151
|
Vos SM, Pöllmann D, Caizzi L, Hofmann KB, Rombaut P, Zimniak T, Herzog F, Cramer P. Architecture and RNA binding of the human negative elongation factor. eLife 2016; 5. [PMID: 27282391 PMCID: PMC4940160 DOI: 10.7554/elife.14981] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022] Open
Abstract
Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF. DOI:http://dx.doi.org/10.7554/eLife.14981.001
Collapse
Affiliation(s)
- Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David Pöllmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katharina B Hofmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomasz Zimniak
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
152
|
Day DS, Zhang B, Stevens SM, Ferrari F, Larschan EN, Park PJ, Pu WT. Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types. Genome Biol 2016; 17:120. [PMID: 27259512 PMCID: PMC4893286 DOI: 10.1186/s13059-016-0984-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/12/2016] [Indexed: 01/02/2023] Open
Abstract
Background For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the extent to which it is involved in control of mammalian gene expression and its relationship to chromatin structure remain poorly understood. Results Here, we analyze 85 RNA polymerase II chromatin immunoprecipitation (ChIP)-sequencing experiments from 35 different murine and human samples, as well as related genome-wide datasets, to gain new insights into the relationship between polymerase II pausing and gene regulation. Across cell and tissue types, paused genes (pausing index > 2) comprise approximately 60 % of expressed genes and are repeatedly associated with specific biological functions. Paused genes also have lower cell-to-cell expression variability. Increased pausing has a non-linear effect on gene expression levels, with moderately paused genes being expressed more highly than other paused genes. The highest gene expression levels are often achieved through a novel pause-release mechanism driven by high polymerase II initiation. In three datasets examining the impact of extracellular signals, genes responsive to stimulus have slightly lower pausing index on average than non-responsive genes, and rapid gene activation is linked to conditional pause-release. Both chromatin structure and local sequence composition near the transcription start site influence pausing, with divergent features between mammals and Drosophila. Most notably, in mammals pausing is positively correlated with histone H2A.Z occupancy at promoters. Conclusions Our results provide new insights into the contribution of RNA polymerase II pausing in mammalian gene regulation and chromatin structure. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0984-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel S Day
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.,Harvard/MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA
| | - Bing Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA. .,Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Sean M Stevens
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA. .,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| |
Collapse
|
153
|
Robinson C, Lowe M, Schwartz A, Kikyo N. Mechanisms and Developmental Roles of Promoter-proximal Pausing of RNA Polymerase II. ACTA ACUST UNITED AC 2016; 6. [PMID: 27158559 PMCID: PMC4855949 DOI: 10.4172/2157-7633.1000330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA polymerase II (Pol II) temporarily stops transcription after synthesizing 30–50 bases, and resumes elongation only after stimulations by various signaling molecules and developmental cues. This phenomenon, called promoter-proximal pausing, is observed in 10–50% of the entire genes from Drosophila embryos to human cells. Release of paused Pol II is primarily mediated by the activated form of positive transcription elongation factor b (P-TEFb) initially sequestered in the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Many proteins and RNAs have been discovered and studied in detail to explain the process of the pausing and release of Pol II in relation to P-TEFb. At the functional level, promoter-proximal pausing regulates genes involved in stimulus-response and development in Drosophila. In mammalian stem cell biology, pausing is important for proliferation and signaling in embryonic stem cells and the formation of induced pluripotent stem cells. Other than this, however, little is known about the biological significance of pausing in mammalian cell differentiation. Further study on pausing mechanisms as well as its functions will contribute to the development of stem cell biology and its clinical applications.
Collapse
Affiliation(s)
- Christine Robinson
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Matthew Lowe
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Amanda Schwartz
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Nobuaki Kikyo
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| |
Collapse
|
154
|
McNamara RP, Bacon CW, D'Orso I. Transcription elongation control by the 7SK snRNP complex: Releasing the pause. Cell Cycle 2016; 15:2115-2123. [PMID: 27152730 DOI: 10.1080/15384101.2016.1181241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability for the eukaryotic cell to transcriptionally respond to various stimuli is critical for the overall homeostasis of the cell, and in turn, the organism. The human RNA polymerase II complex (Pol II), which is responsible for the transcription of protein-encoding genes and non-coding RNAs, is paused at promoter-proximal regions to ensure their rapid activation. In response to stimulation, Pol II pause release is facilitated by the action of positive transcription elongation factors such as the P-TEFb kinase. However, the majority of P-TEFb is held in a catalytically inactivate state, assembled into the 7SK small nuclear ribonucleoprotein (snRNP) complex, and must be dislodged to become catalytically active. In this review, we discuss mechanisms of 7SK snRNP recruitment to promoter-proximal regions and P-TEFb disassembly from the inhibitory snRNP to regulate 'on site' kinase activation and Pol II pause release.
Collapse
Affiliation(s)
- Ryan P McNamara
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Curtis W Bacon
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| |
Collapse
|
155
|
Pance A. Oct-1, to go or not to go? That is the PolII question. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:820-4. [PMID: 27063953 DOI: 10.1016/j.bbagrm.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 10/22/2022]
Abstract
The Oct transcription factors recognise an octamer DNA element from which they regulate transcription of specific target genes. Oct-1 is the only member of the subfamily that is ubiquitously expressed and has a wide role in transcriptional control. Through interaction with various partner proteins, Oct-1 can modulate accessibility to the chromatin to recruit the transcription machinery and form the pre-initiation complex. The recruited PolII is induced to initiate transcription and stalled until elongation is triggered on interaction with signalling transcription factors. In this way, Oct-1 can fulfil general roles in transcription by opening the chromatin as well as transduce extracellular signals by relaying activation through various interacting partners. The emerging picture of Oct-1 is that of a complex and versatile transcription factor with fundamental functions in cell homeostasis and signal response in general as well as cell specific contexts. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
Collapse
Affiliation(s)
- Alena Pance
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
| |
Collapse
|
156
|
Nair SJ, Zhang X, Chiang HC, Jahid MJ, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan JB, Parvin JD, Jin VX, Hu Y, Li R. Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development. Nat Commun 2016; 7:10913. [PMID: 26941120 PMCID: PMC4785232 DOI: 10.1038/ncomms10913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/29/2016] [Indexed: 12/14/2022] Open
Abstract
The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance remains unclear. COBRA1 (also known as NELF-B) is a BRCA1-binding protein that regulates RNA polymerase II (RNAPII) pausing and transcription elongation. Here we interrogate functional interaction between BRCA1 and COBRA1 during mouse mammary gland development. Tissue-specific deletion of Cobra1 reduces mammary epithelial compartments and blocks ductal morphogenesis, alveologenesis and lactogenesis, demonstrating a pivotal role of COBRA1 in adult tissue development. Remarkably, these developmental deficiencies due to Cobra1 knockout are largely rescued by additional loss of full-length Brca1. Furthermore, Brca1/Cobra1 double knockout restores developmental transcription at puberty, alters luminal epithelial homoeostasis, yet remains deficient in homologous recombination-based DSB repair. Thus our genetic suppression analysis uncovers a previously unappreciated, DNA repair-independent function of BRCA1 in antagonizing COBRA1-dependent transcription programme during mammary gland development. COBRA1 is a BRCA1-binding protein and, as part of the negative elongation factor, regulates RNA polymerase II pausing and transcription elongation. Here, the authors show that tissue-specific deletion of mouse Cobra1 inhibits postnatal mammary gland development and that the mammary defects can be rescued by additional deletion of Brca1 in a DNA repair-independent manner.
Collapse
Affiliation(s)
- Sreejith J Nair
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Xiaowen Zhang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Huai-Chin Chiang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Md Jamiul Jahid
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Yao Wang
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Paula Garza
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Craig April
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Neeraj Salathia
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Tapahsama Banerjee
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fahad S Alenazi
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, Texas 78249, USA
| | - Jian-Bing Fan
- Research and Development, Illumina, Inc., San Diego, California 92122, USA
| | - Jeffrey D Parvin
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Yanfen Hu
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rong Li
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| |
Collapse
|
157
|
Takemata N, Oda A, Yamada T, Galipon J, Miyoshi T, Suzuki Y, Sugano S, Hoffman CS, Hirota K, Ohta K. Local potentiation of stress-responsive genes by upstream noncoding transcription. Nucleic Acids Res 2016; 44:5174-89. [PMID: 26945040 PMCID: PMC4914089 DOI: 10.1093/nar/gkw142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/25/2016] [Indexed: 02/06/2023] Open
Abstract
It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chromatin remodeling and fbp1 mRNA expression. Here, we demonstrate that such upstream noncoding transcription facilitates promoter association of the stress-responsive transcriptional activator Atf1 at the sites of transcription, leading to activation of the downstream stress genes. Genome-wide analyses revealed that ∼50 Atf1-binding sites show marked decrease in Atf1 occupancy when cells are treated with a transcription inhibitor. Most of these transcription-enhanced Atf1-binding sites are associated with stress-dependent induction of the adjacent mRNAs or lncRNAs, as observed in fbp1. These Atf1-binding sites exhibit low Atf1 occupancy and high histone density in glucose-rich conditions, and undergo dramatic changes in chromatin status after glucose depletion: enhanced Atf1 binding, histone eviction, and histone H3 acetylation. We also found that upstream transcripts bind to the Groucho-Tup1 type transcriptional corepressors Tup11 and Tup12, and locally antagonize their repressive functions on Atf1 binding. These results reveal a new mechanism in which upstream noncoding transcription locally magnifies the specific activation of stress-inducible genes via counteraction of corepressors.
Collapse
Affiliation(s)
- Naomichi Takemata
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Arisa Oda
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Takatomi Yamada
- Department of Biological Sciences, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Tomoichiro Miyoshi
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | | | - Kouji Hirota
- Department of Chemistry, Tokyo Metropolitan University, Hachi-Ohji, Tokyo 192-0397, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan Department of Biological Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
158
|
Williams AM, Maman Y, Alinikula J, Schatz DG. Bcl6 Is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells. PLoS One 2016; 11:e0149146. [PMID: 26900682 PMCID: PMC4762950 DOI: 10.1371/journal.pone.0149146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/27/2016] [Indexed: 12/20/2022] Open
Abstract
The activation induced cytosine deaminase (AID) mediates diversification of B cell immunoglobulin genes by the three distinct yet related processes of somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion (GCV). SHM occurs in germinal center B cells, and the transcription factor Bcl6 is a key regulator of the germinal center B cell gene expression program, including expression of AID. To test the hypothesis that Bcl6 function is important for the process of SHM, we compared WT chicken DT40 B cells, which constitutively perform SHM/GCV, to their Bcl6-deficient counterparts. We found that Bcl6-deficient DT40 cells were unable to perform SHM and GCV despite enforced high level expression of AID and substantial levels of AID in the nucleus of the cells. To gain mechanistic insight into the GCV/SHM dependency on Bcl6, transcriptional features of a highly expressed SHM target gene were analyzed in Bcl6-sufficient and -deficient DT40 cells. No defect was observed in the accumulation of single stranded DNA in the target gene as a result of Bcl6 deficiency. In contrast, association of Spt5, an RNA polymerase II (Pol II) and AID binding factor, was strongly reduced at the target gene body relative to the transcription start site in Bcl6-deficient cells as compared to WT cells. However, partial reconstitution of Bcl6 function substantially reconstituted Spt5 association with the target gene body but did not restore detectable SHM. Our observations suggest that in the absence of Bcl6, Spt5 fails to associate efficiently with Pol II at SHM targets, perhaps precluding robust AID action on the SHM target DNA. Our data also suggest, however, that Spt5 binding is not sufficient for SHM of a target gene even in DT40 cells with strong expression of AID.
Collapse
Affiliation(s)
- Alan M. Williams
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yaakov Maman
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jukka Alinikula
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - David G. Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
| |
Collapse
|
159
|
Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Mol Cell 2016; 60:435-45. [PMID: 26527278 DOI: 10.1016/j.molcel.2015.09.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/04/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division.
Collapse
Affiliation(s)
- Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
| |
Collapse
|
160
|
Gudipaty SA, D’Orso I. Functional interplay between PPM1G and the transcription elongation machinery. RNA & DISEASE 2016; 3:e1215. [PMID: 27088130 PMCID: PMC4830430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transcription elongation is a critical regulatory step in the gene expression cycle. One key regulator of the switch between transcription initiation and elongation is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) and several negative elongation factors to relieve the elongation block at paused promoters to facilitate productive elongation. Here, we highlight recent findings signifying the role of the PPM1G/PP2Cγ phosphatase in activating and maintaining the active transcription elongation state by regulating the availability of P-TEFb and blocking its assembly into the catalytic inactive 7SK small nuclear ribonucleoprotein (snRNP) complex.
Collapse
Affiliation(s)
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
161
|
Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH. Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Rep 2015; 13:1444-1455. [PMID: 26549458 DOI: 10.1016/j.celrep.2015.10.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/26/2015] [Accepted: 10/06/2015] [Indexed: 01/10/2023] Open
Abstract
Transcription elongation regulates the expression of many genes, including oncogenes. Histone deacetylase (HDAC) inhibitors (HDACIs) block elongation, suggesting that HDACs are involved in gene activation. To understand this, we analyzed nascent transcription and elongation factor binding genome-wide after perturbation of elongation with small molecule inhibitors. We found that HDACI-mediated repression requires heat shock protein 90 (HSP90) activity. HDACIs promote the association of RNA polymerase II (RNAP2) and negative elongation factor (NELF), a complex stabilized by HSP90, at the same genomic sites. Additionally, HDACIs redistribute bromodomain-containing protein 4 (BRD4), a key elongation factor involved in enhancer activity. BRD4 binds to newly acetylated sites, and its occupancy at promoters and enhancers is reduced. Furthermore, HDACIs reduce enhancer activity, as measured by enhancer RNA production. Therefore, HDACs are required for limiting acetylation in gene bodies and intergenic regions. This facilitates the binding of elongation factors to properly acetylated promoters and enhancers for efficient elongation.
Collapse
Affiliation(s)
- Celeste B Greer
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Genetics and Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yoon Jung Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Peng Xie
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Michael Q Zhang
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - In-Hyun Park
- Department of Genetics and Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tae Hoon Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.
| |
Collapse
|
162
|
Functional Consequences for Apoptosis by Transcription Elongation Regulator 1 (TCERG1)-Mediated Bcl-x and Fas/CD95 Alternative Splicing. PLoS One 2015; 10:e0139812. [PMID: 26462236 PMCID: PMC4604205 DOI: 10.1371/journal.pone.0139812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/17/2015] [Indexed: 11/19/2022] Open
Abstract
Here, we present evidence for a specific role of the splicing-related factor TCERG1 in regulating apoptosis in live cells by modulating the alternative splicing of the apoptotic genes Bcl-x and Fas. We show that TCERG1 modulates Bcl-x alternative splicing during apoptosis and its activity in Bcl-x alternative splicing correlates with the induction of apoptosis, as determined by assessing dead cells, sub-G1-phase cells, annexin-V binding, cell viability, and cleavage of caspase-3 and PARP-1. Furthermore, the effect of TCERG1 on apoptosis involved changes in mitochondrial membrane permeabilization. We also found that depletion of TCERG1 reduces the expression of the activated form of the pro-apoptotic mitochondrial membrane protein Bak, which remains inactive by heterodimerizing with Bcl-xL, preventing the initial step of cytochrome c release in Bak-mediated mitochondrial apoptosis. In addition, we provide evidence that TCERG1 also participates in the death receptor-mediated apoptosis pathway. Interestingly, TCERG1 also modulates Fas/CD95 alternative splicing. We propose that TCERG1 sensitizes a cell to apoptotic agents, thus promoting apoptosis by regulating the alternative splicing of both the Bcl-x and Fas/CD95 genes. Our findings may provide a new link between the control of alternative splicing and the molecular events leading to apoptosis.
Collapse
|
163
|
Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
Collapse
|
164
|
Scheidegger A, Nechaev S. RNA polymerase II pausing as a context-dependent reader of the genome. Biochem Cell Biol 2015; 94:82-92. [PMID: 26555214 DOI: 10.1139/bcb-2015-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.
Collapse
Affiliation(s)
- Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| |
Collapse
|
165
|
GC skew defines distinct RNA polymerase pause sites in CpG island promoters. Genome Res 2015; 25:1600-9. [PMID: 26275623 PMCID: PMC4617957 DOI: 10.1101/gr.189068.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 08/14/2015] [Indexed: 12/15/2022]
Abstract
CpG islands (CGIs) are associated with over half of human gene promoters and are characterized by a unique chromatin environment and high levels of bidirectional transcriptional activity relative to surrounding genomic regions, suggesting that RNA polymerase (Pol II) progression past the CGI boundaries is restricted. Here we describe a novel transcriptional regulatory step wherein Pol II encounters an additional barrier to elongation distinct from the promoter-proximal pause and occurring at the downstream boundary of the CGI domain. For most CGI-associated promoters, Pol II exhibits a dominant pause at either the promoter-proximal or this distal site that correlates, both in position and in intensity, with local regions of high GC skew, a sequence feature known to form unique secondary structures. Upon signal-induced gene activation, long-range enhancer contacts at the dominant pause site are selectively enhanced, suggesting a new role for enhancers at the downstream pause. These data point to an additional level of control over transcriptional output at a subset of CGI-associated genes that is linked to DNA sequence and the integrity of the CGI domain.
Collapse
|
166
|
Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res 2015; 43:8746-61. [PMID: 26227968 PMCID: PMC4605296 DOI: 10.1093/nar/gkv766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
Collapse
Affiliation(s)
- Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kurt Zimmer
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Neha Paranjape
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
167
|
Nojima T, Gomes T, Grosso ARF, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, Proudfoot NJ. Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell 2015; 161:526-540. [PMID: 25910207 PMCID: PMC4410947 DOI: 10.1016/j.cell.2015.03.027] [Citation(s) in RCA: 382] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/24/2014] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.
Collapse
Affiliation(s)
- Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Tomás Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Rita Fialho Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 226-8501Yokohama, Japan
| | - Michael J Dye
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| |
Collapse
|
168
|
Kwok RS, Li YH, Lei AJ, Edery I, Chiu JC. The Catalytic and Non-catalytic Functions of the Brahma Chromatin-Remodeling Protein Collaborate to Fine-Tune Circadian Transcription in Drosophila. PLoS Genet 2015; 11:e1005307. [PMID: 26132408 PMCID: PMC4488936 DOI: 10.1371/journal.pgen.1005307] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/28/2015] [Indexed: 11/18/2022] Open
Abstract
Daily rhythms in gene expression play a critical role in the progression of circadian clocks, and are under regulation by transcription factor binding, histone modifications, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Although previous studies have shown that clock-controlled genes exhibit rhythmic chromatin modifications, less is known about the functions performed by chromatin remodelers in animal clockwork. Here we have identified the Brahma (Brm) complex as a regulator of the Drosophila clock. In Drosophila, CLOCK (CLK) is the master transcriptional activator driving cyclical gene expression by participating in an auto-inhibitory feedback loop that involves stimulating the expression of the main negative regulators, period (per) and timeless (tim). BRM functions catalytically to increase nucleosome density at the promoters of per and tim, creating an overall restrictive chromatin landscape to limit transcriptional output during the active phase of cycling gene expression. In addition, the non-catalytic function of BRM regulates the level and binding of CLK to target promoters and maintains transient RNAPII stalling at the per promoter, likely by recruiting repressive and pausing factors. By disentangling its catalytic versus non-catalytic functions at the promoters of CLK target genes, we uncovered a multi-leveled mechanism in which BRM fine-tunes circadian transcription. The circadian clock is an endogenous timing system that enables organisms to anticipate daily changes in their external environment and temporally coordinate key biological functions that are important to their survival. Central to Drosophila clockwork is a key transcription factor CLOCK (CLK). CLK activates expression of target genes only during specific parts of the day, thereby orchestrating rhythmic expression of hundreds of clock-controlled genes, which consequently manifest into daily rhythms in physiology and behavior. In this study, we demonstrated that the Brahma (Brm) chromatin-remodeling protein interacts with CLK and fine-tune the levels of CLK-dependent transcription to maintain the robustness of the circadian clock. Specifically, we uncovered two distinct but collaborative functions of Brm. Brm possesses a non-catalytic function that negatively regulates the binding of CLK to target genes and limits transcriptional output, likely by recruiting repressive protein complexes. Catalytically, Brm functions by condensing the chromatin at CLK target genes, specifically when transcription is active. This serves to precisely control the level of repressive factors likely recruited by Brm as well as other transcriptional regulators. By disentangling these two roles of Brm, our study uncovered a multi-layered mechanism in which a chromatin remodeler regulates the circadian clock.
Collapse
Affiliation(s)
- Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, California, United States of America
| | - Ying H. Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, California, United States of America
| | - Anna J. Lei
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, California, United States of America
| | - Isaac Edery
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, California, United States of America
- * E-mail:
| |
Collapse
|
169
|
Hsu HT, Chen HM, Yang Z, Wang J, Lee NK, Burger A, Zaret K, Liu T, Levine E, Mango SE. TRANSCRIPTION. Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4. Science 2015; 348:1372-6. [PMID: 26089518 PMCID: PMC4861314 DOI: 10.1126/science.aab1223] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pioneer transcription factors initiate cell-fate changes by binding to silent target genes. They are among the first factors to bind key regulatory sites and facilitate chromatin opening. Here, we identify an additional role for pioneer factors. In early Caenorhabditis elegans foregut development, the pioneer factor PHA-4/FoxA binds promoters and recruits RNA polymerase II (Pol II), often in a poised configuration in which Pol II accumulates near transcription start sites. At a later developmental stage, PHA-4 promotes chromatin opening. We found many more genes with poised RNA polymerase than had been observed previously in unstaged embryos, revealing that early embryos accumulate poised Pol II and that poising is dynamic. Our results suggest that Pol II recruitment, in addition to chromatin opening, is an important feature of PHA-4 pioneer factor activity.
Collapse
Affiliation(s)
- H-T Hsu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - H-M Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Z Yang
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - J Wang
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA
| | - N K Lee
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - A Burger
- Department of Physics and Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - K Zaret
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - T Liu
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA. Department of Biostatistics, University at Buffalo, Buffalo, NY 14214, USA
| | - E Levine
- Department of Physics and Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - S E Mango
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
170
|
Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell 2015; 58:1101-12. [PMID: 26028540 DOI: 10.1016/j.molcel.2015.04.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/29/2015] [Accepted: 04/01/2015] [Indexed: 11/26/2022]
Abstract
Anti-sense transcription originating upstream of mammalian protein-coding genes is a well-documented phenomenon, but remarkably little is known about the regulation or function of anti-sense promoters and the non-coding RNAs they generate. Here we define at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNA genes. We find that coupled sense and anti-sense TSSs precisely define the boundaries of a nucleosome-depleted region (NDR) that is highly enriched in transcription factor (TF) motifs. Notably, as the distance between sense and anti-sense TSSs increases, so does the size of the NDR, the level of signal-dependent TF binding, and gene activation. We further discover a group of anti-sense TSSs in macrophages with an enhancer-like chromatin signature. Interestingly, this signature identifies divergent promoters that are activated during immune challenge. We propose that anti-sense promoters serve as platforms for TF binding and establishment of active chromatin to further regulate or enhance sense-strand mRNA expression.
Collapse
Affiliation(s)
- Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Daniel A Gilchrist
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sergei Nechaev
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ginger W Muse
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - David C Fargo
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
171
|
Abstract
UNLABELLED Upon infection, pathogen recognition leads to a rapidly activated gene expression program that induces antimicrobial effectors to clear the invader. We recently found that Nup98 regulates the expression of a subset of rapidly activated antiviral genes to restrict disparate RNA virus infections in Drosophila by promoting RNA polymerase occupancy at the promoters of these antiviral genes. How Nup98 specifically targets these loci was unclear; however, it is known that Nup98 participates with transcription factors to regulate developmental-gene activation. We reasoned that additional transcription factors may facilitate the Nup98-dependent expression of antiviral genes. In a genome-wide RNA interference (RNAi) screen, we identified a relatively understudied forkhead transcription factor, FoxK, as active against Sindbis virus (SINV) in Drosophila. Here we find that FoxK is active against the panel of viruses that are restricted by Nup98, including SINV and vesicular stomatitis virus (VSV). Mechanistically, we show that FoxK coordinately regulates the Nup98-dependent expression of antiviral genes. Depletion of FoxK significantly reduces Nup98-dependent induction of antiviral genes and reduces the expression of a forkhead response element-containing luciferase reporter. Together, these data show that FoxK-mediated activation of gene expression is Nup98 dependent. We extended our studies to mammalian cells and found that the mammalian ortholog FOXK1 is antiviral against two disparate RNA viruses, SINV and VSV, in human cells. Interestingly, FOXK1 also plays a role in the expression of antiviral genes in mammals: depletion of FOXK1 attenuates virus-inducible interferon-stimulated response element (ISRE) reporter expression. Overall, our results demonstrate a novel role for FOXK1 in regulating the expression of antiviral genes, from insects to humans. IMPORTANCE Innate immunity is characterized by rapid gene expression programs, from insects to mammals. Furthermore, we find that Nup98, known for its roles in the nuclear pore, plays a noncanonical role in binding the promoters and poising a subset of loci for rapid antiviral gene induction. It was unclear how Nup98 accesses these specific genes, and we here demonstrate that Nup98 cooperates with the transcription factor FoxK to regulate this gene expression program. Depletion of FoxK specifically reduces the induction of Nup98-dependent genes. Further, we find that the antiviral function of FoxK is conserved, as the human ortholog FOXK1 is also antiviral and regulates gene expression from virus-induced promoters. Although other forkhead transcription factors have been implicated in immunity, a role for FoxK in antiviral defense was previously unappreciated. Our findings reveal a conserved and novel role for FoxK in coordinating with Nup98 to promote a robust and complex antiviral transcriptional response.
Collapse
|
172
|
Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet 2015; 11:e1005108. [PMID: 25815464 PMCID: PMC4376892 DOI: 10.1371/journal.pgen.1005108] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/26/2015] [Indexed: 11/28/2022] Open
Abstract
Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters. Transcriptional regulation is critical for proper gene expression in response to environmental changes and developmental programs. Eukaryotes have evolved multiple mechanisms by which transcription factors regulate transcription. One mechanism is the reorganization of chromatin to allow Pol II recruitment. Another is the release of promoter-proximal paused Pol II, where Pol II transcription that is halted 20–60 bases downstream of the transcription start site (TSS) is allowed to enter into productive elongation through the gene body. The Drosophila transcription factor GAF binds to genes that undergo pausing and interacts with nucleosome remodelers and the pausing factor NELF. Thus, GAF can regulate multiple points necessary for transcription, but its mechanistic role is not fully understood genome-wide. We depleted GAF from cells and examined the genome-wide changes in Pol II and nucleosome distributions across genes. We found that GAF depletion reduces polymerase density at genes where GAF binds just upstream of the TSS, and results in nucleosomes moving into the promoter region. Our results show that GAF is important for maintaining the promoter accessibility, allowing Pol II to be recruited to promoters and enter the pause sites downstream of the TSS. Thus, GAF is critical for providing the chromatin environment necessary for the proper control of gene expression.
Collapse
Affiliation(s)
- Nicholas J. Fuda
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael J. Guertin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sumeet Sharma
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Charles G. Danko
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - André L. Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
173
|
Samarakkody A, Abbas A, Scheidegger A, Warns J, Nnoli O, Jokinen B, Zarns K, Kubat B, Dhasarathy A, Nechaev S. RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic Acids Res 2015; 43:3938-49. [PMID: 25820424 PMCID: PMC4417172 DOI: 10.1093/nar/gkv263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/17/2015] [Indexed: 12/26/2022] Open
Abstract
Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.
Collapse
Affiliation(s)
- Ann Samarakkody
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Ata Abbas
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Jessica Warns
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Oscar Nnoli
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Bradley Jokinen
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kris Zarns
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Brooke Kubat
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Archana Dhasarathy
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| |
Collapse
|
174
|
Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks. Mol Cell 2015; 58:311-322. [PMID: 25773599 DOI: 10.1016/j.molcel.2015.02.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/16/2015] [Accepted: 01/30/2015] [Indexed: 11/21/2022]
Abstract
The remarkable capacity for pluripotency and self-renewal in embryonic stem cells (ESCs) requires a finely tuned transcriptional circuitry wherein the pathways and genes that initiate differentiation are suppressed, but poised to respond rapidly to developmental signals. To elucidate transcriptional control in mouse ESCs in the naive, ground state, we defined the distribution of engaged RNA polymerase II (Pol II) at high resolution. We find that promoter-proximal pausing of Pol II is most enriched at genes regulating cell cycle and signal transduction and not, as expected, at developmental or bivalent genes. Accordingly, ablation of the primary pause-inducing factor NELF does not increase expression of lineage markers, but instead causes proliferation defects, embryonic lethality, and dysregulation of ESC signaling pathways. Indeed, ESCs lacking NELF have dramatically attenuated FGF/ERK activity, rendering them resistant to differentiation. This work thus uncovers a key role for NELF-mediated pausing in establishing the responsiveness of stem cells to developmental cues.
Collapse
|
175
|
Jimeno-González S, Ceballos-Chávez M, Reyes JC. A positioned +1 nucleosome enhances promoter-proximal pausing. Nucleic Acids Res 2015; 43:3068-78. [PMID: 25735750 PMCID: PMC4381062 DOI: 10.1093/nar/gkv149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 02/13/2015] [Indexed: 02/07/2023] Open
Abstract
Chromatin distribution is not uniform along the human genome. In most genes there is a promoter-associated nucleosome free region (NFR) followed by an array of nucleosomes towards the gene body in which the first (+1) nucleosome is strongly positioned. The function of this characteristic chromatin distribution in transcription is not fully understood. Here we show in vivo that the +1 nucleosome plays a role in modulating RNA polymerase II (RNAPII) promoter-proximal pausing. When a +1 nucleosome is strongly positioned, elongating RNAPII has a tendency to stall at the promoter-proximal region, recruits more negative elongation factor (NELF) and produces less mRNA. The nucleosome-induced pause favors pre-mRNA quality control by promoting the addition of the cap to the nascent RNA. Moreover, the uncapped RNAs produced in the absence of a positioned nucleosome are degraded by the 5′-3′ exonuclease XRN2. Interestingly, reducing the levels of the chromatin remodeler ISWI factor SNF2H decreases +1 nucleosome positioning and increases RNAPII pause release. This work demonstrates a function for +1 nucleosome in regulation of transcription elongation, pre-mRNA processing and gene expression.
Collapse
Affiliation(s)
- Silvia Jimeno-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), E-41012, Seville, Spain
| | - María Ceballos-Chávez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), E-41012, Seville, Spain
| | - José C Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), E-41012, Seville, Spain
| |
Collapse
|
176
|
Chen F, Gao X, Shilatifard A. Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide. Genes Dev 2015; 29:39-47. [PMID: 25561494 PMCID: PMC4281563 DOI: 10.1101/gad.246173.114] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. Here, Chen et al. used the small molecule triptolide (TPL), an XPB/TFIIH inhibitor, to block transcriptional initiation and then measured Pol II occupancy by ChIP-seq. This revealed that most genes with paused Pol II show significant clearance of Pol II during the period of TPL treatment. They also identified a group of genes with unexpectedly stably paused Pol II, with unchanged Pol II occupancy during 1 h of inhibition of initiation. Transcription by RNA polymerase II (Pol II) in metazoans is regulated in several steps, including preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional RNA processing, and termination. Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. However, a mechanistic understanding of the paused Pol II state at promoters is limited. For example, at a global level, it is unclear to what extent the engaged paused Pol II is stably tethered to the promoter or undergoes rapid cycles of initiation and termination. Here we used the small molecule triptolide (TPL), an XPB/TFIIH inhibitor, to block transcriptional initiation and then measured Pol II occupancy by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq). This inhibition of initiation enabled us to investigate different states of paused Pol II. Specifically, our global analysis revealed that most genes with paused Pol II, as defined by a pausing index, show significant clearance of Pol II during the period of TPL treatment. Our study further identified a group of genes with unexpectedly stably paused Pol II, with unchanged Pol II occupancy even after 1 h of inhibition of initiation. This group of genes constitutes a small portion of all paused genes defined by the conventional criterion of pausing index. These findings could pave the way for evaluating the contribution of different elongation/pausing factors on different states of Pol II pausing in developmental and other stimulus-responsive pathways.
Collapse
Affiliation(s)
- Fei Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Xin Gao
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| |
Collapse
|
177
|
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res 2015; 24:1224-35. [PMID: 24985916 PMCID: PMC4079976 DOI: 10.1101/gr.168807.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Annotation of regulatory elements and identification of the transcription-related factors (TRFs) targeting these elements are key steps in understanding how cells interpret their genetic blueprint and their environment during development, and how that process goes awry in the case of disease. One goal of the modENCODE (model organism ENCyclopedia of DNA Elements) Project is to survey a diverse sampling of TRFs, both DNA-binding and non-DNA-binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TRFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA regions with demonstrated enhancer activity. Regions of high TRF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TRF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. Together these data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
Collapse
Affiliation(s)
- Matthew Slattery
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Lijia Ma
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rebecca F Spokony
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert K Arthur
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Anshul Kundaje
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Nicolas Nègre
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA; Université de Montpellier II and INRA, UMR1333 DGIMI, F-34095 Montpellier, France
| | - Alex Crofts
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Ryan Ptashkin
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer Zieba
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander Ostapenko
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah Suchy
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alec Victorsen
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Nader Jameel
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - A Jason Grundstad
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Wenxuan Gao
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer R Moran
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - E Jay Rehm
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert L Grossman
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
178
|
Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2015; 16:167-77. [PMID: 25693130 DOI: 10.1038/nrm3953] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.
Collapse
|
179
|
Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol 2015; 16:155-66. [PMID: 25693131 DOI: 10.1038/nrm3951] [Citation(s) in RCA: 589] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-coding RNA genes and is globally regulated by Mediator - a large, conformationally flexible protein complex with a variable subunit composition (for example, a four-subunit cyclin-dependent kinase 8 module can reversibly associate with it). These biochemical characteristics are fundamentally important for Mediator's ability to control various processes that are important for transcription, including the organization of chromatin architecture and the regulation of Pol II pre-initiation, initiation, re-initiation, pausing and elongation. Although Mediator exists in all eukaryotes, a variety of Mediator functions seem to be specific to metazoans, which is indicative of more diverse regulatory requirements.
Collapse
Affiliation(s)
- Benjamin L Allen
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| |
Collapse
|
180
|
Dahlberg O, Shilkova O, Tang M, Holmqvist PH, Mannervik M. P-TEFb, the super elongation complex and mediator regulate a subset of non-paused genes during early Drosophila embryo development. PLoS Genet 2015; 11:e1004971. [PMID: 25679530 PMCID: PMC4334199 DOI: 10.1371/journal.pgen.1004971] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 12/22/2014] [Indexed: 02/07/2023] Open
Abstract
Positive Transcription Elongation Factor b (P-TEFb) is a kinase consisting of Cdk9 and Cyclin T that releases RNA Polymerase II (Pol II) into active elongation. It can assemble into a larger Super Elongation Complex (SEC) consisting of additional elongation factors. Here, we use a miRNA-based approach to knock down the maternal contribution of P-TEFb and SEC components in early Drosophila embryos. P-TEFb or SEC depletion results in loss of cells from the embryo posterior and in cellularization defects. Interestingly, the expression of many patterning genes containing promoter-proximal paused Pol II is relatively normal in P-TEFb embryos. Instead, P-TEFb and SEC are required for expression of some non-paused, rapidly transcribed genes in pre-cellular embryos, including the cellularization gene Serendipity-α. We also demonstrate that another P-TEFb regulated gene, terminus, has an essential function in embryo development. Similar morphological and gene expression phenotypes were observed upon knock down of Mediator subunits, providing in vivo evidence that P-TEFb, the SEC and Mediator collaborate in transcription control. Surprisingly, P-TEFb depletion does not affect the ratio of Pol II at the promoter versus the 3’ end, despite affecting global Pol II Ser2 phosphorylation levels. Instead, Pol II occupancy is reduced at P-TEFb down-regulated genes. We conclude that a subset of non-paused, pre-cellular genes are among the most susceptible to reduced P-TEFb, SEC and Mediator levels in Drosophila embryos. Embryo development involves formation of various cell types through the regulation of gene transcription, resulting in expression of cell type specific RNAs and proteins. A key regulatory step in transcription of animal genes involves the transition of RNA polymerase II (Pol II) into active elongation. At many genes, Pol II is transiently paused approximately 50 basepairs downstream of the transcription start site. Release from this promoter-proximal pausing involves the kinase P-TEFb, which phosphorylates negative elongation factors, allowing Pol II to enter into productive elongation. In this work, we have depleted a considerable amount of P-TEFb from early Drosophila embryos. We find that several genes with paused Pol II can be expressed relatively normally in P-TEFb depleted embryos, whereas expression of some non-paused genes is substantially reduced. This result suggests that also non-paused genes transit through a P-TEFb-dependent checkpoint before entering active elongation. Unexpectedly, we find less Pol II associated with these non-paused genes in P-TEFb embryos. We demonstrate that a protein complex involved in recruitment of Pol II to promoters, the Mediator complex, show the same morphological and gene expression phenotypes as P-TEFb. We propose that Mediator and P-TEFb function together in recruiting Pol II to a subset of developmental genes.
Collapse
Affiliation(s)
- Olle Dahlberg
- Dept. Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Olga Shilkova
- Dept. Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Min Tang
- Dept. Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Dept. Biochemistry & Biology, South China University, Hengyang, Hunan Province, China
| | - Per-Henrik Holmqvist
- Dept. Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mattias Mannervik
- Dept. Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
181
|
Analysis of methylation microarray for tissue specific detection. Gene 2014; 553:31-41. [DOI: 10.1016/j.gene.2014.09.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
|
182
|
Stadelmayer B, Micas G, Gamot A, Martin P, Malirat N, Koval S, Raffel R, Sobhian B, Severac D, Rialle S, Parrinello H, Cuvier O, Benkirane M. Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat Commun 2014; 5:5531. [PMID: 25410209 PMCID: PMC4263189 DOI: 10.1038/ncomms6531] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/10/2014] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. Here, we show that negative elongation factor (NELF) interacts with Integrator complex subunits (INTScom), RNAPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated INTScom subunits. Interestingly, in addition to controlling RNAPII pause-release INTS11 catalytic subunit of the INTScom is required for RNAPII processivity. Finally, INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3' box sequence required for small nuclear RNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle. RNA polymerase II (RNAPII) pausing at transcriptional start sites is an important element of gene transcription regulation. Here, the authors implicate the Integrator complex as a regulator of RNAPII pause-release and completion of mRNA synthesis at a subset of the negative elongation factor target genes.
Collapse
Affiliation(s)
- Bernd Stadelmayer
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
| | - Gaël Micas
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Adrien Gamot
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Pascal Martin
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France
| | - Nathalie Malirat
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Slavik Koval
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Raoul Raffel
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Bijan Sobhian
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | | | | | | | - Olivier Cuvier
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [3] IGF, MGX-Montpellier GenomiX, France
| | - Monsef Benkirane
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
| |
Collapse
|
183
|
Sawicka A, Hartl D, Goiser M, Pusch O, Stocsits RR, Tamir IM, Mechtler K, Seiser C. H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress. Genome Res 2014; 24:1808-20. [PMID: 25135956 PMCID: PMC4216922 DOI: 10.1101/gr.176255.114] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/14/2014] [Indexed: 12/26/2022]
Abstract
The selectivity of transcriptional responses to extracellular cues is reflected by the deposition of stimulus-specific chromatin marks. Although histone H3 phosphorylation is a target of numerous signaling pathways, its role in transcriptional regulation remains poorly understood. Here, for the first time, we report a genome-wide analysis of H3S28 phosphorylation in a mammalian system in the context of stress signaling. We found that this mark targets as many as 50% of all stress-induced genes, underlining its importance in signal-induced transcription. By combining ChIP-seq, RNA-seq, and mass spectrometry we identified the factors involved in the biological interpretation of this histone modification. We found that MSK1/2-mediated phosphorylation of H3S28 at stress-responsive promoters contributes to the dissociation of HDAC corepressor complexes and thereby to enhanced local histone acetylation and subsequent transcriptional activation of stress-induced genes. Our data reveal a novel function of the H3S28ph mark in the activation of mammalian genes in response to MAP kinase pathway activation.
Collapse
Affiliation(s)
- Anna Sawicka
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Dominik Hartl
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria; Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Ido M Tamir
- Campus Science Support Facilities GmbH, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, 1030 Vienna, Austria; Protein Chemistry Facility, IMBA Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Christian Seiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria;
| |
Collapse
|
184
|
Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone-induced and DNA demethylation-induced relief of a tissue-specific and developmentally regulated block in transcriptional elongation. J Biol Chem 2014; 289:35087-101. [PMID: 25331959 DOI: 10.1074/jbc.m114.615435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox gene recruits polymerase II and begins elongating in all tissues and cell lines that we tested, but it only completes elongation in a tissue-specific and developmentally regulated manner. Relief of the elongation block is associated with recruitment of the elongation factor P-TEFb, the co-activator GRIP1, the chromatin remodeling factor BRG1, and specific histone modifications. We provide evidence that two mechanisms relieve the elongation block at the proximal promoter: demethylation and recruitment of androgen receptor. Together, our findings support a model in which promoter proximal pausing helps confer tissue-specific and developmental gene expression through a mechanism regulated by DNA demethylation-dependent nuclear hormone receptor recruitment.
Collapse
Affiliation(s)
- Manjeet K Rao
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Yuiko Matsumoto
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Marcy E Richardson
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Subbarayalu Panneerdoss
- the Greehey Children's Cancer Research Institute, Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Anjana Bhardwaj
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Jacqueline M Ward
- the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Sreenath Shanker
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Anilkumar Bettegowda
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| | - Miles F Wilkinson
- From the Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, the Department of Reproductive Medicine, University of California at San Diego, La Jolla, California 92037, the Institute of Genomic Medicine, University of California at San Diego, La Jolla, California 92093, and
| |
Collapse
|
185
|
Schaukowitch K, Joo JY, Liu X, Watts JK, Martinez C, Kim TK. Enhancer RNA facilitates NELF release from immediate early genes. Mol Cell 2014; 56:29-42. [PMID: 25263592 DOI: 10.1016/j.molcel.2014.08.023] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 08/06/2014] [Accepted: 08/19/2014] [Indexed: 12/14/2022]
Abstract
Enhancer RNAs (eRNAs) are a class of long noncoding RNAs (lncRNA) expressed from active enhancers, whose function and action mechanism are yet to be firmly established. Here we show that eRNAs facilitate the transition of paused RNA polymerase II (RNAPII) into productive elongation by acting as a decoy for the negative elongation factor (NELF) complex upon induction of immediate early genes (IEGs) in neurons. eRNAs are synthesized prior to the culmination of target gene transcription and interact with the NELF complex. Knockdown of eRNAs expressed at neuronal enhancers impairs transient release of NELF from the specific target promoters during transcriptional activation, coinciding with a decrease in target mRNA induction. The enhancer-promoter interaction was unaffected by eRNA knockdown. Instead, chromatin looping might enable eRNAs to act locally at a specific promoter. Our findings highlight the spatiotemporally regulated action mechanism of eRNAs during early transcriptional elongation.
Collapse
Affiliation(s)
- Katie Schaukowitch
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9111, USA
| | - Jae-Yeol Joo
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9111, USA
| | - Xihui Liu
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9111, USA
| | - Jonathan K Watts
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9111, USA
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines Drive, The Woodlands, TX 77380, USA
| | - Tae-Kyung Kim
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9111, USA.
| |
Collapse
|
186
|
Gardini A, Baillat D, Cesaroni M, Hu D, Marinis JM, Wagner EJ, Lazar MA, Shilatifard A, Shiekhattar R. Integrator regulates transcriptional initiation and pause release following activation. Mol Cell 2014; 56:128-139. [PMID: 25201415 DOI: 10.1016/j.molcel.2014.08.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022]
Abstract
In unicellular organisms, initiation is the rate-limiting step in transcription; in metazoan organisms, the transition from initiation to productive elongation is also important. Here, we show that the RNA polymerase II (RNAPII)-associated multiprotein complex, Integrator, plays a critical role in both initiation and the release of paused RNAPII at immediate early genes (IEGs) following transcriptional activation by epidermal growth factor (EGF) in human cells. Integrator is recruited to the IEGs in a signal-dependent manner and is required to engage and recruit the super elongation complex (SEC) to EGF-responsive genes to allow release of paused RNAPII and productive transcription elongation.
Collapse
Affiliation(s)
- Alessandro Gardini
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,The Wistar Institute, Philadelphia, PA 19104, USA
| | - David Baillat
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Matteo Cesaroni
- The Fels Institute, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Deqing Hu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jill M Marinis
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Mitchell A Lazar
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,The Wistar Institute, Philadelphia, PA 19104, USA
| |
Collapse
|
187
|
Ferrer-Vicens I, Riffo‐Campos ÁL, Zaragozá R, García C, López-Rodas G, Viña JR, Torres L, García-Trevijano ER. In vivo genome-wide binding of Id2 to E2F4 target genes as part of a reversible program in mice liver. Cell Mol Life Sci 2014; 71:3583-97. [PMID: 24573694 PMCID: PMC11113549 DOI: 10.1007/s00018-014-1588-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/30/2014] [Accepted: 02/12/2014] [Indexed: 12/14/2022]
Abstract
The inhibitor of differentiation Id2, a protein lacking the basic DNA-binding domain, is involved in the modulation of a number of biological processes. The molecular mechanisms explaining Id2 pleiotropic functions are poorly understood. Id2 and E2F4 are known to bind simultaneously to c-myc promoter. To study whether Id2 plays a global role on transcriptional regulation, we performed in vivo genome-wide ChIP/chip experiments for Id2 and E2F4 in adult mouse liver. An Id2-containing complex was bound to a common sequence downstream from the TSS on a subset of 442 E2F4 target genes mainly related to cell development and chromatin structure. We found a positive correlation between Id2 protein levels and the expression of E2F4/Id2 targets in fetal and adult liver. Id2 protein stability increased in fetal liver by interaction with USP1 de-ubiquitinating enzyme, which was induced during development. In adult liver, USP1 and Id2 levels dramatically decreased. In differentiated liver tissue, when Id2 concentration was low, E2F4/Id2 was bound to the same region as paused Pol II and target genes remained transcriptionally inactive. Conversely, in fetal liver when Id2 levels were increased, Id2 and Pol II were released from gene promoters and target genes up-regulated. During liver regeneration after partial hepatectomy, we obtained the same results as in fetal liver. Our results suggest that Id2 might be part of a reversible development-related program involved in the paused-ON/OFF state of Pol II on selected genes that would remain responsive to specific stimuli.
Collapse
Affiliation(s)
- Ivan Ferrer-Vicens
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Ángela L. Riffo‐Campos
- Facultad de Ciencias Biológicas. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Rosa Zaragozá
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Concha García
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Gerardo López-Rodas
- Facultad de Ciencias Biológicas. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Juan R. Viña
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Luis Torres
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| | - Elena R. García-Trevijano
- Departamento de Bioquímica y Biología Molecular. Facultad de Medicina. Fundación Investigación Hospital Clínico-INCLIVA, Universidad de Valencia, Avda. Blasco Ibañez, 17, 46010 Valencia, Spain
| |
Collapse
|
188
|
Amariei C, Machné R, Stolc V, Soga T, Tomita M, Murray DB. Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. MICROBIAL CELL 2014; 1:279-288. [PMID: 28357254 PMCID: PMC5349131 DOI: 10.15698/mic2014.09.166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The structural dynamics of chromatin have been implicated in the regulation of
fundamental eukaryotic processes, such as DNA transcription, replication and
repair. Although previous studies have revealed that the chromatin landscape,
nucleosome remodeling and histone modification events are intimately tied into
cellular energetics and redox state, few studies undertake defined time-resolved
measurements of these state variables. Here, we use metabolically synchronous,
continuously-grown yeast cultures to measure DNA occupancy and track global
patterns with respect to the metabolic state of the culture. Combined with
transcriptome analyses and ChIP-qPCR experiments, these paint an intriguing
picture where genome-wide nucleosome focusing occurs during the recovery of
energy charge, followed by clearance of the promoter regions and global
transcriptional slow-down, thus indicating a nucleosome-mediated “reset point”
for the cycle. The reset begins at the end of the catabolic and stress-response
transcriptional programs and ends prior to the start of the anabolic and
cell-growth transcriptional program, and the histones on genes from both the
catabolic and anabolic superclusters are deacetylated.
Collapse
Affiliation(s)
- Cornelia Amariei
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Rainer Machné
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstrasse 43, D-10115, Berlin, Germany. ; Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090, Vienna, Austria
| | - Viktor Stolc
- NASA Ames Research Center, Moffett Field, California, United States of America
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. ; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Douglas B Murray
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| |
Collapse
|
189
|
Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 2014; 158:673-88. [PMID: 25083876 PMCID: PMC4137894 DOI: 10.1016/j.cell.2014.06.027] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 04/03/2014] [Accepted: 06/10/2014] [Indexed: 12/15/2022]
Abstract
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.
Collapse
Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA
| | - Duygu Ucar
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | | | | | - Anshul B Kundaje
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Elena Mancini
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Rakhi Gupta
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Thomas A Rando
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford CA 94305, USA; RR&D REAP, VA Palo Alto Health Care Systems, Palo Alto, CA 94304,USA
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA.
| |
Collapse
|
190
|
Gyenis Á, Umlauf D, Újfaludi Z, Boros I, Ye T, Tora L. UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells. PLoS Genet 2014; 10:e1004483. [PMID: 25058334 PMCID: PMC4109906 DOI: 10.1371/journal.pgen.1004483] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 05/19/2014] [Indexed: 11/19/2022] Open
Abstract
Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair (TCR) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. Moreover, numerous efforts investigated the fate of blocked RNA polymerase II (Pol II) during DNA repair mechanisms and suggested that stopped Pol II complexes can either backtrack, be removed and degraded or bypass the lesions to allow TCR. We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We found that the used UVB dose did not induce Pol II degradation however surprisingly at about 93% of the promoters of all expressed genes Pol II occupancy was seriously reduced 2-4 hours following UVB irradiation. The presence of Pol II at these cleared promoters was restored 5-6 hours after irradiation, indicating that the negative regulation is very dynamic. We also identified a small set of genes (including several p53 regulated genes), where the UVB-induced Pol II clearing did not operate. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH, but not TBP, follows the behavior of Pol II, suggesting that at these genes upon UVB treatment TFIIH is sequestered for DNA repair by the TCR machinery. In agreement, in cells where the TCR factor, the Cockayne Syndrome B protein, was depleted UVB did not induce Pol II and TFIIH clearance at promoters. Thus, our study reveals a UVB induced negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed gene promoters, and a small subset of genes, where Pol II escapes this negative regulation.
Collapse
Affiliation(s)
- Ákos Gyenis
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - David Umlauf
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Zsuzsanna Újfaludi
- University of Szeged, Faculty of Sciences and Informatics, Department of Biochemistry and Molecular Biology, Szeged, Hungary
| | - Imre Boros
- University of Szeged, Faculty of Sciences and Informatics, Department of Biochemistry and Molecular Biology, Szeged, Hungary
| | - Tao Ye
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Microarrays and deep sequencing platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Làszlò Tora
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- * E-mail:
| |
Collapse
|
191
|
Rogatsky I, Adelman K. Preparing the first responders: building the inflammatory transcriptome from the ground up. Mol Cell 2014; 54:245-54. [PMID: 24766888 DOI: 10.1016/j.molcel.2014.03.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In cells of the immune system, inflammatory stimuli trigger highly coordinated cascades of gene activation that are precisely calibrated to the nature and strength of the stimulus. Herein, we describe the forces that control inflammatory gene transcription and highlight that many critical determinants of responsiveness are established prior to challenge. We discuss key steps in the transcription cycle that are regulated during gene activation and the importance of the underlying enhancer landscape. Further, we illustrate how the diversity in regulatory strategies employed at inflammatory genes provides novel opportunities for therapeutic intervention.
Collapse
Affiliation(s)
- Inez Rogatsky
- Hospital for Special Surgery Research Division and the David Rosensweig Genomics Center, New York, NY 10021, USA; Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Karen Adelman
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
192
|
Quinodoz M, Gobet C, Naef F, Gustafson KB. Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biol 2014; 15:R85. [PMID: 24972996 PMCID: PMC4197824 DOI: 10.1186/gb-2014-15-6-r85] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 06/12/2014] [Indexed: 01/15/2023] Open
Abstract
Background In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. Results Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3. Conclusions We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.
Collapse
|
193
|
Grzechnik P, Tan-Wong SM, Proudfoot NJ. Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 2014; 39:319-27. [PMID: 24928762 PMCID: PMC4085477 DOI: 10.1016/j.tibs.2014.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 01/28/2023]
Abstract
Transcriptional directionality is controlled by premature transcription termination. Transcriptional directionality is enforced by gene looping. mRNA-specific termination signals and factors are required for gene looping.
Bidirectional promoters are a common feature of many eukaryotic organisms from yeast to humans. RNA Polymerase II that is recruited to this type of promoter can start transcribing in either direction using alternative DNA strands as the template. Such promiscuous transcription can lead to the synthesis of unwanted transcripts that may have negative effects on gene expression. Recent studies have identified transcription termination and gene looping as critical players in the enforcement of promoter directionality. Interestingly, both mechanisms share key components. Here, we focus on recent findings relating to the transcriptional output of bidirectional promoters.
Collapse
Affiliation(s)
- Pawel Grzechnik
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| |
Collapse
|
194
|
Lhoumaud P, Hennion M, Gamot A, Cuddapah S, Queille S, Liang J, Micas G, Morillon P, Urbach S, Bouchez O, Severac D, Emberly E, Zhao K, Cuvier O. Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes. EMBO J 2014; 33:1599-613. [PMID: 24916307 DOI: 10.15252/embj.201385965] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosomal domains in Drosophila are marked by the insulator-binding proteins (IBPs) dCTCF/Beaf32 and cofactors that participate in regulating long-range interactions. Chromosomal borders are further enriched in specific histone modifications, yet the role of histone modifiers and nucleosome dynamics in this context remains largely unknown. Here, we show that IBP depletion impairs nucleosome dynamics specifically at the promoters and coding sequence of genes flanked by IBP binding sites. Biochemical purification identifies the H3K36 histone methyltransferase NSD/dMes-4 as a novel IBP cofactor, which specifically co-regulates the chromatin accessibility of hundreds of genes flanked by dCTCF/Beaf32. NSD/dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-dependent H3K36 trimethylation, nucleosome positioning, and RNA splicing. Our results unveil a model for how IBPs regulate nucleosome dynamics and gene expression through NSD/dMes-4, which may regulate H3K27me3 spreading. Our data uncover how IBPs dynamically regulate chromatin organization depending on distinct cofactors.
Collapse
Affiliation(s)
- Priscillia Lhoumaud
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Magali Hennion
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Suresh Cuddapah
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sophie Queille
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Jun Liang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Gael Micas
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Pauline Morillon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| | - Serge Urbach
- Mass-Spectrometry Facility, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Olivier Bouchez
- UMR444-Laboratoire de Génétique Cellulaire & GeT-PlaGe, INRA Genotoul, Auzeville, Toulouse, France
| | - Dany Severac
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Eldon Emberly
- Physics Department, Simon Fraser University (SFU), Burnaby, BC, Canada
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute National Institutes of Health (NIH), Bethesda, MD, USA
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS Université de Toulouse (UPS), Toulouse, France
| |
Collapse
|
195
|
Abstract
Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
Collapse
|
196
|
Abstract
In pluripotent stem cells, the interplay between signaling cues, epigenetic regulators and transcription factors orchestrates developmental potency. Flexibility in gene expression control is imparted by molecular changes to the nucleosomes, the building block of chromatin. Here, we review the current understanding of the role of chromatin as a plastic and integrative platform to direct gene expression changes in pluripotent stem cells, giving rise to distinct pluripotent states. We will further explore the concept of epigenetic asymmetry, focusing primarily on histone stoichiometry and their associated modifications, that is apparent at both the nucleosome and chromosome-wide levels, and discuss the emerging importance of these asymmetric chromatin configurations in diversifying epigenetic states and their implications for cell fate control.
Collapse
Affiliation(s)
- Wee-Wei Tee
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
197
|
Bowman EA, Kelly WG. RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus 2014; 5:224-36. [PMID: 24879308 DOI: 10.4161/nucl.29347] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.
Collapse
Affiliation(s)
- Elizabeth A Bowman
- National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
| | | |
Collapse
|
198
|
Affiliation(s)
- Amanda L. Hughes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| |
Collapse
|
199
|
Abstract
The rapid expansion of genomics methods has enabled developmental biologists to address fundamental questions of developmental gene regulation on a genome-wide scale. These efforts have demonstrated that transcription of developmental control genes by RNA polymerase II (Pol II) is commonly regulated at the transition to productive elongation, resulting in the promoter-proximal accumulation of transcriptionally engaged but paused Pol II prior to gene induction. Here we review the mechanisms and possible functions of Pol II pausing and their implications for development.
Collapse
Affiliation(s)
- Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, 64110 MO, USA
| | | |
Collapse
|
200
|
Iwaki H, Sasaki S, Matsushita A, Ohba K, Matsunaga H, Misawa H, Oki Y, Ishizuka K, Nakamura H, Suda T. Essential role of TEA domain transcription factors in the negative regulation of the MYH 7 gene by thyroid hormone and its receptors. PLoS One 2014; 9:e88610. [PMID: 24781449 PMCID: PMC4004540 DOI: 10.1371/journal.pone.0088610] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 01/14/2014] [Indexed: 12/20/2022] Open
Abstract
MYH7 (also referred to as cardiac myosin heavy chain β) gene expression is known to be repressed by thyroid hormone (T3). However, the molecular mechanism by which T3 inhibits the transcription of its target genes (negative regulation) remains to be clarified, whereas those of transcriptional activation by T3 (positive regulation) have been elucidated in detail. Two MCAT (muscle C, A, and T) sites and an A/T-rich region in the MYH7 gene have been shown to play a critical role in the expression of this gene and are known to be recognized by the TEAD/TEF family of transcription factors (TEADs). Using a reconstitution system with CV-1 cells, which has been utilized in the analysis of positive as well as negative regulation, we demonstrate that both T3 receptor (TR) β1 and α1 inhibit TEAD-dependent activation of the MYH7 promoter in a T3 dose-dependent manner. TRβ1 bound with GC-1, a TRβ-selective T3 analog, also repressed TEAD-induced activity. Although T3-dependent inhibition required the DNA-binding domain (DBD) of TRβ1, it remained after the putative negative T3-responsive elements were mutated. A co-immunoprecipitation study demonstrated the in vivo association of TRβ1 with TEAD-1, and the interaction surfaces were mapped to the DBD of the TRβ1 and TEA domains of TEAD-1, both of which are highly conserved among TRs and TEADs, respectively. The importance of TEADs in MYH7 expression was also validated with RNA interference using rat embryonic cardiomyocyte H9c2 cells. These results indicate that T3-bound TRs interfere with transactivation by TEADs via protein-protein interactions, resulting in the negative regulation of MYH7 promoter activity.
Collapse
Affiliation(s)
- Hiroyuki Iwaki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Shigekazu Sasaki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
- * E-mail:
| | - Akio Matsushita
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Kenji Ohba
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hideyuki Matsunaga
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hiroko Misawa
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Yutaka Oki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Keiko Ishizuka
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | | | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| |
Collapse
|