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Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
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2
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Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet 2023; 39:672-685. [PMID: 37236814 PMCID: PMC10524715 DOI: 10.1016/j.tig.2023.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Transcription of eukaryotic genes by RNA polymerase II (Pol II) yields RNA precursors containing introns that must be spliced out and the flanking exons ligated together. Splicing is catalyzed by a dynamic ribonucleoprotein complex called the spliceosome. Recent evidence has shown that a large fraction of splicing occurs cotranscriptionally as the RNA chain is extruded from Pol II at speeds of up to 5 kb/minute. Splicing is more efficient when it is tethered to the transcription elongation complex, and this linkage permits functional coupling of splicing with transcription. We discuss recent progress that has uncovered a network of connections that link splicing to transcript elongation and other cotranscriptional RNA processing events.
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Affiliation(s)
- Hossein Shenasa
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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3
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The upstream 5' splice site remains associated to the transcription machinery during intron synthesis. Nat Commun 2021; 12:4545. [PMID: 34315864 PMCID: PMC8316553 DOI: 10.1038/s41467-021-24774-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/02/2021] [Indexed: 12/28/2022] Open
Abstract
In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF along with other proteins. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns in human cells, we discovered that the nascent 5′ splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. This association functionally corresponds with splicing outcome, involves bona fide 5′ splice sites and cryptic intronic sites, and occurs transcriptome-wide. Overall, our findings reveal that the upstream 5′ splice sites remain attached to the transcriptional machinery during intron synthesis and are thus brought into proximity of the 3′ splice sites; potentially mediating the rapid splicing of long introns. We know that most splicing reactions take place co-transcriptionally, but how the transcription machinery facilitate splicing of introns is unknown. Here the authors show that the 5′ splice site remains associated with the transcription machinery during intron synthesis through U1 snRNP, providing a basis for the rapid splicing reaction of introns.
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4
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An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation. Essays Biochem 2020; 64:907-918. [PMID: 33034346 DOI: 10.1042/ebc20200004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation.
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5
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Yamamoto T, Yamazaki T, Hirose T. Phase separation driven by production of architectural RNA transcripts. SOFT MATTER 2020; 16:4692-4698. [PMID: 32396591 DOI: 10.1039/c9sm02458a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We here use an extension of the Flory-Huggins theory to predict that phase separation is driven by the production of architectural RNA (arcRNA) at a DNA locus with a constant rate. The arcRNA molecules diffuse in the nucleoplasm and show attractive interactions via proteins that are bound to the arcRNA. Our theory predicts that when the Flory interaction parameter is larger than the value at the critical point, the volume fraction of arcRNA jumps between the two values corresponding to the volume fraction of the two coexisting phases at equilibrium at a distance from the DNA locus due to the local equilibrium condition. The distance defines the radius of the condensate that is assembled by the phase separation. When the interaction parameter is large, the volume of the condensates is proportional to the production rate of arcRNA and inversely proportional to the degradation rate of arcRNA. These results imply that most arcRNA molecules are degraded before they diffuse out from the condensates due to the strong segregation of arcRNA.
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Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan.
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6
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Minocha R, Popova V, Kopytova D, Misiak D, Hüttelmaier S, Georgieva S, Sträßer K. Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. Nucleic Acids Res 2019; 46:9749-9763. [PMID: 30053068 PMCID: PMC6182176 DOI: 10.1093/nar/gky640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 07/20/2018] [Indexed: 01/31/2023] Open
Abstract
The different steps of gene expression are intimately linked to coordinate and regulate this complex process. During transcription, numerous RNA-binding proteins are already loaded onto the nascent mRNA and package the mRNA into a messenger ribonucleoprotein particle (mRNP). These RNA-binding proteins are often also involved in other steps of gene expression than mRNA packaging. For example, TREX functions in transcription, mRNP packaging and nuclear mRNA export. Previously, we showed that the Prp19 splicing complex (Prp19C) is needed for efficient transcription as well as TREX occupancy at transcribed genes. Here, we show that the splicing factor Mud2 interacts with Prp19C and is needed for Prp19C occupancy at transcribed genes in Saccharomyces cerevisiae. Interestingly, Mud2 is not only recruited to intron-containing but also to intronless genes indicating a role in transcription. Indeed, we show for the first time that Mud2 functions in transcription. Furthermore, these functions of Mud2 are likely evolutionarily conserved as Mud2 is also recruited to an intronless gene and interacts with Prp19C in Drosophila melanogaster. Taken together, we classify Mud2 as a novel transcription factor that is necessary for the recruitment of mRNA-binding proteins to the transcription machinery. Thus, Mud2 is a multifunctional protein important for transcription, splicing and most likely also mRNP packaging.
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Affiliation(s)
- Rashmi Minocha
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Danny Misiak
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Sofia Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Katja Sträßer
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
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7
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Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019; 11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
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Affiliation(s)
- Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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8
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Biamonti G, Maita L, Montecucco A. The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism. Front Oncol 2018; 8:408. [PMID: 30319972 PMCID: PMC6168629 DOI: 10.3389/fonc.2018.00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a pervasive mechanism that molds the transcriptome to meet cell and organism needs. However, how this layer of gene expression regulation is coordinated with other aspects of the cell metabolism is still largely undefined. Glucose is the main energy and carbon source of the cell. Not surprisingly, its metabolism is finely tuned to satisfy growth requirements and in response to nutrient availability. A number of studies have begun to unveil the connections between glucose metabolism and splicing programs. Alternative splicing modulates the ratio between M1 and M2 isoforms of pyruvate kinase in this way determining the choice between aerobic glycolysis and complete glucose oxidation in the Krebs cycle. Reciprocally, intermediates in the Krebs cycle may impact splicing programs at different levels by modulating the activity of 2-oxoglutarate-dependent oxidases. In this review we discuss the molecular mechanisms that coordinate alternative splicing programs with glucose metabolism, two aspects with profound implications in human diseases.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Lucia Maita
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
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9
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Herzel L, Ottoz DSM, Alpert T, Neugebauer KM. Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. Nat Rev Mol Cell Biol 2017; 18:637-650. [PMID: 28792005 DOI: 10.1038/nrm.2017.63] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Diana S M Ottoz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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10
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Hou Y, Huang H, Hu W, Liu H, Sun X. Histone modifications influence skipped exons inclusion. J Bioinform Comput Biol 2017; 15:1750003. [PMID: 28178888 DOI: 10.1142/s0219720017500032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons. We revealed that the inclusion levels of skipped exons (SEs) were negatively correlated with the enrichment of active histone marks in SEs, indicating a role of histone modifications in AS. We also found that active histone modifications were enriched in the upstream exons of SEs, especially around 5[Formula: see text] splicing sites. We inferred that the histone modifications around the 5[Formula: see text] splicing sites in upstream exon of the SEs could help RNA Polymerase II complex to recruit the effector proteins and facilitate AS. It was indicated that nucleosome occupancy had little influence on the inclusion levels of SEs. At last, we proposed an integrated model that describe how histone modifications affected the pre-mRNA splicing.
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Affiliation(s)
- Yue Hou
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Huan Huang
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Wenqiao Hu
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Hongde Liu
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Xiao Sun
- 1 State Key Laboratory of Bioelectronics, School of Biology Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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11
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Alpert T, Herzel L, Neugebauer KM. Perfect timing: splicing and transcription rates in living cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27873472 DOI: 10.1002/wrna.1401] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
An important step toward understanding gene regulation is the elucidation of the time necessary for the completion of individual steps. Measurement of reaction rates can reveal potential nodes for regulation. For example, measurements of in vivo transcription elongation rates reveal regulation by DNA sequence, gene architecture, and chromatin. Pre-mRNA splicing is regulated by transcription elongation rates and vice versa, yet the rates of RNA processing reactions remain largely elusive. Since the 1980s, numerous model systems and approaches have been used to determine the precise timing of splicing in vivo. Because splicing can be co-transcriptional, the position of Pol II when splicing is detected has been used as a proxy for time by some investigators. In addition to these 'distance-based' measurements, 'time-based' measurements have been possible through live cell imaging, metabolic labeling of RNA, and gene induction. Yet splicing rates can be convolved by the time it takes for transcription, spliceosome assembly and spliceosome disassembly. The variety of assays and systems used has, perhaps not surprisingly, led to reports of widely differing splicing rates in vivo. Recently, single molecule RNA-seq has indicated that splicing occurs more quickly than previously deduced. Here we comprehensively review these findings and discuss evidence that splicing and transcription rates are closely coordinated, facilitating the efficiency of gene expression. On the other hand, introduction of splicing delays through as yet unknown mechanisms provide opportunity for regulation. More work is needed to understand how cells optimize the rates of gene expression for a range of biological conditions. WIREs RNA 2017, 8:e1401. doi: 10.1002/wrna.1401 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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12
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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13
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Hollander D, Naftelberg S, Lev-Maor G, Kornblihtt AR, Ast G. How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing? Trends Genet 2016; 32:596-606. [PMID: 27507607 DOI: 10.1016/j.tig.2016.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/19/2022]
Abstract
The splice sites (SSs) delimiting an intron are brought together in the earliest step of spliceosome assembly yet it remains obscure how SS pairing occurs, especially when introns are thousands of nucleotides long. Splicing occurs in vivo in mammals within minutes regardless of intron length, implying that SS pairing can instantly follow transcription. Also, factors required for SS pairing, such as the U1 small nuclear ribonucleoprotein (snRNP) and U2AF65, associate with RNA polymerase II (RNAPII), while nucleosomes preferentially bind exonic sequences and associate with U2 snRNP. Based on recent publications, we assume that the 5' SS-bound U1 snRNP can remain tethered to RNAPII until complete synthesis of the downstream intron and exon. An additional U1 snRNP then binds the downstream 5' SS, whereas the RNAPII-associated U2AF65 binds the upstream 3' SS to facilitate SS pairing along with exon definition. Next, the nucleosome-associated U2 snRNP binds the branch site to advance splicing complex assembly. This may explain how RNAPII and chromatin are involved in spliceosome assembly and how introns lengthened during evolution with a relatively minimal compromise in splicing.
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Affiliation(s)
- Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Shiran Naftelberg
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.
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14
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Saldi T, Cortazar MA, Sheridan RM, Bentley DL. Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol 2016; 428:2623-2635. [PMID: 27107644 DOI: 10.1016/j.jmb.2016.04.017] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/27/2016] [Accepted: 04/12/2016] [Indexed: 01/07/2023]
Abstract
Pre-mRNA maturation frequently occurs at the same time and place as transcription by RNA polymerase II. The co-transcriptionality of mRNA processing has permitted the evolution of mechanisms that functionally couple transcription elongation with diverse events that occur on the nascent RNA. This review summarizes the current understanding of the relationship between transcriptional elongation through a chromatin template and co-transcriptional splicing including alternative splicing decisions that affect the expression of most human genes.
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Affiliation(s)
- Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Michael A Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA.
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15
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Kralovicova J, Knut M, Cross NCP, Vorechovsky I. Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins. Nucleic Acids Res 2015; 43:3747-63. [PMID: 25779042 PMCID: PMC4402522 DOI: 10.1093/nar/gkv194] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 02/24/2015] [Indexed: 01/05/2023] Open
Abstract
The auxiliary factor of U2 small nuclear RNA (U2AF) is a heterodimer consisting of 65- and 35-kD proteins that bind the polypyrimidine tract (PPT) and AG dinucleotides at the 3′ splice site (3′ss). The gene encoding U2AF35 (U2AF1) is alternatively spliced, giving rise to two isoforms U2AF35a and U2AF35b. Here, we knocked down U2AF35 and each isoform and characterized transcriptomes of HEK293 cells with varying U2AF35/U2AF65 and U2AF35a/b ratios. Depletion of both isoforms preferentially modified alternative RNA processing events without widespread failure to recognize 3′ss or constitutive exons. Over a third of differentially used exons were terminal, resulting largely from the use of known alternative polyadenylation (APA) sites. Intronic APA sites activated in depleted cultures were mostly proximal whereas tandem 3′UTR APA was biased toward distal sites. Exons upregulated in depleted cells were preceded by longer AG exclusion zones and PPTs than downregulated or control exons and were largely activated by PUF60 and repressed by CAPERα. The U2AF(35) repression and activation was associated with a significant interchange in the average probabilities to form single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream. Although most differentially used exons were responsive to both U2AF subunits and their inclusion correlated with U2AF levels, a small number of transcripts exhibited distinct responses to U2AF35a and U2AF35b, supporting the existence of isoform-specific interactions. These results provide new insights into function of U2AF and U2AF35 in alternative RNA processing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Marcin Knut
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Nicholas C P Cross
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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16
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Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet 2014; 15:163-75. [PMID: 24514444 DOI: 10.1038/nrg3662] [Citation(s) in RCA: 544] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maturation of mRNA precursors often occurs simultaneously with their synthesis by RNA polymerase II (Pol II). The co-transcriptional nature of mRNA processing has permitted the evolution of coupling mechanisms that coordinate transcription with mRNA capping, splicing, editing and 3' end formation. Recent experiments using sophisticated new methods for analysis of nascent RNA have provided important insights into the relative amount of co-transcriptional and post-transcriptional processing, the relationship between mRNA elongation and processing, and the role of the Pol II carboxy-terminal domain (CTD) in regulating these processes.
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Affiliation(s)
- David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, MS8101, PO BOX 6511, Aurora, Colorado 80045, USA
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17
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Hartzog GA, Fu J. The Spt4-Spt5 complex: a multi-faceted regulator of transcription elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:105-15. [PMID: 22982195 DOI: 10.1016/j.bbagrm.2012.08.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/21/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
Abstract
In all domains of life, elongating RNA polymerases require the assistance of accessory factors to maintain their processivity and regulate their rate. Among these elongation factors, the Spt5/NusG factors stand out. Members of this protein family appear to be the only transcription accessory proteins that are universally conserved across all domains of life. In archaea and eukaryotes, Spt5 associates with a second protein, Spt4. In addition to regulating elongation, the eukaryotic Spt4-Spt5 complex appears to couple chromatin modification states and RNA processing to transcription elongation. This review discusses the experimental bases for our current understanding of Spt4-Spt5 function and recent studies that are beginning to elucidate the structure of Spt4-Spt5/RNA polymerase complexes and mechanism of Spt4-Spt5 action. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Grant A Hartzog
- Department of MCD Biology, University of California, Santa Cruz, CA 95064, USA.
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18
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David CJ, Boyne AR, Millhouse SR, Manley JL. The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes Dev 2011; 25:972-83. [PMID: 21536736 DOI: 10.1101/gad.2038011] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pre-mRNA splicing is frequently coupled to transcription by RNA polymerase II (RNAPII). This coupling requires the C-terminal domain of the RNAPII largest subunit (CTD), although the underlying mechanism is poorly understood. Using a biochemical complementation assay, we previously identified an activity that stimulates CTD-dependent splicing in vitro. We purified this activity and found that it consists of a complex of two well-known splicing factors: U2AF65 and the Prp19 complex (PRP19C). We provide evidence that both U2AF65 and PRP19C are required for CTD-dependent splicing activation, that U2AF65 and PRP19C interact both in vitro and in vivo, and that this interaction is required for activation of splicing. Providing the link to the CTD, we show that U2AF65 binds directly to the phosphorylated CTD, and that this interaction results in increased recruitment of U2AF65 and PRP19C to the pre-mRNA. Our results not only provide a mechanism by which the CTD enhances splicing, but also describe unexpected interactions important for splicing and its coupling to transcription.
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Affiliation(s)
- Charles J David
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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19
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Spiluttini B, Gu B, Belagal P, Smirnova AS, Nguyen VT, Hébert C, Schmidt U, Bertrand E, Darzacq X, Bensaude O. Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells. J Cell Sci 2010; 123:2085-93. [PMID: 20519584 DOI: 10.1242/jcs.061358] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Numerous non-coding RNAs are known to be involved in the regulation of gene expression. In this work, we analyzed RNAs that co-immunoprecipitated with human RNA polymerase II from mitotic cell extracts and identified U1 small nuclear RNA (snRNA) as a major species. To investigate a possible splicing-independent recruitment of U1 snRNA to transcription units, we established cell lines having integrated a reporter gene containing a functional intron or a splicing-deficient construction. Recruitment of U snRNAs and some splicing factors to transcription sites was evaluated using fluorescence in situ hybridization (FISH) and immunofluorescence. To analyze imaging data, we developed a quantitative procedure, 'radial analysis', based on averaging data from multiple fluorescence images. The major splicing snRNAs (U2, U4 and U6 snRNAs) as well as the U2AF65 and SC35 splicing factors were found to be recruited only to transcription units containing a functional intron. By contrast, U1 snRNA, the U1-70K (also known as snRNP70) U1-associated protein as well as the ASF/SF2 (also known as SFRS1) serine/arginine-rich (SR) protein were efficiently recruited both to normally spliced and splicing-deficient transcription units. The constitutive association of U1 small nuclear ribonucleoprotein (snRNP) with the transcription machinery might play a role in coupling transcription with pre-mRNA maturation.
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Affiliation(s)
- Béatrice Spiluttini
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France
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20
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Allele-specific recognition of the 3' splice site of INS intron 1. Hum Genet 2010; 128:383-400. [PMID: 20628762 PMCID: PMC2939332 DOI: 10.1007/s00439-010-0860-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 06/30/2010] [Indexed: 10/27/2022]
Abstract
Genetic predisposition to type 1 diabetes (T1D) has been associated with a chromosome 11 locus centered on the proinsulin gene (INS) and with differential steady-state levels of INS RNA from T1D-predisposing and -protective haplotypes. Here, we show that the haplotype-specific expression is determined by INS variants that control the splicing efficiency of intron 1. The adenine allele at IVS1-6 (rs689), which rapidly expanded in modern humans, renders the 3' splice site of this intron more dependent on the auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF). This interaction required both zinc fingers of the 35-kD U2AF subunit (U2AF35) and was associated with repression of a competing 3' splice site in INS exon 2. Systematic mutagenesis of reporter constructs showed that intron 1 removal was facilitated by conserved guanosine-rich enhancers and identified additional splicing regulatory motifs in exon 2. Sequencing of intron 1 in primates revealed that relaxation of its 3' splice site in Hominidae coevolved with the introduction of a short upstream open reading frame, providing a more efficient coupled splicing and translation control. Depletion of SR proteins 9G8 and transformer-2 by RNA interference was associated with exon 2 skipping whereas depletion of SRp20 with increased representation of transcripts containing a cryptic 3' splice site in the last exon. Together, these findings reveal critical interactions underlying the allele-dependent INS expression and INS-mediated risk of T1D and suggest that the increased requirement for U2AF35 in higher primates may hinder thymic presentation of autoantigens encoded by transcripts with weak 3' splice sites.
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21
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RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol 2010; 17:815-21. [PMID: 20562857 PMCID: PMC2921552 DOI: 10.1038/nsmb.1827] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/08/2010] [Indexed: 01/11/2023]
Abstract
The transition from transcription initiation to elongation at the HIV-1 promoter is controlled by Tat, which recruits P-TEFb to TAR RNA to phosphorylate RNA polymerase II. It has long been unclear why the HIV-1 promoter is incompetent for elongation. We report that P-TEFb is recruited to the promoter in a catalytically inactive state bound to the inhibitory 7SK snRNP, thereby preventing elongation. It also has long been believed that TAR functions to recruit Tat to the promoter, but we find that Tat is recruited to the DNA template before TAR is synthesized. We propose that TAR binds Tat and P-TEFb as it emerges on the nascent transcript, competitively displacing the inhibitory 7SK snRNP and activating the P-TEFb kinase. Recruitment of an inhibitory snRNP complex at an early stage in the transcription cycle provides a new paradigm for controlling gene expression with a non-coding RNA.
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22
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Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat Struct Mol Biol 2009; 16:916-22. [PMID: 19701200 PMCID: PMC2755206 DOI: 10.1038/nsmb.1652] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 06/29/2009] [Indexed: 02/06/2023]
Abstract
We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis delta ribozyme, but not the slower hammerhead, inhibited splicing. Therefore, exon tethering to RNA polymerase II (Pol II) cannot rescue splicing of a transcript severed by a ribozyme that cleaves rapidly relative to the rate of splicing. Ribozyme cutting also released cap-binding complex (CBC) from the gene, suggesting that exon 1 is not tethered. Unexpectedly, cutting within exons inhibited splicing of distal introns, where exon definition is not affected, probably owing to disruption of the interactions with the CBC and the Pol II C-terminal domain that facilitate splicing. Ribozyme cutting within the mRNA also inhibited 3' processing and transcription termination. We propose that damaging the nascent transcript aborts pre-mRNA processing and that this mechanism may help to prevent association of processing factors with Pol II that is not productively engaged in transcription.
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23
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Rigo F, Martinson HG. Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA (NEW YORK, N.Y.) 2009; 15:823-36. [PMID: 19304926 PMCID: PMC2673064 DOI: 10.1261/rna.1409209] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
When transcription is coupled to pre-mRNA processing in HeLa nuclear extracts nascent transcripts become attached to RNA polymerase II during assembly of the cleavage/polyadenylation apparatus (CPA), and are not released even after cleavage at the poly(A) site. Here we show that these cleaved transcripts are anchored to the polymerase at their 3' ends by the CPA or, when introns are present, by the larger 3'-terminal exon definition complex (EDC), which consists of splicing factors complexed with the CPA. Poly(A) addition releases the RNA from the polymerase when the RNA is anchored only by the CPA. When anchored by the EDC, poly(A) addition remains a requirement, but it triggers release only after being licensed by splicing. The process by which RNA must first be attached to the polymerase by the EDC, and then can only be released following dual inputs from splicing and polyadenylation, provides an obvious opportunity for surveillance as the RNA enters the transport pathway.
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Affiliation(s)
- Frank Rigo
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569, USA
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24
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Abstract
A large share of mRNA processing and packaging events occurs cotranscriptionally. To explore the hypothesis that transcription defects may affect mRNA fate, we analyzed poly(A)(+) RNA distribution in Saccharomyces cerevisiae strains harboring mutations in Rpb1p, the largest subunit of RNA polymerase II. In certain rpb1 mutants, a poly(A)(+) RNA granule, distinct from any known structure, strongly accumulated in a confined space of the cytoplasm. RNA and protein expressed from Ty1 retrovirus-like elements colocalized with this new granule, which we have consequently named the T body. A visual screen revealed that the deletion of most genes with proposed functions in Ty1 biology unexpectedly does not alter T-body levels. In contrast, the deletion of genes encoding the Mediator transcription initiation factor subunits Srb2p and Srb5p as well as the Ty1 transcriptional regulator Spt21p greatly enhances T-body formation. Our data disclose a new cellular body putatively involved in the assembly of Ty1 particles and suggest that the cytoplasmic fate of mRNA can be affected by transcription initiation events.
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25
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Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. J Virol 2008; 82:9492-504. [PMID: 18667497 DOI: 10.1128/jvi.00763-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) transcription is regulated by the viral Tat protein, which relieves a block to elongation by recruiting an elongation factor, P-TEFb, to the viral promoter. Here, we report the discovery of potent Tat inhibitors that utilize a localization signal to target a dominant negative protein to its site of action. Fusing the Tat activation domain to some splicing factors, particularly to the Arg-Ser (RS) domain of U2AF65, creates Tat inhibitors that localize to subnuclear speckles, sites where pre-mRNA processing factors are stored for assembly into transcription complexes. A U2AF65 fusion named T-RS interacts with the nonphosphorylated C-terminal domain of RNA polymerase II (RNAP II) via its RS domain and is loaded into RNAP II holoenzyme complexes. T-RS is recruited efficiently to the HIV-1 promoter in a TAR-independent manner before RNAP II hyperphosphorylation but not to cellular promoters. The "preloading" of T-RS into HIV-1 preinitiation complexes prevents the entry of active Tat molecules, leaving the complexes in an elongation-incompetent state and effectively suppressing HIV-1 replication. The ability to deliver inhibitors to transcription complexes through the use of targeting/localization signals may provide new avenues for designing viral and transcription inhibitors.
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26
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Abstract
The time taken to transcribe most metazoan genes is significant because of the substantial length of introns. Developmentally regulated gene networks, where timing and dynamic patterns of expression are critical, may be particularly sensitive to intron delays. We revisit and comment on a perspective last presented by Thummel 16 years ago: transcriptional delays may contribute to timing mechanisms during development. We discuss the presence of intron delays in genetic networks. We consider how delays can impact particular moments during development, which mechanistic attributes of transcription can influence them, how they can be modeled, and how they can be studied using recent technological advances as well as classical genetics.
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Affiliation(s)
- Ian A Swinburne
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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27
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Functional coupling of last-intron splicing and 3'-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage. Mol Cell Biol 2007; 28:849-62. [PMID: 17967872 DOI: 10.1128/mcb.01410-07] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed an in vitro transcription system, using HeLa nuclear extract, that supports not only efficient splicing of a multiexon transcript but also efficient cleavage and polyadenylation. In this system, both last-intron splicing and cleavage/polyadenylation are functionally coupled to transcription via the tether of nascent RNA that extends from the terminal exon to the transcribing polymerase downstream. Communication between the 3' splice site and the poly(A) site across the terminal exon is established within minutes of their transcription, and multiple steps leading up to 3'-end processing of this exon can be distinguished. First, the 3' splice site establishes connections to enhance 3'-end processing, while the nascent 3'-end processing apparatus makes reciprocal functional connections to enhance splicing. Then, commitment to poly(A) site cleavage itself occurs and the connections of the 3'-end processing apparatus to the transcribing polymerase are strengthened. Finally, the chemical steps in the processing of the terminal exon take place, beginning with poly(A) site cleavage, continuing with polyadenylation of the 3' end, and then finishing with splicing of the last intron.
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28
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Das R, Yu J, Zhang Z, Gygi MP, Krainer AR, Gygi SP, Reed R. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol Cell 2007; 26:867-81. [PMID: 17588520 DOI: 10.1016/j.molcel.2007.05.036] [Citation(s) in RCA: 265] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 03/06/2007] [Accepted: 05/25/2007] [Indexed: 01/11/2023]
Abstract
Transcription and splicing are functionally coupled, resulting in highly efficient splicing of RNA polymerase II (RNAP II) transcripts. The mechanism involved in this coupling is not known. To identify potential coupling factors, we carried out a comprehensive proteomic analysis of immunopurified human RNAP II, identifying >100 specifically associated proteins. Among these are the SR protein family of splicing factors and all of the components of U1 snRNP, but no other snRNPs or splicing factors. We show that SR proteins function in coupling transcription to splicing and provide evidence that the mechanism involves cotranscriptional recruitment of SR proteins to RNAP II transcripts. We propose that the exclusive association of U1 snRNP/SR proteins with RNAP II positions these splicing factors, which are known to function early in spliceosome assembly, close to the nascent pre-mRNA. Thus, these factors readily out-compete inhibitory hnRNP proteins, resulting in efficient spliceosome assembly on nascent RNAP II transcripts.
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Affiliation(s)
- Rita Das
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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29
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Dye MJ, Gromak N, Haussecker D, West S, Proudfoot NJ. Turnover and function of noncoding RNA polymerase II transcripts. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:275-84. [PMID: 17381307 DOI: 10.1101/sqb.2006.71.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the past few years, especially since the discovery of RNA interference (RNAi), our understanding of the role of RNA in gene expression has undergone a significant transformation. This change has been brought about by growing evidence that RNA is more complex and transcription more promiscuous than has previously been thought. Many of the new transcripts are of so-called noncoding RNA (ncRNA); i.e., RNA that does not code for proteins such as mRNA, or intrinsic parts of the cellular machinery such as the highly structured RNA components of ribosomes (rRNA) and the small nuclear RNA (snRNA) components of the splicing machinery. It is becoming increasingly apparent that ncRNAs have very important roles in gene expression. This paper focuses on work from our laboratory in which we have investigated the roles and turnover of ncRNA located within the gene pre-mRNA, which we refer to as intragenic ncRNA. Also discussed are some investigations of intergenic ncRNA transcription and how these two classes of ncRNA may interrelate.
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Affiliation(s)
- M J Dye
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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30
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Cheng B, Price DH. Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J Biol Chem 2007; 282:21901-12. [PMID: 17548348 DOI: 10.1074/jbc.m702936200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The positive transcription elongation factor, P-TEFb, controls the fraction of initiated RNA polymerase II molecules that enter into the productive mode of elongation necessary to generate mRNAs. To better understand the mechanism of this transition into productive elongation we optimized a defined in vitro transcription system and compared results obtained with it to those obtained with a crude system. We found that controlling the function of TFIIF is a key aspect of RNA polymerase II elongation control. Before P-TEFb function, early elongation complexes under the control of negative factors are completely unresponsive to the robust elongation stimulatory activity of TFIIF. P-TEFb-mediated phosphorylation events, targeting the elongation complex containing DSIF and NELF, reverse the negative effect of DSIF and NELF and simultaneously facilitate the action of TFIIF. We also found that productive elongation complexes are completely resistant to negative elongation factors. Our data suggest that an additional factor(s) is involved in establishing the unique resistance activities of the elongation complexes before and after P-TEFb function. Furthermore, we provide evidence for the existence of another positive activity required for efficient function of P-TEFb. A model of the mechanism of P-TEFb-mediated elongation control is proposed in which P-TEFb induces the transition into productive elongation by changing the accessibility of elongation factors to elongation complexes. Our results have uncovered important properties of elongation complexes that allow a more complete understanding of how P-TEFb controls the elongation phases of transcription by RNA polymerase II.
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Affiliation(s)
- Bo Cheng
- Department of Biochemistry, Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242, USA
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31
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Gendra E, Colgan DF, Meany B, Konarska MM. A sequence motif in the simian virus 40 (SV40) early core promoter affects alternative splicing of transcribed mRNA. J Biol Chem 2007; 282:11648-57. [PMID: 17331949 DOI: 10.1074/jbc.m611126200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To identify new sequence elements in the promoter that affect splicing patterns of pre-mRNAs, we analyzed effects of different promoters on alternative splicing of model reporter genes. We compared the E1a alternative splicing pattern in transcripts expressed from the full-length cytomegalovirus, SV40 early, or a hybrid cytomegalovirus/SV40 early promoter and found that the hybrid promoter improved selection of the suboptimal E1a 5'SS-1. Expressing RNA from the hybrid promoter also enhanced selection of suboptimal splice sites in other alternatively spliced reporter genes, demonstrating the generality of this effect. Unlike previously defined promoter elements shown to affect alternative splicing, which were located in the enhancer/upstream activating sequences, the motif identified in this work is positioned within the core promoter; it is comprised of eight T-residues directly upstream of the SV40 early TATA box. This motif was previously implicated in DNA bending and negative regulation of transcription. Together, these results suggest that the identity of transcription complex assembled in the core promoter-dependent fashion can affect splice site selection during pre-mRNA splicing, perhaps by influencing the processivity of transcription elongation.
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32
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Abstract
Numerous studies support the idea that the complex process of gene expression is composed of multiple highly coordinated and integrated steps. While such an extensive coupling ensures the efficiency and accuracy of each step during the gene expression pathway, recent studies have suggested an evolutionarily conserved function for cotranscriptional processes in the maintenance of genome stability. Specifically, such processes prevent a detrimental effect of nascent transcripts on the integrity of the genome. Here we describe studies indicating that nascent transcripts can rehybridize with template DNA, and that this can lead to DNA strand breaks and rearrangements. We present an overview of the diverse mechanisms that different species employ to keep nascent RNA away from DNA during transcription. We also discuss possible mechanisms by which nascent transcripts impact genome stability, as well as the possibility that transcription-induced genomic instability may contribute to disease.
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Affiliation(s)
- Xialu Li
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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33
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Listerman I, Sapra AK, Neugebauer KM. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 2006; 13:815-22. [PMID: 16921380 DOI: 10.1038/nsmb1135] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 07/24/2006] [Indexed: 01/09/2023]
Abstract
Coupling between transcription and RNA processing is a key gene regulatory mechanism. Here we use chromatin immunoprecipitation to detect transcription-dependent accumulation of the precursor mRNA (pre-mRNA) splicing factors hnRNP A1, U2AF65 and U1 and U5 snRNPs on the intron-containing human FOS gene. These factors were poorly detected on intronless heat-shock and histone genes, a result that opposes direct recruitment by RNA polymerase II (Pol II) or the cap-binding complex in vivo. However, an observed RNA-dependent interaction between U2AF65 and active forms of Pol II may stabilize U2AF65 binding to intron-containing nascent RNA. We establish chromatin-RNA immunoprecipitation and show that FOS pre-mRNA is cotranscriptionally spliced. Notably, the topoisomerase I inhibitor camptothecin, which stalls elongating Pol II, increased cotranscriptional splicing factor accumulation and splicing in parallel. This provides direct evidence for a kinetic link between transcription, splicing factor recruitment and splicing catalysis.
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Affiliation(s)
- Imke Listerman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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34
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Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res 2006; 16:912-21. [PMID: 16769980 PMCID: PMC1484458 DOI: 10.1101/gr.5211806] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA binding proteins by chromatin immunoprecipitation (ChIP) as a way of determining their sites of action on the encoded mRNA. Here, we used ChIP combined with high-density microarrays to localize on the human genome three functionally distinct RNA binding proteins: the splicing factor polypyrimidine tract binding protein (PTBP1/hnRNP I), the mRNA export factor THO complex subunit 4 (ALY/THOC4), and the 3' end cleavage stimulation factor 64 kDa (CSTF2). We observed interactions at promoters, internal exons, and 3' ends of active genes. PTBP1 had biases toward promoters and often coincided with RNA polymerase II (RNA Pol II). The 3' processing factor, CSTF2, had biases toward 3' ends but was also observed at promoters. The mRNA processing and export factor, ALY, mapped to some exons but predominantly localized to introns and did not coincide with RNA Pol II. Because the RNA binding proteins did not consistently coincide with RNA Pol II, the data support a processing mechanism driven by reorganization of transcription complexes as opposed to a scanning mechanism. In sum, we present the mapping in mammalian cells of RNA binding proteins across a portion of the genome that provides insight into the transcriptional assembly of RNA-protein complexes.
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Affiliation(s)
- Ian A. Swinburne
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Clifford A. Meyer
- Departments of Biostatistics and Computational Biology, The Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - X. Shirley Liu
- Departments of Biostatistics and Computational Biology, The Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Corresponding authors.E-mail ; fax (401) 863-9653.E-mail ; fax (401) 863-9653
| | - Alexander S. Brodsky
- Department of Cancer Biology, The Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Corresponding authors.E-mail ; fax (401) 863-9653.E-mail ; fax (401) 863-9653
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35
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Dye MJ, Gromak N, Proudfoot NJ. Exon tethering in transcription by RNA polymerase II. Mol Cell 2006; 21:849-59. [PMID: 16543153 DOI: 10.1016/j.molcel.2006.01.032] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 12/12/2005] [Accepted: 01/30/2006] [Indexed: 10/24/2022]
Abstract
There is an emerging consensus that RNA polymerase II (RNA Pol II) transcription and pre-mRNA processing are tightly coupled events. We show here that exons flanking an intron that has been engineered to be co-transcriptionally cleaved are accurately and efficiently spliced together. These data underline the close coupling of processes in the initial stages of protein-encoding gene expression and provide evidence for a molecular tether connecting emergent splice sites in the pre-mRNA to transcribing RNA Pol II. This observation suggests that for some genes a continuous intron transcript is not required for pre-mRNA splicing in vivo.
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Affiliation(s)
- Michael J Dye
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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Ujvári A, Luse DS. RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit. Nat Struct Mol Biol 2005; 13:49-54. [PMID: 16327806 DOI: 10.1038/nsmb1026] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Accepted: 10/25/2005] [Indexed: 01/22/2023]
Abstract
Structural studies of RNA polymerase II have suggested two possible exit paths for the nascent RNA: groove 1, which points toward the subcomplex of subunits Rpb4 and Rpb7, and groove 2, which points toward Rpb8. These alternatives could not be distinguished previously because less than 10 nucleotides (nt) of transcript were resolved in the structures. We have approached this question by UV cross-linking nascent RNA to components of the transcription complex through uridine analogs located within the first six nucleotides of the RNA. We find that the emerging transcript cross-links to the Rpb7 subunit of RNA polymerase II in various complexes containing 26- to 32-nt transcripts. This interaction is greatly reduced in complexes with 41- or 43-nt RNAs and absent when the transcript is 125 nt. Our results are consistent with groove 1 being the exit path for nascent RNA.
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Affiliation(s)
- Andrea Ujvári
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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Abstract
Transcription is coupled with the concomitant assembly of RNA-binding proteins to the nascent mRNA to generate a stable and export-competent mRNP particle. RNA-binding factors recruited at active transcription sites specify the processing, nuclear export, subcellular localization, translation and stability of the mRNA. The assembly of the mRNP particle starts with the association of the cap-binding protein complex followed by the splicing-dependent assembly of the exon-junction complex in intron-containing genes and by the binding of RNA-export adaptor proteins. New findings suggest that mRNP assembly is a genetically controlled process that plays a key role in gene expression and other cellular processes, including the maintenance of genome integrity.
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Affiliation(s)
- Andrés Aguilera
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Avd. Reina Mercedes 6, 41012 Sevilla, Spain.
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Görnemann J, Kotovic KM, Hujer K, Neugebauer KM. Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 2005; 19:53-63. [PMID: 15989964 DOI: 10.1016/j.molcel.2005.05.007] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Coupling between transcription and pre-mRNA splicing is a key regulatory mechanism in gene expression. Here, we investigate cotranscriptional spliceosome assembly in yeast, using in vivo crosslinking to determine the distribution of spliceosome components along intron-containing genes. Accumulation of the U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) and the 3' splice site binding factors Mud2p and BBP was detected in patterns indicative of progressive and complete spliceosome assembly; recruitment of the nineteen complex (NTC) component Prp19p suggests that splicing catalysis is also cotranscriptional. The separate dynamics of the U1, U2, and U5 snRNPs are consistent with stepwise recruitment of individual snRNPs rather than a preformed "penta-snRNP", as recently proposed. Finally, we show that the cap binding complex (CBC) is necessary, but not sufficient, for cotranscriptional spliceosome assembly. Thus, the demonstration of an essential link between CBC and spliceosome assembly in vivo indicates that 5' end capping couples pre-mRNA splicing to transcription.
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Affiliation(s)
- Janina Görnemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol 2005; 6:R64. [PMID: 16086846 PMCID: PMC1273631 DOI: 10.1186/gb-2005-6-8-r64] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 04/07/2005] [Accepted: 06/17/2005] [Indexed: 11/15/2022] Open
Abstract
Determination of the distribution of RNA Polymerase II within regions of the human genome identifies novel sites of transcription and suggests that a major factor of transcription elongation control in mammals is the coordination of transcription and pre-mRNA processing to define exons. Background Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation. RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows. Results To further understand transcriptional regulation at a global level, we determined the distribution of RNA polymerase II within regions of the human genome designated by the ENCODE project. Hypophosphorylated RNA polymerase II localizes almost exclusively to 5' ends of genes. On the other hand, localization of total RNA polymerase II reveals a variety of distinct landscapes across many genes with 74% of the observed enriched locations at exons. RNA polymerase II accumulates at many annotated constitutively spliced exons, but is biased for alternatively spliced exons. Finally, RNA polymerase II is also observed at locations not in gene regions. Conclusion Localizing RNA polymerase II across many millions of base pairs in the human genome identifies novel sites of transcription and provides insights into the regulation of transcription elongation. These data indicate that RNA polymerase II accumulates most often at exons during transcription. Thus, a major factor of transcription elongation control in mammalian cells is the coordination of transcription and pre-mRNA processing to define exons.
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Affiliation(s)
- Alexander S Brodsky
- Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
| | - Clifford A Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02155, USA
| | - Ian A Swinburne
- Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
| | - Giles Hall
- Department of Medicine, Harvard Medical School and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Benjamin J Keenan
- Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
| | - Xiaole S Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02155, USA
| | - Edward A Fox
- Department of Medicine, Harvard Medical School and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
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Brès V, Gomes N, Pickle L, Jones KA. A human splicing factor, SKIP, associates with P-TEFb and enhances transcription elongation by HIV-1 Tat. Genes Dev 2005; 19:1211-26. [PMID: 15905409 PMCID: PMC1132007 DOI: 10.1101/gad.1291705] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
HIV-1 Tat binds human CyclinT1 and recruits the CDK9/P-TEFb complex to the viral TAR RNA in a step that links RNA polymerase II (RNAPII) C-terminal domain (CTD) Ser 2 phosphorylation with transcription elongation. Previous studies have suggested a connection between Tat and pre-mRNA splicing factors. Here we show that the splicing-associated c-Ski-interacting protein, SKIP, is required for Tat transactivation in vivo and stimulates HIV-1 transcription elongation, but not initiation, in vitro. SKIP associates with CycT1:CDK9/P-TEFb and Tat:P-TEFb complexes in nuclear extracts and interacts with recombinant Tat:P-TEFb:TAR RNA complexes in vitro, indicating that it may act through nascent RNA to overcome pausing by RNAPII. SKIP also associates with U5snRNP proteins and tri-snRNP110K in nuclear extracts, and facilitates recognition of an alternative Tat-specific splice site in vivo. The effects of SKIP on transcription elongation, binding to P-TEFb, and splicing are mediated through the SNW domain. HIV-1 Tat transactivation is accompanied by the recruitment of P-TEFb, SKIP, and tri-snRNP110K to the integrated HIV-1 promoter in vivo, whereas the U5snRNPs associate only with the transcribed coding region. These findings suggest that SKIP plays independent roles in transcription elongation and pre-mRNA splicing.
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Affiliation(s)
- Vanessa Brès
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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