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Sharma S, Anand R, Zhang X, Francia S, Michelini F, Galbiati A, Williams H, Ronato DA, Masson JY, Rothenberg E, Cejka P, d'Adda di Fagagna F. MRE11-RAD50-NBS1 Complex Is Sufficient to Promote Transcription by RNA Polymerase II at Double-Strand Breaks by Melting DNA Ends. Cell Rep 2021; 34:108565. [PMID: 33406426 PMCID: PMC7788559 DOI: 10.1016/j.celrep.2020.108565] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex supports the synthesis of damage-induced long non-coding RNA (dilncRNA) by RNA polymerase II (RNAPII) from DNA double-strand breaks (DSBs) by an unknown mechanism. Here, we show that recombinant human MRN and native RNAPII are sufficient to reconstitute a minimal functional transcriptional apparatus at DSBs. MRN recruits and stabilizes RNAPII at DSBs. Unexpectedly, transcription is promoted independently from MRN nuclease activities. Rather, transcription depends on the ability of MRN to melt DNA ends, as shown by the use of MRN mutants and specific allosteric inhibitors. Single-molecule FRET assays with wild-type and mutant MRN show a tight correlation between the ability to melt DNA ends and to promote transcription. The addition of RPA enhances MRN-mediated transcription, and unpaired DNA ends allow MRN-independent transcription by RNAPII. These results support a model in which MRN generates single-strand DNA ends that favor the initiation of transcription by RNAPII.
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Affiliation(s)
- Sheetal Sharma
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Xuzhu Zhang
- NYU Langone Medical Center, 450 East 29th Street, New York, NY, USA
| | - Sofia Francia
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia 2700, Italy
| | - Flavia Michelini
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | | | - Daryl A Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 2J6, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 2J6, Canada
| | - Eli Rothenberg
- NYU Langone Medical Center, 450 East 29th Street, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland.
| | - Fabrizio d'Adda di Fagagna
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia 2700, Italy.
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Voss C, Schmitt B, Werner-Simon S, Lutz C, Simon W, Anderl J. A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity. BMC Mol Biol 2014; 15:7. [PMID: 24694320 PMCID: PMC4021065 DOI: 10.1186/1471-2199-15-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 03/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Many studies of the eukaryotic transcription mechanism and its regulation rely on in vitro assays. Conventional RNA polymerase II transcription assays are based on radioactive labelling of the newly synthesized RNA. Due to the inefficient in vitro transcription, the detection of the RNA involving purification and gel electrophoresis is laborious and not always quantitative. Results Herein, we describe a new, non-radioactive, robust and reproducible eukaryotic in vitro transcription assay that has been established in our laboratory. Upon transcription, the newly synthesized RNA is directly detected and quantified using the QuantiGene assay. Alternatively, the RNA can be purified and a primer extension followed by PCR detection or qPCR quantification can be performed. When applied to assess the activity of RNA polymerase II inhibitors, this new method allowed an accurate estimation of their relative potency. Conclusions Our novel assay provides a non-radioactive alternative to a standard in vitro transcription assay that allows for sensitive detection and precise quantification of the newly transcribed, unlabelled RNA and is particularly useful for quantification of strong transcriptional inhibitors like α-amanitin. Moreover, the method can be easily adapted to quantify the reaction yield and the transcription efficiency of other eukaryotic in vitro systems, thus providing a complementary tool for the field of transcriptional research.
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Affiliation(s)
- Cristina Voss
- Department of Biochemistry and Cell Biology, Heidelberg-Pharma GmbH, Schriesheimer Str, 101, Ladenburg D-68526, Germany.
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Biochemical analyses of nuclear receptor-dependent transcription with chromatin templates. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:137-92. [PMID: 20374704 DOI: 10.1016/s1877-1173(09)87005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Chromatin, the physiological template for transcription, plays important roles in gene regulation by nuclear receptors (NRs). It can (1) restrict the binding of NRs or the transcriptional machinery to their genomic targets, (2) serve as a target of regulatory posttranslational modifications by NR coregulator proteins with histone-directed enzymatic activities, and (3) function as a binding scaffold for a variety of transcription-related proteins. The advent of in vitro or "cell-free" systems that accurately recapitulate ligand-dependent transcription by NRs with chromatin templates has allowed detailed analyses of these processes. Biochemical studies have advanced our understanding of the mechanisms of gene regulation, including the role of ligands, coregulators, and nucleosome remodeling. In addition, they have provided new insights about the dynamics of NR-mediated transcription. This chapter reviews the current methodologies for assembling, transcribing, and analyzing chromatin in vitro, as well as the new information that has been gained from these studies.
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Transcription of in vitro assembled chromatin templates in a highly purified RNA polymerase II system. Methods 2009; 48:353-60. [PMID: 19272450 DOI: 10.1016/j.ymeth.2009.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 02/25/2009] [Indexed: 11/20/2022] Open
Abstract
In mammalian cells RNA polymerase II efficiently transcribes nucleosome-packaged DNA. In this regard, a fundamental question concerns the nature and mechanism of action of the accessory factors that are necessary and sufficient for, or enhance, transcription through nucleosomal arrays by RNA polymerase II. Here we describe a highly purified system that allows for efficient activator-dependent transcription by RNA polymerase II from the promoter through several contiguous nucleosomes on defined chromatin templates. The system contains natural or recombinant histones, chromatin assembly factors, the histone-acetyltransferase p300, all components of the general transcription machinery, general coactivators and the elongation factor SII (TFIIS). As examples of the applicability of this system for mechanistic analyses of these and other factors, representative experiments show (i) that activated transcription from chromatin templates is concomitantly dependent on the activator, p300-mediated histone acetylation and elongation factor SII/TFIIS. (ii) that SII/TFIIS acts in a highly synergistic manner with p300 (and histone acetylation) at a step subsequent to preinitiation complex (PIC) formation and (iii) that SII/TFIIS works directly at the elongation step of chromatin transcription. Here we describe purification methods for the different factors employed and the specific transcriptional assays that led to the above-mentioned conclusions. This purified system will be very useful as an assay system for the discovery of new factors or the mechanistic analysis of known or candidate factors involved in transcription initiation or elongation on chromatin templates, including factors that effect specific histone modifications or nucleosomal remodeling.
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Abstract
Transcription of protein-coding genes is one of the most fundamental processes that underlies all life and is a primary mechanism of biological regulation. In eukaryotic cells, transcription depends on the formation of a complex at the promoter region of the gene that minimally includes RNA polymerase II and several auxiliary proteins known as the general transcription factors. Transcription initiation follows at the promoter site given the availability of nucleoside triphosphates and ATP. Soon after the polymerase begins the synthesis of the nascent mRNA chain, it enters a critical stage, referred to as promoter escape, that is characterized by physical and functional instability of the transcription complex. These include formation of abortive transcripts, strong dependence on ATP cofactor, the general transcription factor TFIIH and downstream template. These criteria are no longer in effect when the nascent RNA reaches a length of 14-15 nucleotides. Towards the end of promoter escape, disruption or adjustment of protein-protein and protein-DNA interactions, including the release of some of the general transcription factors from the early transcription complex is to be expected, allowing the transition to the elongation stage of transcription. In this review, we examine the experimental evidence that defines promoter escape as a distinct stage in transcription, and point out areas where critical information is missing.
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MESH Headings
- HeLa Cells
- Humans
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/physiology
- RNA Polymerase II/chemistry
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/metabolism
- Sarcosine/analogs & derivatives
- Sarcosine/pharmacology
- Transcription Factor TFIIH
- Transcription Factors, General/chemistry
- Transcription Factors, General/metabolism
- Transcription Factors, TFII/genetics
- Transcription Factors, TFII/metabolism
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Arik Dvir
- Department of Biological Sciences, Oakland University, Rochester, MI 48309-4401, USA.
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Mizuguchi G, Vassilev A, Tsukiyama T, Nakatani Y, Wu C. ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J Biol Chem 2001; 276:14773-83. [PMID: 11279013 DOI: 10.1074/jbc.m100125200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Drosophila nucleosome remodeling factor (NURF) is an ISWI-containing protein complex that facilitates nucleosome mobility and transcriptional activation in an ATP-dependent manner. Numerous studies have implicated histone acetylation in transcriptional activation. We investigated the relative contributions of these two chromatin modifications to transcription in vitro of a chromatinized adenovirus E4 minimal promoter that contains binding sites for the GAL4-VP16 activator. We found that NURF could remodel chromatin and stimulate transcription irrespective of the acetylation status of histones. In contrast, hyperacetylation of histones in the absence of NURF was unable to stimulate transcription, suggesting that NURF-dependent chromatin remodeling is an obligatory step in E4 promoter activation. When chromatin templates were first hyperacetylated and then incubated with NURF, significantly greater transcription stimulation was observed. The results suggest that changes in chromatin induced by acetylation of histones and the mobilization of nucleosomes by NURF combine synergistically to facilitate transcription. Experiments using single and multiple rounds of transcription indicate that these chromatin modifications stimulate transcription preinitiation as well as reinitiation.
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Affiliation(s)
- G Mizuguchi
- Laboratory of Molecular Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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