1
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Francette AM, Arndt KM. Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications. Cell Rep 2024; 43:114730. [PMID: 39244754 DOI: 10.1016/j.celrep.2024.114730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/17/2024] [Accepted: 08/23/2024] [Indexed: 09/10/2024] Open
Abstract
The polymerase-associated factor 1 (Paf1) complex (Paf1C) is a conserved protein complex with critical functions during eukaryotic transcription. Previous studies showed that Paf1C is multi-functional, controlling specific aspects of transcription ranging from RNA polymerase II (RNAPII) processivity to histone modifications. However, it is unclear how specific Paf1C subunits directly impact transcription and coupled processes. We have compared conditional depletion to steady-state deletion for each Paf1C subunit to determine the direct and indirect contributions to gene expression in Saccharomyces cerevisiae. Using nascent transcript sequencing, RNAPII profiling, and modeling of transcription elongation dynamics, we have demonstrated direct effects of Paf1C subunits on RNAPII processivity and elongation rate and indirect effects on transcript splicing and repression of antisense transcripts. Further, our results suggest that the direct transcriptional effects of Paf1C cannot be readily assigned to any particular histone modification. This work comprehensively analyzes both the immediate and the extended roles of each Paf1C subunit in transcription elongation and transcript regulation.
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Affiliation(s)
- Alex M Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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2
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Merens HE, Choquet K, Baxter-Koenigs AR, Churchman LS. Timing is everything: advances in quantifying splicing kinetics. Trends Cell Biol 2024:S0962-8924(24)00070-9. [PMID: 38777664 DOI: 10.1016/j.tcb.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
Splicing is a highly regulated process critical for proper pre-mRNA maturation and the maintenance of a healthy cellular environment. Splicing events are impacted by ongoing transcription, neighboring splicing events, and cis and trans regulatory factors on the respective pre-mRNA transcript. Within this complex regulatory environment, splicing kinetics have the potential to influence splicing outcomes but have historically been challenging to study in vivo. In this review, we highlight recent technological advancements that have enabled measurements of global splicing kinetics and of the variability of splicing kinetics at single introns. We demonstrate how identifying features that are correlated with splicing kinetics has increased our ability to form potential models for how splicing kinetics may be regulated in vivo.
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Affiliation(s)
- Hope E Merens
- Harvard University, Department of Genetics, Boston, MA, USA
| | - Karine Choquet
- University of Sherbrooke, Department of Biochemistry and Functional Genomics, Sherbrooke, Québec, Canada
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3
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Francette AM, Arndt KM. Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591159. [PMID: 38712269 PMCID: PMC11071476 DOI: 10.1101/2024.04.25.591159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Paf1C is a highly conserved protein complex with critical functions during eukaryotic transcription. Previous studies have shown that Paf1C is multi-functional, controlling specific aspects of transcription, ranging from RNAPII processivity to histone modifications. However, it is unclear how specific Paf1C subunits directly impact transcription and coupled processes. We have compared conditional depletion to steady-state deletion for each Paf1C subunit to determine the direct and indirect contributions to gene expression in Saccharomyces cerevisiae. Using nascent transcript sequencing, RNAPII profiling, and modeling of transcription elongation dynamics, we have demonstrated direct effects of Paf1C subunits on RNAPII processivity and elongation rate and indirect effects on transcript splicing and repression of antisense transcripts. Further, our results suggest that the direct transcriptional effects of Paf1C cannot be readily assigned to any particular histone modification. This work comprehensively analyzes both the immediate and extended roles of each Paf1C subunit in transcription elongation and transcript regulation.
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Affiliation(s)
- Alex M. Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
- Lead contact
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4
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Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A. Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife 2024; 12:RP91357. [PMID: 38577979 PMCID: PMC10997330 DOI: 10.7554/elife.91357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
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Affiliation(s)
- Allison Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Aoife O'Farrell
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Ian Dardani
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Margaret Dunagin
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Chris Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Yihan Wan
- School of Life Sciences, Westlake UniversityHangzhouChina
| | - Sareh Bayatpour
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Heather L Drexler
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Katherine A Alexander
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Fei Chen
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Asmamaw T Wassie
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Rohan Patel
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Kenneth Pham
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Edward S Boyden
- Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Shelly Berger
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | | | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Arjun Raj
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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5
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Cuevas-Bermúdez A, Martínez-Fernández V, Garrido-Godino AI, Jordán-Pla A, Peñate X, Martín-Expósito M, Gutiérrez G, Govind CK, Chávez S, Pelechano V, Navarro F. The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:194995. [PMID: 37967810 DOI: 10.1016/j.bbagrm.2023.194995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023]
Abstract
The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin in gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely due to pausing or arrest. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.
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Affiliation(s)
- Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Antonio Jordán-Pla
- Instituto Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Xenia Peñate
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Manuel Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | | | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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6
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McNeil JB, Lee SK, Oliinyk A, Raina S, Garg J, Moallem M, Urquhart-Cox V, Fillingham J, Cheung P, Rosonina E. 1,10-phenanthroline inhibits sumoylation and reveals that yeast SUMO modifications are highly transient. EMBO Rep 2024; 25:68-81. [PMID: 38182817 PMCID: PMC10897377 DOI: 10.1038/s44319-023-00010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 01/07/2024] Open
Abstract
The steady-state levels of protein sumoylation depend on relative rates of conjugation and desumoylation. Whether SUMO modifications are generally long-lasting or short-lived is unknown. Here we show that treating budding yeast cultures with 1,10-phenanthroline abolishes most SUMO conjugations within one minute, without impacting ubiquitination, an analogous post-translational modification. 1,10-phenanthroline inhibits the formation of the E1~SUMO thioester intermediate, demonstrating that it targets the first step in the sumoylation pathway. SUMO conjugations are retained after treatment with 1,10-phenanthroline in yeast that express a defective form of the desumoylase Ulp1, indicating that Ulp1 is responsible for eliminating existing SUMO modifications almost instantly when de novo sumoylation is inhibited. This reveals that SUMO modifications are normally extremely transient because of continuous desumoylation by Ulp1. Supporting our findings, we demonstrate that sumoylation of two specific targets, Sko1 and Tfg1, virtually disappears within one minute of impairing de novo sumoylation. Altogether, we have identified an extremely rapid and potent inhibitor of sumoylation, and our work reveals that SUMO modifications are remarkably short-lived.
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Affiliation(s)
- J Bryan McNeil
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Su-Kyong Lee
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Anna Oliinyk
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Sehaj Raina
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
| | - Marjan Moallem
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Verne Urquhart-Cox
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
| | - Peter Cheung
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Emanuel Rosonina
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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7
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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8
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Maudlin IE, Beggs JD. Conditional depletion of transcriptional kinases Ctk1 and Bur1 and effects on co-transcriptional spliceosome assembly and pre-mRNA splicing. RNA Biol 2021; 18:782-793. [PMID: 34705599 PMCID: PMC8782173 DOI: 10.1080/15476286.2021.1991673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022] Open
Abstract
From yeast to humans, pre-mRNA splicing occurs mainly co-transcriptionally, with splicing and transcription functionally coupled such that they influence one another. The recruitment model of co-transcriptional splicing proposes that core members of the transcription elongation machinery have the potential to influence co-transcriptional spliceosome assembly and pre-mRNA splicing. Here, we tested whether the transcription elongation kinases Bur1 and Ctk1 affect co-transcriptional spliceosome assembly and pre-mRNA splicing in the budding yeast Saccharomyces cerevisiae. In S. cerevisiae, Ctk1 is the major kinase that phosphorylates serine 2 of the carboxy-terminal domain of the largest subunit of RNA polymerase II, whilst Bur1 augments the kinase activity of Ctk1 and is the major kinase for elongation factor Spt5. We used the auxin-inducible degron system to conditionally deplete Bur1 and Ctk1 kinases, and investigated the effects on co-transcriptional spliceosome assembly and pre-mRNA splicing. Depletion of Ctk1 effectively reduced phosphorylation of serine 2 of the carboxy-terminal domain but did not impact co-transcriptional spliceosome assembly or pre-mRNA splicing. In striking contrast, depletion of Bur1 did not reduce phosphorylation of serine 2 of the carboxy-terminal domain, but reduced Spt5 phosphorylation and enhanced co-transcriptional spliceosome assembly and pre-mRNA splicing, suggesting a role for this kinase in modulating co-transcriptional splicing.
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Affiliation(s)
- Isabella E. Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jean D. Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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9
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Caizzi L, Monteiro-Martins S, Schwalb B, Lysakovskaia K, Schmitzova J, Sawicka A, Chen Y, Lidschreiber M, Cramer P. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol Cell 2021; 81:1920-1934.e9. [PMID: 33689748 DOI: 10.1016/j.molcel.2021.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
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Affiliation(s)
- Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sara Monteiro-Martins
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ying Chen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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10
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Zhang S, Aibara S, Vos SM, Agafonov DE, Lührmann R, Cramer P. Structure of a transcribing RNA polymerase II–U1 snRNP complex. Science 2021; 371:305-309. [DOI: 10.1126/science.abf1870] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Suyang Zhang
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shintaro Aibara
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Seychelle M. Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dmitry E. Agafonov
- Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Reinhard Lührmann
- Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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11
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Shao W, Ding Z, Zheng ZZ, Shen JJ, Shen YX, Pu J, Fan YJ, Query CC, Xu YZ. Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription. Nucleic Acids Res 2020; 48:5799-5813. [PMID: 32399566 PMCID: PMC7293005 DOI: 10.1093/nar/gkaa311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 04/08/2020] [Accepted: 05/03/2020] [Indexed: 01/23/2023] Open
Abstract
Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome assembly and splicing proofreading at the branch-point region. From an open UV mutagenesis screen for genetic suppressors of prp5 defects and subsequent targeted testing, we identify components of the TBP-binding module of the Spt–Ada–Gcn5 Acetyltransferase (SAGA) complex, Spt8p and Spt3p. Spt8Δ and spt3Δ rescue the cold-sensitivity of prp5-GAR allele, and prp5 mutants restore growth of spt8Δ and spt3Δ strains on 6-azauracil. By chromatin immunoprecipitation (ChIP), we find that prp5 alleles decrease recruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Δ. Further ChIP-seq reveals that global effects on Pol II-binding are mutually rescued by prp5-GAR and spt8Δ. Inhibited splicing caused by prp5-GAR is also restored by spt8Δ. In vitro assays indicate that Prp5p directly interacts with Spt8p, but not Spt3p. We demonstrate that Prp5p's splicing proofreading is modulated by Spt8p and Spt3p. Therefore, this study reveals that interactions between the TBP-binding module of SAGA and the spliceosomal ATPase Prp5p mediate a balance between transcription initiation/elongation and pre-spliceosome assembly.
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Affiliation(s)
- Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhan Ding
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zeng-Zhang Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ji-Jia Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yu-Xian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jia Pu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Jie Fan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Yong-Zhen Xu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
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12
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Aslanzadeh V, Beggs JD. Revisiting the window of opportunity for cotranscriptional splicing in budding yeast. RNA (NEW YORK, N.Y.) 2020; 26:1081-1085. [PMID: 32439718 PMCID: PMC7430680 DOI: 10.1261/rna.075895.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We reported previously that, in budding yeast, transcription rate affects both the efficiency and fidelity of pre-mRNA splicing, especially of ribosomal protein transcripts. Here, we report that the majority of ribosomal protein transcripts with non-consensus 5' splice sites are spliced less efficiently when transcription is faster, and more efficiently with slower transcription. These results support the "window of opportunity" model, and we suggest a possible mechanism to explain these findings.
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Affiliation(s)
- Vahid Aslanzadeh
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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13
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Tellier M, Maudlin I, Murphy S. Transcription and splicing: A two-way street. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1593. [PMID: 32128990 DOI: 10.1002/wrna.1593] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
RNA synthesis by RNA polymerase II and RNA processing are closely coupled during the transcription cycle of protein-coding genes. This coupling affords opportunities for quality control and regulation of gene expression and the effects can go in both directions. For example, polymerase speed can affect splice site selection and splicing can increase transcription and affect the chromatin landscape. Here we review the many ways that transcription and splicing influence one another, including how splicing "talks back" to transcription. We will also place the connections between transcription and splicing in the context of other RNA processing events that define the exons that will make up the final mRNA. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Isabella Maudlin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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14
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Geisberg JV, Moqtaderi Z, Struhl K. The transcriptional elongation rate regulates alternative polyadenylation in yeast. eLife 2020; 9:e59810. [PMID: 32845240 PMCID: PMC7532003 DOI: 10.7554/elife.59810] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Yeast cells undergoing the diauxic response show a striking upstream shift in poly(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3' mRNA isoforms for most genes. This altered poly(A) pattern is extremely similar to that observed in cells containing Pol II derivatives with slow elongation rates. Conversely, cells containing derivatives with fast elongation rates show a subtle downstream shift in poly(A) sites. Polyadenylation patterns of many genes are sensitive to both fast and slow elongation rates, and a global shift of poly(A) utilization is strongly linked to increased purine content of sequences flanking poly(A) sites. Pol II processivity is impaired in diauxic cells, but strains with reduced processivity and normal Pol II elongation rates have normal polyadenylation profiles. Thus, Pol II elongation speed is important for poly(A) site selection and for regulating poly(A) patterns in response to environmental conditions.
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Affiliation(s)
- Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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15
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Taylor K, Sobczak K. Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control. Int J Mol Sci 2020; 21:ijms21145161. [PMID: 32708277 PMCID: PMC7404189 DOI: 10.3390/ijms21145161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
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16
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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17
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Turowski TW, Petfalski E, Goddard BD, French SL, Helwak A, Tollervey D. Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates. Mol Cell 2020; 79:488-503.e11. [PMID: 32585128 PMCID: PMC7427326 DOI: 10.1016/j.molcel.2020.06.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/01/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Transcription elongation rates influence RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S. cerevisiae. Mapping RNAPI by Miller chromatin spreads or UV crosslinking revealed 5' enrichment and strikingly uneven local polymerase occupancy along the rDNA, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution: folding energy and GC content in the transcription bubble. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high GC in the transcription bubble slows elongation. A mathematical model for RNAPI elongation confirmed the importance of nascent RNA folding in transcription. RNAPI from S. pombe was similarly sensitive to transcript folding, as were S. cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use, indicating regulatory significance for transcript folding.
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Affiliation(s)
- Tomasz W Turowski
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK.
| | - Elisabeth Petfalski
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
| | - Benjamin D Goddard
- School of Mathematics and Maxwell Institute for Mathematical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Sarah L French
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK.
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18
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Zhao SP, Song XY, Guo LL, Zhang XZ, Zheng WJ. Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean. Int J Mol Sci 2020; 21:E1810. [PMID: 32155727 PMCID: PMC7084930 DOI: 10.3390/ijms21051810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 11/25/2022] Open
Abstract
The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.
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Affiliation(s)
- Shu-Ping Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xin-Yuan Song
- Agro-biotechnology Research Institute, Jilin Academy of Agriculture Sciences, Changchun 130033, China;
| | - Lin-Lin Guo
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xiang-Zhan Zhang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Wei-Jun Zheng
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
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19
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Maudlin IE, Beggs JD. Spt5 modulates cotranscriptional spliceosome assembly in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2019; 25:1298-1310. [PMID: 31289129 PMCID: PMC6800482 DOI: 10.1261/rna.070425.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
There is increasing evidence from yeast to humans that pre-mRNA splicing occurs mainly cotranscriptionally, such that splicing and transcription are functionally coupled. Currently, there is little insight into the contribution of the core transcription elongation machinery to cotranscriptional spliceosome assembly and pre-mRNA splicing. Spt5 is a member of the core transcription elongation machinery and an essential protein, whose absence in budding yeast causes defects in pre-mRNA splicing. To determine how Spt5 affects pre-mRNA splicing, we used the auxin-inducible degron system to conditionally deplete Spt5 in Saccharomyces cerevisiae and assayed effects on cotranscriptional spliceosome assembly and splicing. We show that Spt5 is needed for efficient splicing and for the accumulation of U5 snRNPs at intron-containing genes, and therefore for stable cotranscriptional assembly of spliceosomes. The defect in cotranscriptional spliceosome assembly can explain the relatively mild splicing defect as being a consequence of the failure of cotranscriptional splicing. Coimmunoprecipitation of Spt5 with core spliceosomal proteins and all spliceosomal snRNAs suggests a model whereby Spt5 promotes cotranscriptional pre-mRNA splicing by stabilizing the association of U5 snRNP with spliceosome complexes as they assemble on the nascent transcript. If this phenomenon is conserved in higher eukaryotes, it has the potential to be important for cotranscriptional regulation of alternative splicing.
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Affiliation(s)
- Isabella E Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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20
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A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia. Noncoding RNA Res 2019; 4:96-108. [PMID: 31891018 PMCID: PMC6926186 DOI: 10.1016/j.ncrna.2019.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/09/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022] Open
Abstract
Noncoding RNAs are increasingly being accredited with key roles in gene regulation during development and disease. Here we report the discovery and characterization of a novel long noncoding RNA, Hmrhl, which shares synteny and partial sequence similarity with the mouse lncRNA, Mrhl. The human homolog, Hmrhl, transcribed from intron 14 of phkb gene, is 5.5 kb in size, expressed in all tissues examined and is associated with chromatin. Analysis of Hmrhl locus using ENCODE database revealed that it exhibits hallmarks of enhancers like the open chromatin configuration, binding of transcription factors, enhancer specific histone signature etc. in the K562 Chronic Myelogenous Leukemia (CML) cells. We compared the expression of Hmrhl in the normal lymphoblast cell line, GM12878, with that of K562 cells and lymphoma samples and show that it is highly upregulated in leukemia as well as several cases of lymphoma. Further, we validated the enhancer properties of Hmrhl locus in K562 cells with the help of ChIP-qPCR and Luciferase assay. Moreover, siRNA mediated down-regulation of Hmrhl in K562 cells leads to a concomitant down regulation of its parent gene, phkb, showing that Hmrhl functions as an enhancer RNA and positively regulates its host gene, phkb, in chronic myelogenous leukemia. This study is significant in view of the fact that a better understanding of mechanism of gene regulation under normal conditions and its perturbation in cancer could in turn help in its therapeutic intervention through molecular medicine/RNA based drug discovery.
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21
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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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22
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Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019; 20:631-656. [DOI: 10.1038/s41576-019-0150-2] [Citation(s) in RCA: 679] [Impact Index Per Article: 135.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
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23
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RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing. Mol Cell 2019; 72:369-379.e4. [PMID: 30340024 PMCID: PMC6201815 DOI: 10.1016/j.molcel.2018.09.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 07/23/2018] [Accepted: 08/31/2018] [Indexed: 01/22/2023]
Abstract
The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in footprints of approximately 60 nucleotides. Also, splicing intermediates formed by cleavage at the 5′ splice site are associated with nearly all spliced exons. These spliceosome-bound intermediates are frequently ligated to upstream exons, implying a sequential, constitutive, and U12-dependent splicing process. Finally, lack of detectable spliced products connected to the Pol II active site in human HeLa or murine lymphoid cells suggests that splicing does not occur immediately following 3′ splice site synthesis. Our results imply that most mammalian splicing requires exon definition for completion. S5P CTD Pol II associates with the catalytic spliceosome Elongating Pol II complexes protect about 60 newly synthesized nucleotides Co-transcriptional splicing associated with dominant 5′ ss intermediate U12-dependent introns are sequentially spliced in association with Pol II
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24
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Xia X. RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns. Methods 2019; 176:25-33. [PMID: 30926533 DOI: 10.1016/j.ymeth.2019.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 01/21/2023] Open
Abstract
Introns in different genes, or even different introns within the same gene, often have different splice sites and differ in splicing efficiency (SE). One expects mass-transcribed genes to have introns with higher SE than weakly transcribed genes. However, such a simple expectation cannot be tested directly because variable SE for these genes is often not measured. Mechanistically, SE should depend on signal strength at key splice sites (SS) such as 5'SS, 3'SS and branchpoint site (BPS), i.e., SE = F(5'SS, 3'SS, BPS). However, without SE, we again cannot model how these splice sites contribute to SE. Here I present an RNA-Seq approach to quantify SE for each of the 304 introns in yeast (Saccharomyces cerevisiae) genes, including 24 in the 5'UTR, by measuring 1) number of reads mapped to exon-exon junctions (NEE) as a proxy for the abundance of spliced form, and 2) number of reads mapped to exon-intron junction (NEI5 and NEI3 at 5' and 3' ends of intron) as a proxy for the abundance of unspliced form. The total mRNA is NTotal = NEE + p * NEI5 + (1-p) * NEI3, with the simplest p = 0.5 but statistical methods were presented to estimate p from data. An estimated p is needed because NEI5 is expected to be smaller than NEI3 due to 1) step 1 splicing occurs before step 2 so EI5 is broken before EI3, 2) enrichment of poly(A) mRNA by oligo-dT, and 3) 5' degradation. SE is defined as the proportion (NEE/NTotal). Application of the method shows that ribosomal protein messages are efficiently and mostly cotranscriptionally spliced. Yeast genes with long introns are also spliced efficiently. HAC1/YFL031W is poorly spliced partly because its splicing involves a nonspliceosome mechanism and partly because Ire1p, which participate in splicing HAC1, is hardly expressed. Many putative yeast genes have low SE, and some splice sites are incorrectly annotated.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa K1N 6N5, Canada; Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada.
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25
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Tan J, Yang L, Ong AAL, Shi J, Zhong Z, Lye ML, Liu S, Lisowiec-Wachnicka J, Kierzek R, Roca X, Chen G. A Disease-Causing Intronic Point Mutation C19G Alters Tau Exon 10 Splicing via RNA Secondary Structure Rearrangement. Biochemistry 2019; 58:1565-1578. [DOI: 10.1021/acs.biochem.9b00001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiazi Tan
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Lixia Yang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Alan Ann Lerk Ong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jiahao Shi
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Zhensheng Zhong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Mun Leng Lye
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Shiyi Liu
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Gang Chen
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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26
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Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5'-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.
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Affiliation(s)
- Tucker J Carrocci
- 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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27
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Herzel L, Straube K, Neugebauer KM. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res 2018; 28:1008-1019. [PMID: 29903723 PMCID: PMC6028129 DOI: 10.1101/gr.232025.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
Abstract
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2, the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3′ end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Korinna Straube
- 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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28
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Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast. Genome Res 2017; 28:203-213. [PMID: 29254943 PMCID: PMC5793784 DOI: 10.1101/gr.225615.117] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/14/2017] [Indexed: 01/24/2023]
Abstract
The functional consequences of alternative splicing on altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimize the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.
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29
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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: 230] [Impact Index Per Article: 32.9] [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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Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol 2017; 91:145-155. [PMID: 28673892 DOI: 10.1016/j.biocel.2017.06.016] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 01/18/2023]
Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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