251
|
Abstract
A longstanding endeavor to define the genetic lesions that drive myeloid malignances has stimulated a period of remarkable discovery. Enabled by technological advances that have sharply decreased the cost of DNA sequencing, the full compendium of common, recurrent somatic mutations in the coding genome of myeloid malignancies is nearly complete. As the focus of genetic discovery shifts to the noncoding genome, renewed attention is being applied to the clinical and biological implications of recent genomic advances. Although the potential for this newfound knowledge to influence the care of patients has not yet been realized, broad genetic surveys of patient samples are now being used to improve the accuracy of disease diagnosis, define a molecular taxonomy of myeloid malignancies, refine prognostic and predictive models, and identify novel therapeutic strategies. Here, we will review recent advances in the genetics of myeloid malignancies and discuss their potential impact on clinical practice.
Collapse
Affiliation(s)
- R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; and
| | | |
Collapse
|
252
|
Khan DH, Gonzalez C, Cooper C, Sun JM, Chen HY, Healy S, Xu W, Smith KT, Workman JL, Leygue E, Davie JR. RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing. Nucleic Acids Res 2013; 42:1656-70. [PMID: 24234443 PMCID: PMC3919583 DOI: 10.1093/nar/gkt1134] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Histone deacetylases (HDACs) and lysine acetyltransferases (KATs) catalyze dynamic histone acetylation at regulatory and coding regions of transcribed genes. Highly phosphorylated HDAC2 is recruited within corepressor complexes to regulatory regions, while the nonphosphorylated form is associated with the gene body. In this study, we characterized the nonphosphorylated HDAC2 complexes recruited to the transcribed gene body and explored the function of HDAC-complex-mediated dynamic histone acetylation. HDAC1 and 2 were coimmunoprecipitated with several splicing factors, including serine/arginine-rich splicing factor 1 (SRSF1) which has roles in alternative splicing. The co-chromatin immunoprecipitation of HDAC1/2 and SRSF1 to the gene body was RNA-dependent. Inhibition of HDAC activity and knockdown of HDAC1, HDAC2 or SRSF1 showed that these proteins were involved in alternative splicing of MCL1. HDAC1/2 and KAT2B were associated with nascent pre-mRNA in general and with MCL1 pre-mRNA specifically. Inhibition of HDAC activity increased the occupancy of KAT2B and acetylation of H3 and H4 of the H3K4 methylated alternative MCL1 exon 2 nucleosome. Thus, nonphosphorylated HDAC1/2 is recruited to pre-mRNA by splicing factors to act at the RNA level with KAT2B and other KATs to catalyze dynamic histone acetylation of the MCL1 alternative exon and alter the splicing of MCL1 pre-mRNA.
Collapse
Affiliation(s)
- Dilshad H Khan
- Department of Biochemistry and Medical Genetics, University of Manitoba, Manitoba Institute of Child Health, Winnipeg, Manitoba, R3E 3P4, Canada, Department of Biochemistry and Medical Genetics, University of Manitoba, Manitoba Institute of Cell Biology, Winnipeg, Manitoba, R3E0V9, Canada and Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
253
|
Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol Cell 2013; 52:517-28. [PMID: 24184211 DOI: 10.1016/j.molcel.2013.10.001] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/03/2013] [Accepted: 09/26/2013] [Indexed: 01/17/2023]
Abstract
Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of the short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 min at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent, and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions.
Collapse
|
254
|
Iannone C, Valcárcel J. Chromatin's thread to alternative splicing regulation. Chromosoma 2013; 122:465-74. [PMID: 23912688 DOI: 10.1007/s00412-013-0425-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
Abstract
Intron removal (pre-mRNA splicing) is a necessary step for expression of most genes in higher eukaryotes. Alternative splice site selection is a prevalent mechanism that diversifies genome outputs and offers ample opportunities for gene regulation in these organisms. Pre-mRNA splicing occurs co-transcriptionally and is influenced by features in chromatin structure, including nucleosome density and epigenetic modifications. We review here the molecular mechanisms by which the reciprocal interplay between chromatin and RNA processing can contribute to alternative splicing regulation.
Collapse
|
255
|
Cherrier T, Le Douce V, Eilebrecht S, Riclet R, Marban C, Dequiedt F, Goumon Y, Paillart JC, Mericskay M, Parlakian A, Bausero P, Abbas W, Herbein G, Kurdistani SK, Grana X, Van Driessche B, Schwartz C, Candolfi E, Benecke AG, Van Lint C, Rohr O. CTIP2 is a negative regulator of P-TEFb. Proc Natl Acad Sci U S A 2013; 110:12655-60. [PMID: 23852730 PMCID: PMC3732990 DOI: 10.1073/pnas.1220136110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is involved in physiological and pathological events including inflammation, cancer, AIDS, and cardiac hypertrophy. The balance between its active and inactive form is tightly controlled to ensure cellular integrity. We report that the transcriptional repressor CTIP2 is a major modulator of P-TEFb activity. CTIP2 copurifies and interacts with an inactive P-TEFb complex containing the 7SK snRNA and HEXIM1. CTIP2 associates directly with HEXIM1 and, via the loop 2 of the 7SK snRNA, with P-TEFb. In this nucleoprotein complex, CTIP2 significantly represses the Cdk9 kinase activity of P-TEFb. Accordingly, we show that CTIP2 inhibits large sets of P-TEFb- and 7SK snRNA-sensitive genes. In hearts of hypertrophic cardiomyopathic mice, CTIP2 controls P-TEFb-sensitive pathways involved in the establishment of this pathology. Overexpression of the β-myosin heavy chain protein contributes to the pathological cardiac wall thickening. The inactive P-TEFb complex associates with CTIP2 at the MYH7 gene promoter to repress its activity. Taken together, our results strongly suggest that CTIP2 controls P-TEFb function in physiological and pathological conditions.
Collapse
Affiliation(s)
- Thomas Cherrier
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Laboratory of Protein Signaling and Interactions, University of Liège, Liège, Belgium
| | - Valentin Le Douce
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Sebastian Eilebrecht
- Vaccine Research Institute, Institut National de la Santé et de la Recherche Médicale, Unité 955, 94010 Créteil, France
- Institut des Hautes Études Scientifiques, Centre National de la Recherche Scientifique, 91440 Bures sur Yvette, France
| | - Raphael Riclet
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Céline Marban
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Department of Biological Chemistry, University of California, Los Angeles, CA 92093
| | - Franck Dequiedt
- Laboratory of Protein Signaling and Interactions, University of Liège, Liège, Belgium
| | - Yannick Goumon
- Institut des Neurosciences Cellulaires et Intégratives, University of Strasbourg, Centre National de la Recherche Scientifique, 67000 Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique Unité Propre de Recherche 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67000 Strasbourg, France
| | - Mathias Mericskay
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Ara Parlakian
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Pedro Bausero
- Unité de Recherche 4, Aging, Stress, Inflammation Department, Université Pierre et Marie Curie Université Paris 6, 75005 Paris, France
| | - Wasim Abbas
- Department of Virology, Institut Fédératif de Recherche 133, Institut National de la Santé et de la Recherche Médicale, University of Franche-Comté, 25000 Besançon, France
| | - Georges Herbein
- Department of Virology, Institut Fédératif de Recherche 133, Institut National de la Santé et de la Recherche Médicale, University of Franche-Comté, 25000 Besançon, France
| | | | - Xavier Grana
- Fels Institute for Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140
| | - Benoit Van Driessche
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Christian Schwartz
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Ermanno Candolfi
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
| | - Arndt G. Benecke
- Vaccine Research Institute, Institut National de la Santé et de la Recherche Médicale, Unité 955, 94010 Créteil, France
- Institut des Hautes Études Scientifiques, Centre National de la Recherche Scientifique, 91440 Bures sur Yvette, France
| | - Carine Van Lint
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 6041 Gosselies, Belgium; and
| | - Olivier Rohr
- Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 67000 Strasbourg, France
- Institut Universitaire de France, 75005 Paris, France
| |
Collapse
|
256
|
Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T. The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome Biol 2013; 14:R98. [PMID: 24044525 PMCID: PMC4053805 DOI: 10.1186/gb-2013-14-9-r98] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pluripotency is characterized by a unique transcriptional state, in which lineage-specification genes are poised for transcription upon exposure to appropriate stimuli, via a bivalency mechanism involving the simultaneous presence of activating and repressive methylation marks at promoter-associated histones. Recent evidence suggests that other mechanisms, such as RNA polymerase II pausing, might be operational in this process, but their regulation remains poorly understood. RESULTS Here we identify the non-coding snRNA 7SK as a multifaceted regulator of transcription in embryonic stem cells. We find that 7SK represses a specific cohort of transcriptionally poised genes with bivalent or activating chromatin marks in these cells, suggesting a novel poising mechanism independent of Polycomb activity. Genome-wide analysis shows that 7SK also prevents transcription downstream of polyadenylation sites at several active genes, indicating that 7SK is required for normal transcriptional termination or control of 3′-UTR length. In addition, 7SK suppresses divergent upstream antisense transcription at more than 2,600 loci, including many that encode divergent long non-coding RNAs, a finding that implicates the 7SK snRNA in the control of transcriptional bidirectionality. CONCLUSIONS Our study indicates that a single non-coding RNA, the snRNA 7SK, is a gatekeeper of transcriptional termination and bidirectional transcription in embryonic stem cells and mediates transcriptional poising through a mechanism independent of chromatin bivalency.
Collapse
Affiliation(s)
- Gonçalo Castelo-Branco
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet,SE-17177 Stockholm, Sweden
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Pär G Engström
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Present address: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Samuel C Robson
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sueli C Marques
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet,SE-17177 Stockholm, Sweden
| | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| |
Collapse
|