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Sheinboim D, Parikh S, Parikh R, Menuchin A, Shapira G, Kapitansky O, Elkoshi N, Ruppo S, Shaham L, Golan T, Elgavish S, Nevo Y, Bell RE, Malcov H, Shomron N, Taub JW, Izraeli S, Levy C. Slow transcription of the 99a/let-7c/125b-2 cluster results in differential miRNA expression and promotes melanoma phenotypic plasticity. J Invest Dermatol 2021; 141:2944-2956.e6. [PMID: 34186058 DOI: 10.1016/j.jid.2021.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Almost half of human miRNAs are encoded in clusters. Although transcribed as a single unit, the levels of individual mature miRNAs often differ. The mechanisms underlying differential biogenesis of clustered miRNAs and the resulting physiological implications are mostly unknown. Here, we report that the melanoma master transcription regulator MITF regulates the differential expression of the 99a/let-7c/125b-2 cluster by altering the distribution of RNA polymerase II (Pol-II) along the cluster. We discovered that MITF interacts with TRIM28, a known inhibitor of Pol-II transcription elongation, at the let-7c region resulting in Pol-II pausing and causing its elevated expression, whereas low levels of Pol-II occupation over miR-99a and miR-125b-2 regions decreases their biogenesis. Furthermore, we showed that this differential expression affects the phenotypic state of melanoma cells. RNA-seq analysis of proliferative melanoma cells that express miR-99a and miR-125b mimics revealed a transcriptomic shift toward an invasive phenotype. Conversely, expression of a let-7c mimic in invasive melanoma cells induced a shift to a more proliferative state. We confirmed direct target genes of these miRNAs: FGFR3, BAP1, Bcl2, TGFBR1, and CDKN1A. Our study demonstrates a MITF-governed biogenesis mechanism that results in differential expression of clustered 99a/let-7c/125b-2 miRNAs that control melanoma progression.
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Affiliation(s)
- Danna Sheinboim
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shivang Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roma Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amitai Menuchin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oxana Kapitansky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nadav Elkoshi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shmuel Ruppo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Lital Shaham
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Division of Pediatric Hematology-Oncology Department, Schneider Children's Medical Center, Petah Tikva 49202, Israel
| | - Tamar Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Rachel E Bell
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hagar Malcov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Edmond J. Safra Center of Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jeffrey W Taub
- Wayne State University School of Medicine, Detroit, MI 48201, USA; Division of Pediatric Hematology and Oncology, Children's Hospital of Michigan, Detroit, MI 48201, USA
| | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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2
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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3
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Slobodin B, Bahat A, Sehrawat U, Becker-Herman S, Zuckerman B, Weiss AN, Han R, Elkon R, Agami R, Ulitsky I, Shachar I, Dikstein R. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell 2020; 78:434-444.e5. [PMID: 32294471 DOI: 10.1016/j.molcel.2020.03.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 02/02/2023]
Abstract
Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced m6A deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirly Becker-Herman
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amanda N Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Slobodin B, Han R, Calderone V, Vrielink JAFO, Loayza-Puch F, Elkon R, Agami R. Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell 2017; 169:326-337.e12. [PMID: 28388414 PMCID: PMC5388891 DOI: 10.1016/j.cell.2017.03.031] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 01/15/2023]
Abstract
Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency. Using a CRISPR-Cas9-mediated approach, genome-wide analyses, and in vitro experiments, we show that the rate of transcription regulates the efficiency of translation. Furthermore, we demonstrate that m6A modification of mRNAs is co-transcriptional and depends upon the dynamics of the transcribing RNAPII. Suboptimal transcription rates lead to elevated m6A content, which may result in reduced translation. This study uncovers a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs. Transcription rates of mRNAs positively correlate with rates of their translation Dynamics of RNA polymerase II impact the deposition of m6A on mRNAs Suboptimal transcription enhances m6A modification of mRNAs Excessive m6A modification is detrimental for the translation process
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Affiliation(s)
- Boris Slobodin
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| | - Ruiqi Han
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vittorio Calderone
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joachim A F Oude Vrielink
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Reuven Agami
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
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Diamant G, Bahat A, Dikstein R. The elongation factor Spt5 facilitates transcription initiation for rapid induction of inflammatory-response genes. Nat Commun 2016; 7:11547. [PMID: 27180651 PMCID: PMC4873663 DOI: 10.1038/ncomms11547] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/07/2016] [Indexed: 12/11/2022] Open
Abstract
A subset of inflammatory-response NF-κB target genes is activated immediately following pro-inflammatory signal. Here we followed the kinetics of primary transcript accumulation after NF-κB activation when the elongation factor Spt5 is knocked down. While elongation rate is unchanged, the transcript synthesis at the 5'-end and at the earliest time points is delayed and reduced, suggesting an unexpected role in early transcription. Investigating the underlying mechanism reveals that the induced TFIID-promoter association is practically abolished by Spt5 depletion. This effect is associated with a decrease in promoter-proximal H3K4me3 and H4K5Ac histone modifications that are differentially required for rapid transcriptional induction. In contrast, the displacement of TFIIE and Mediator, which occurs during promoter escape, is attenuated in the absence of Spt5. Our findings are consistent with a central role of Spt5 in maintenance of TFIID-promoter association and promoter escape to support rapid transcriptional induction and re-initiation of inflammatory-response genes.
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Affiliation(s)
- Gil Diamant
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7600, Israel
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7600, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7600, Israel
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A Novel Allosteric Mechanism of NF-κB Dimerization and DNA Binding Targeted by an Anti-Inflammatory Drug. Mol Cell Biol 2016; 36:1237-47. [PMID: 26830231 DOI: 10.1128/mcb.00895-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/25/2016] [Indexed: 11/20/2022] Open
Abstract
The NF-κB family plays key roles in immune and stress responses, and its deregulation contributes to several diseases. Therefore its modulation has become an important therapeutic target. Here, we used a high-throughput screen for small molecules that directly inhibit dimerization of the NF-κB protein p65. One of the identified inhibitors is withaferin A (WFA), a documented anticancer and anti-inflammatory compound. Computational modeling suggests that WFA contacts the dimerization interface on one subunit and surface residues E285 and Q287 on the other. Despite their locations far from the dimerization site, E285 and Q287 substitutions diminished both dimerization and the WFA effect. Further investigation revealed that their effects on dimerization are associated with their proximity to a conserved hydrophobic core domain (HCD) that is crucial for dimerization and DNA binding. Our findings established NF-κB dimerization as a drug target and uncovered an allosteric domain as a target of WFA action.
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Marbach-Bar N, Bahat A, Ashkenazi S, Golan-Mashiach M, Haimov O, Wu SY, Chiang CM, Puzio-Kuter A, Hirshfield KM, Levine AJ, Dikstein R. DTIE, a novel core promoter element that directs start site selection in TATA-less genes. Nucleic Acids Res 2015; 44:1080-94. [PMID: 26464433 PMCID: PMC4756809 DOI: 10.1093/nar/gkv1032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/26/2015] [Indexed: 12/16/2022] Open
Abstract
The transcription start site (TSS) determines the length and composition of the 5′ UTR and therefore can have a profound effect on translation. Yet, little is known about the mechanism underlying start site selection, particularly from promoters lacking conventional core elements such as TATA-box and Initiator. Here we report a novel mechanism of start site selection in the TATA- and Initiator-less promoter of miR-22, through a strictly localized downstream element termed DTIE and an upstream distal element. Changing the distance between them reduced promoter strength, altered TSS selection and diminished Pol II recruitment. Biochemical assays suggest that DTIE does not serve as a docking site for TFIID, the major core promoter-binding factor. TFIID is recruited to the promoter through DTIE but is dispensable for TSS selection. We determined DTIE consensus and found it to be remarkably prevalent, present at the same TSS downstream location in ≈20.8% of human promoters, the vast majority of which are TATA-less. Analysis of DTIE in the tumor suppressor p53 confirmed a similar function. Our findings reveal a novel mechanism of transcription initiation from TATA-less promoters.
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Affiliation(s)
- Nadav Marbach-Bar
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anat Bahat
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shaked Ashkenazi
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Golan-Mashiach
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ora Haimov
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anna Puzio-Kuter
- Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Kim M Hirshfield
- Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Arnold J Levine
- Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Rivka Dikstein
- Dept. of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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8
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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Tamarkin-Ben-Harush A, Schechtman E, Dikstein R. Co-occurrence of transcription and translation gene regulatory features underlies coordinated mRNA and protein synthesis. BMC Genomics 2014; 15:688. [PMID: 25134423 PMCID: PMC4158080 DOI: 10.1186/1471-2164-15-688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/14/2014] [Indexed: 01/08/2023] Open
Abstract
Background Variability in protein levels is generated through intricate control of the different gene decoding phases. Presently little is known about the links between the various gene expression stages. Here we investigated the relationship between transcription and translation regulatory properties encoded in mammalian genes. Results We found that the TATA-box, a core promoter element known to enhance transcriptional output, is associated not only with higher mRNA levels but also with positive translation regulatory features and elevated translation efficiency. Further investigation revealed general association between transcription and translation regulatory trends. Specifically, translation inhibitory features such as the presence of upstream AUG (uAUG) and increased lengths of the 5′UTR, the coding sequence and the 3′UTR, are strongly associated with lower translation as well as lower transcriptional rate. Conclusions Our findings reveal that co-occurrence of several gene-encoded transcription and translation regulatory features with the same trend substantially contributes to the final mRNA and protein expression levels and enables their coordination. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-688) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Rivka Dikstein
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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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.
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Affiliation(s)
- Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, 64110 MO, USA
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