environmental Sciences and COE 21, 52-1 Yada, Shizuoka-shi, Shizuoka 422-8526, Japan
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990
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Li Q, Cooper JJ, Altwerger GH, Feldkamp MD, Shea MA, Price DH. HEXIM1 is a promiscuous double-stranded RNA-binding protein and interacts with RNAs in addition to 7SK in cultured cells. Nucleic Acids Res 2007; 35:2503-12. [PMID: 17395637 PMCID: PMC1885667 DOI: 10.1093/nar/gkm150] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
P-TEFb regulates eukaryotic gene expression at the level of transcription elongation, and is itself controlled by the reversible association of 7SK RNA and an RNA-binding protein HEXIM1 or HEXIM2. In an effort to determine the minimal region of 7SK needed to interact with HEXIM1 in vitro, we found that an oligo comprised of nucleotides 10-48 sufficed. A bid to further narrow down the minimal region of 7SK led to a surprising finding that HEXIM1 binds to double-stranded RNA in a sequence-independent manner. Both dsRNA and 7SK (10-48), but not dsDNA, competed efficiently with full-length 7SK for HEXIM1 binding in vitro. Upon binding dsRNA, a large conformational change was observed in HEXIM1 that allowed the recruitment and inhibition of P-TEFb. Both subcellular fractionation and immunofluorescence demonstrated that, while most HEXIM1 is found in the nucleus, a significant fraction is found in the cytoplasm. Immunoprecipitation experiments demonstrated that both nuclear and cytoplasmic HEXIM1 is associated with RNA. Interestingly, the one microRNA examined (mir-16) was found in HEXIM1 immunoprecipitates, while the small nuclear RNAs, U6 and U2, were not. Our study illuminates novel properties of HEXIM1 both in vitro and in vivo, and suggests that HEXIM1 may be involved in other nuclear and cytoplasmic processes besides controlling P-TEFb.
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Affiliation(s)
| | | | | | | | | | - David H. Price
- *To whom correspondence should be addressed +1-319-335-7910+1-319-335-9570
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991
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Williams SA, Kwon H, Chen LF, Greene WC. Sustained induction of NF-kappa B is required for efficient expression of latent human immunodeficiency virus type 1. J Virol 2007; 81:6043-56. [PMID: 17376917 PMCID: PMC1900291 DOI: 10.1128/jvi.02074-06] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cells harboring infectious, but transcriptionally latent, human immunodeficiency virus type 1 (HIV-1) proviruses currently pose an insurmountable barrier to viral eradication in infected patients. To better understand the molecular basis for HIV-1 latency, we used the J-Lat model of postintegration HIV-1 latency to assess the kinetic relationship between the induction of NF-kappaB and the activation of latent HIV-1 gene expression. Chromatin immunoprecipitation analyses revealed an oscillating pattern of RelA recruitment to the HIV-1 long terminal repeat (LTR) during continuous tumor necrosis factor alpha (TNF-alpha) stimulation. RNA polymerase II (Pol II) recruitment to the HIV-1 LTR closely mirrored RelA binding. Transient stimulation of cells with TNF-alpha for 15 min induced only a single round of RelA and RNA Pol II binding and failed to induce robust expression of latent HIV-1. Efficient formation of elongated HIV-1 transcripts required sustained induction by NF-kappaB, which promoted de novo synthesis of Tat. Cyclin-dependent kinase 9 (CDK9) and serine-2-phosphorylated RNA Pol II were rapidly recruited to the HIV-1 LTR after NF-kappaB induction; however, these elongating polymerase complexes were progressively dephosphorylated in the absence of Tat. Okadaic acid promoted sustained serine-2 phosphorylation of the C-terminal domain of RNA Pol II and stimulated efficient transcriptional elongation and HIV-1 expression in the absence of Tat. These findings underscore important differences between NF-kappaB and Tat stimulation of RNA Pol II elongation. While NF-kappaB binding to the HIV-1 LTR induces serial waves of efficient RNA Pol II initiation, elongation is impaired by the action of an okadaic acid-sensitive phosphatase that dephosphorylates the C-terminal domain of RNA Pol II. Conversely, the action of this phosphatase is overcome in the presence of Tat, promoting very efficient RNA Pol II elongation.
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Affiliation(s)
- Samuel A Williams
- Gladstone Institute of Virology and Immunology, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA
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992
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Shimizu S, Urano E, Futahashi Y, Miyauchi K, Isogai M, Matsuda Z, Nohtomi K, Onogi T, Takebe Y, Yamamoto N, Komano J. Inhibiting lentiviral replication by HEXIM1, a cellular negative regulator of the CDK9/cyclin T complex. AIDS 2007; 21:575-82. [PMID: 17314519 DOI: 10.1097/qad.0b013e32801424a5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Tat-dependent transcriptional elongation is crucial for the replication of HIV-1 and depends on positive transcription elongation factor b complex (P-TEFb), composed of cyclin dependent kinase 9 (CDK9) and cyclin T. Hexamethylene bisacetamide-induced protein 1 (HEXIM1) inhibits P-TEFb in cooperation with 7SK RNA, but direct evidence that this inhibition limits the replication of HIV-1 has been lacking. In the present study we examined whether the expression of FLAG-tagged HEXIM1 (HEXIM1-f) affected lentiviral replication in human T cell lines. METHODS HEXIM1-f was introduced to five human T cell lines, relevant host for HIV-1, by murine leukemia virus vector and cells expressing HEXIM1-f were collected by fluorescence activated cell sorter. The lentiviral replication kinetics in HEXIM1-f-expressing cells was compared with that in green fluorescent protein (GFP)-expressing cells. RESULTS HIV-1 and simian immunodeficiency virus replicated less efficiently in HEXIM1-f-expressing cells than in GFP-expressing cells of the five T cell lines tested. The viral revertants were not immediately selected in culture. In contrast, the replication of vaccinia virus, adenovirus, and herpes simplex virus type 1 was not limited. The quantitative PCR analyses revealed that the early phase of viral life cycle was not blocked by HEXIM1. On the other hand, Tat-dependent transcription in HEXIM1-f-expressing cells was substantially repressed as compared with that in GFP-expressing cells. CONCLUSION These data indicate that HEXIM1 is a host factor that negatively regulates lentiviral replication specifically. Elucidating the regulatory mechanism of HEXIM1 might lead to ways to control lentiviral replication.
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Affiliation(s)
- Saki Shimizu
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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993
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Barboric M, Yik JHN, Czudnochowski N, Yang Z, Chen R, Contreras X, Geyer M, Matija Peterlin B, Zhou Q. Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription. Nucleic Acids Res 2007; 35:2003-12. [PMID: 17341462 PMCID: PMC1874611 DOI: 10.1093/nar/gkm063] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) transcriptional transactivator (Tat) recruits the positive transcription elongation factor b (P-TEFb) to the viral promoter. Consisting of cyclin dependent kinase 9 (Cdk9) and cyclin T1, P-TEFb phosphorylates RNA polymerase II and the negative transcription elongation factor to stimulate the elongation of HIV-1 genes. A major fraction of nuclear P-TEFb is sequestered into a transcriptionally inactive 7SK small nuclear ribonucleoprotein (snRNP) by the coordinated actions of the 7SK small nuclear RNA (snRNA) and hexamethylene bisacetamide (HMBA) induced protein 1 (HEXIM1). In this study, we demonstrate that Tat prevents the formation of and also releases P-TEFb from the 7SK snRNP in vitro and in vivo. This ability of Tat depends on the integrity of its N-terminal activation domain and stems from the high affinity interaction between Tat and cyclin T1, which allows Tat to directly displace HEXIM1 from cyclin T1. Furthermore, we find that in contrast to the Tat-independent activation of the HIV-1 promoter, Tat-dependent HIV-1 transcription is largely insensitive to the inhibition by HEXIM1. Finally, primary blood lymphocytes display a reduced amount of the endogenous 7SK snRNP upon HIV-1 infection. All these data are consistent with the model that Tat not only recruits but also increases the active pool of P-TEFb for efficient HIV-1 transcription.
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Affiliation(s)
- Matjaz Barboric
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Jasper H. N. Yik
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Nadine Czudnochowski
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Zhiyuan Yang
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Ruichuan Chen
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Xavier Contreras
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - Matthias Geyer
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
| | - B. Matija Peterlin
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
- *To whom correspondence should be addressed. +1 510 643 1697+1 510 643 6334 Correspondence may also be addressed to B. Matija Peterlin. +1 415 502 1902+1 415 502 1901
| | - Qiang Zhou
- Departments of Medicine, Microbiology, and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143 0703, USA, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA, Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany and School of Life Sciences, Xiamen University, Xiamen 361005, P.R. China
- *To whom correspondence should be addressed. +1 510 643 1697+1 510 643 6334 Correspondence may also be addressed to B. Matija Peterlin. +1 415 502 1902+1 415 502 1901
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994
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Guiguen A, Soutourina J, Dewez M, Tafforeau L, Dieu M, Raes M, Vandenhaute J, Werner M, Hermand D. Recruitment of P-TEFb (Cdk9-Pch1) to chromatin by the cap-methyl transferase Pcm1 in fission yeast. EMBO J 2007; 26:1552-9. [PMID: 17332744 PMCID: PMC1829387 DOI: 10.1038/sj.emboj.7601627] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 02/05/2007] [Indexed: 12/31/2022] Open
Abstract
Capping of nascent pre-mRNAs is thought to be a prerequisite for productive elongation and associated serine 2 phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (PolII). The mechanism mediating this link is unknown, but is likely to include the capping machinery and P-TEPb. We report that the fission yeast P-TEFb (Cdk9-Pch1) forms a complex with the cap-methyltransferase Pcm1 and these proteins colocalise on chromatin. Ablation of Cdk9 function through chemical genetics causes growth arrest and abolishes serine 2 phosphorylation on the PolII CTD. Strikingly, depletion of Pcm1 also leads to a dramatic decrease of phospho-serine 2. Chromatin immunoprecipitations show a severe decrease of chromatin-bound Cdk9-Pch1 when Pcm1 is depleted. On the contrary, Cdk9 is not required for association of Pcm1 with chromatin. Furthermore, compromising Cdk9 activity leads to a promoter-proximal PolII stalling and sensitivity to 6-azauracil, reflecting elongation defects. The in vivo data presented here strongly support the existence of a molecular mechanism where the cap-methyltransferase recruits P-TEFb to chromatin, thereby ensuring that only properly capped transcripts are elongated.
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Affiliation(s)
- Allan Guiguen
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | | | - Monique Dewez
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | - Lionel Tafforeau
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | - Marc Dieu
- Unité de spectrométrie de masse, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | - Martine Raes
- Unité de spectrométrie de masse, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | - Jean Vandenhaute
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
| | | | - Damien Hermand
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
- Laboratoire de Génétique Moléculaire (GEMO), Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles 61, Namur 5000, Belgium. Tel: +32 81 724241; Fax: +32 81 724297; E-mail:
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995
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Wu SY, Chiang CM. The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J Biol Chem 2007; 282:13141-5. [PMID: 17329240 DOI: 10.1074/jbc.r700001200] [Citation(s) in RCA: 531] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Brd4 is a double bromodomain-containing protein that binds preferentially to acetylated chromatin. It belongs to the BET (bromodomains and extraterminal) family that includes mammalian Brd2, Brd3, Brd4, Brdt, Drosophila Fsh, yeast Bdf1, Bdf2, and corresponding homologues in other species. Brd4 is essential for cellular growth and has been implicated in cell cycle control, DNA replication, and gene rearrangement found in t(15;19)-associated carcinomas. Recently, Brd4 has been found in several transcription complexes, including the general cofactor Mediator and the P-TEFb elongation factor, and is capable of stimulating HIV-1 transcription in a Tat-independent manner. In addition, Brd4 is used as a cellular adaptor by some animal and human papillomaviruses (HPV) for anchoring viral genomes to mitotic chromosomes. This tethering, mediated by Brd4 interaction with virus-encoded E2 protein, facilitates viral genome segregation during mitosis. Interestingly, Brd4 is also identified in a transcriptional silencing complex assembled by HPV E2 and turns out to be the long sought cellular corepressor that inhibits the expression of HPV-encoded E6 and E7 oncoproteins that antagonize p53 and pRB tumor suppressor activity, respectively. The dual role of Brd4 in gene activation and repression illustrates how a dynamic chromatin-binding adaptor is able to recruit distinct transcriptional regulators to modulate promoter activity through cell cycle progression.
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MESH Headings
- Animals
- Cell Cycle Proteins
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 19/genetics
- Drosophila
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Gene Products, tat/genetics
- Gene Products, tat/metabolism
- Genome, Viral/genetics
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Mitosis
- Neoplasms/genetics
- Neoplasms/metabolism
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Papillomaviridae/genetics
- Papillomaviridae/metabolism
- Positive Transcriptional Elongation Factor B/genetics
- Positive Transcriptional Elongation Factor B/metabolism
- Protein Binding/genetics
- Retinoblastoma Protein/genetics
- Retinoblastoma Protein/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Translocation, Genetic
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Shwu-Yuan Wu
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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996
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Sénéchal H, Poirier GG, Coulombe B, Laimins LA, Archambault J. Amino acid substitutions that specifically impair the transcriptional activity of papillomavirus E2 affect binding to the long isoform of Brd4. Virology 2007; 358:10-7. [PMID: 17023018 DOI: 10.1016/j.virol.2006.08.035] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2006] [Revised: 07/18/2006] [Accepted: 08/23/2006] [Indexed: 10/24/2022]
Abstract
The E2 protein of papillomaviruses binds to specific sites in the viral genome to regulate its transcription, replication and segregation in mitosis. Amino acid substitutions in the transactivation domain (TAD) of E2, of Arg37 and Ile73, have been shown previously to impair the transcriptional activity of the protein but not its ability to support viral DNA replication. To understand the biochemical basis of this defect, we have used the TADs of a low-risk (HPV11) and a high-risk (HPV31) human papillomavirus (HPV) as affinity ligands to capture proteins from whole cell extracts that can associate with these domains. The major TAD-binding protein was identified by mass spectrometry and western blotting as the long isoform of Brd4. Binding to Brd4 was also demonstrated for the E2 TADs of other papillomaviruses including cutaneous and animal types. For HPV11, HPV31 and CRPV E2, we found that binding to Brd4 is significantly reduced by substitutions of Arg37 and Ile73. Since these amino acids are located near each other in the 3-dimensional structure of the TAD, we suggest that they define a conserved surface involved in binding Brd4 to regulate viral gene transcription.
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Affiliation(s)
- Hélène Sénéchal
- Laboratory of Molecular Virology, Institut de recherches cliniques de Montréal, 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7
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997
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Nagashima T, Maruyama T, Furuya M, Kajitani T, Uchida H, Masuda H, Ono M, Arase T, Ozato K, Yoshimura Y. Histone acetylation and subcellular localization of chromosomal protein BRD4 during mouse oocyte meiosis and mitosis. Mol Hum Reprod 2007; 13:141-8. [PMID: 17267518 DOI: 10.1093/molehr/gal115] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most specific and general transcription factors (TFs) become dissociated from hypoacetylated mitotic chromosomes, which may contribute to transcriptional silencing during mitosis. Only some chromosomal proteins, such as bromodomain containing protein 4 (BRD4), have a potential to associate with mitotic chromosomes in a histone acetylation-dependent manner. It remains to be fully demonstrated whether similar displacement of nuclear factors takes place in meiotic oocytes whose chromosomes become globally deacetylated. To address this, we here examined the subcellular localization of BRD4 in conjunction with the acetylation status of histones in mouse oocytes. Immunofluorescence studies revealed that BRD4 preferentially localized to mitotic chromosomes in early embryos. In contrast, not only endogenous BRD4 but also exogenous BRD4 overexpressed by mRNA microinjection were displaced from meiotic chromosomes whose histones H3 and H4 were deacetylated. Treatment with trichostatin A (TSA), an inhibitor of histone deacetylases, induced histone hyperacetylation of meiotic chromosomes from which endogenous BRD4, however, remained dissociated. Finally, meiotic chromosomal localization of BRD4 could be achieved by BRD4 overexpression together with TSA-induced histone hyperacetylation. These results indicate that, unlike mitosis, histone acetylation is necessary but not sufficient for chromosomal localization of BRD4 during meiosis, suggesting that meiotic oocytes may have additional mechanism(s) for displacement of chromosomal proteins and TFs.
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Affiliation(s)
- Takashi Nagashima
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
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998
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Parish JL, Bean AM, Park RB, Androphy EJ. ChlR1 is required for loading papillomavirus E2 onto mitotic chromosomes and viral genome maintenance. Mol Cell 2007; 24:867-76. [PMID: 17189189 DOI: 10.1016/j.molcel.2006.11.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/08/2006] [Accepted: 11/01/2006] [Indexed: 02/07/2023]
Abstract
Autonomously replicating DNA viruses must evade mitotic checkpoints and actively partition their genomes to maintain persistent infection. The E2 protein serves these functions by tethering papillomavirus episomes to mitotic chromosomes; however, the mechanism remains unresolved. We show that E2 binds ChlR1, a DNA helicase that plays a role in sister chromatid cohesion. The E2 mutation W130R fails to bind ChlR1 and correspondingly does not associate with mitotic chromosomes. Viral genomes encoding this E2 mutation are not episomally maintained in cell culture. Notably, E2 W130R binds Brd4, which reportedly acts as a mitotic tether, indicating this interaction is insufficient for E2 association with mitotic chromosomes. RNAi-induced depletion of ChlR1 significantly reduced E2 localization to mitotic chromosomes. These studies provide compelling evidence that ChlR1 association is required for loading the papillomavirus E2 protein onto mitotic chromosomes and represents a kinetochore-independent mechanism for viral genome maintenance and segregation.
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Affiliation(s)
- Joanna L Parish
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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999
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Abbate EA, Voitenleitner C, Botchan MR. Structure of the papillomavirus DNA-tethering complex E2:Brd4 and a peptide that ablates HPV chromosomal association. Mol Cell 2007; 24:877-89. [PMID: 17189190 DOI: 10.1016/j.molcel.2006.11.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 09/15/2006] [Accepted: 11/01/2006] [Indexed: 11/26/2022]
Abstract
Many DNA viruses that are latent in dividing cells are noncovalent passengers on mitotic chromosomes and require specific viral-encoded and cellular factors for this activity. The chromosomal protein Brd4 is implicated in the hitchhiking of bovine papillomavirus-1 (BPV-1), and the viral protein E2 binds to both plasmids and Brd4. Here, we present the X-ray crystal structure of the carboxy-terminal domain of Brd4 in complex with HPV-16 E2, and with this information have developed a Brd4-Tat fusion protein that is efficiently taken up by different transformed cells harboring HPV plasmids. In cells treated with these fusion proteins for only 2 hr and arrested in metaphase, the HPV DNA, either HPV-16 or -31, is displaced from mitotic chromosomes. Mutant Brd4 peptides are deficient in ablating this association. We suggest that such peptides may lead to the development of inhibitors of latency for many, if not all, papillomaviruses.
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Affiliation(s)
- Eric A Abbate
- Department of Molecular and Cell Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, Berkeley, California 94720, USA
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1000
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Wang Q, Young TM, Mathews MB, Pe’ery T. Developmental regulators containing the I-mfa domain interact with T cyclins and Tat and modulate transcription. J Mol Biol 2007; 367:630-46. [PMID: 17289077 PMCID: PMC1868487 DOI: 10.1016/j.jmb.2007.01.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Revised: 12/21/2006] [Accepted: 01/04/2007] [Indexed: 11/28/2022]
Abstract
Positive transcription elongation factor b (P-TEFb) complexes, composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1 or T2, are engaged by many cellular transcription regulators that activate or inhibit transcription from specific promoters. The related I-mfa (inhibitor of MyoD family a) and HIC (human I-mfa-domain-containing) proteins function in myogenic differentiation and embryonic development by participating in the Wnt signaling pathway. We report that I-mfa is a novel regulator of P-TEFb. Both HIC and I-mfa interact through their homologous I-mfa domains with cyclin T1 and T2 at two binding sites. One site is the regulatory histidine-rich domain that interacts with CDK9 substrates including RNA polymerase II. The second site contains a lysine and arginine-rich motif that is highly conserved between the two T cyclins. This site overlaps and includes the previously identified Tat/TAR recognition motif of cyclin T1 required for activation of human immunodeficiency virus type 1 (HIV-1) transcription. HIC and I-mfa can serve as substrates for P-TEFb. Their I-mfa domains also bind the activation domain of HIV-1 Tat and inhibit Tat- and P-TEFb-dependent transcription from the HIV-1 promoter. This transcriptional repression is cell-type specific and can operate via Tat and cyclin T1. Genomic and sequence comparisons indicate that the I-mf and HIC genes, as well as flanking genes, diverged from a duplicated chromosomal region. Our findings link I-mfa and HIC to viral replication, and suggest that P-TEFb is modulated in the Wnt signaling pathway.
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Affiliation(s)
- Qi Wang
- Department of Biochemistry and Molecular Biology, New Jersey Medical School
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave., Newark, NJ 07103-2714
| | - Tara M. Young
- Department of Biochemistry and Molecular Biology, New Jersey Medical School
| | - Michael B. Mathews
- Department of Biochemistry and Molecular Biology, New Jersey Medical School
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave., Newark, NJ 07103-2714
| | - Tsafi Pe’ery
- Department of Biochemistry and Molecular Biology, New Jersey Medical School
- Department of Medicine, New Jersey Medical School
- Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave., Newark, NJ 07103-2714
- *Corresponding author: Ph:(973) 972-8763; Fax:(973) 972-5594 E-mail:
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