1
|
Biernat E, Verma M, Govind CK. Genome-wide regulation of Pol II, FACT, and Spt6 occupancies by RSC in Saccharomyces cerevisiae. Gene 2024; 893:147959. [PMID: 37923091 PMCID: PMC10872467 DOI: 10.1016/j.gene.2023.147959] [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: 06/23/2023] [Revised: 10/17/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
RSC (remodels the structure of chromatin) is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. RSC utilizes its ATPase subunit, Sth1, to slide or remove nucleosomes. RSC has been shown to regulate the width of the nucleosome-depleted regions (NDRs) by sliding the flanking nucleosomes away from NDRs. As such, when RSC is depleted, nucleosomes encroach NDRs, leading to transcription initiation defects. In this study, we examined the effects of the catalytic-dead Sth1 on transcription and compared them to those observed during acute and rapid Sth1 depletion by auxin-induced degron strategy. We found that rapid depletion of Sth1 reduces recruitment of TBP and Pol II in highly transcribed genes, as would be expected considering its role in regulating chromatin structure at promoters. In contrast, cells harboring the catalytic-dead Sth1 (sth1-K501R) exhibited a severe reduction in TBP binding, but, surprisingly, also displayed a substantial accumulation in Pol II occupancies within coding regions. The Pol II occupancies further increased upon depleting endogenous Sth1 in the catalytic-dead mutant, suggesting that the inactive Sth1 contributes to Pol II accumulation in coding regions. Notwithstanding the Pol II increase, the ORF occupancies of histone chaperones, FACT and Spt6 were significantly reduced in the mutant. These results suggest a potential role for RSC in recruiting/retaining these chaperones in coding regions. Pol II accumulation despite substantial reductions in TBP, FACT, and Spt6 occupancies in the catalytic-dead mutant could indicate severe transcription elongation and termination defects. Such defects would be consistent with studies showing that RSC is recruited to coding regions in a transcription-dependent manner. Thus, these findings imply a role for RSC in transcription elongation and termination processes, in addition to its established role in transcription initiation.
Collapse
Affiliation(s)
- Emily Biernat
- Department of Biological Sciences, Mathematics and Science Center, Oakland University, Rochester, MI 48309, USA
| | - Mansi Verma
- Department of Biological Sciences, Mathematics and Science Center, Oakland University, Rochester, MI 48309, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Mathematics and Science Center, Oakland University, Rochester, MI 48309, USA.
| |
Collapse
|
2
|
Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
Collapse
Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
3
|
Miller CLW, Warner JL, Winston F. Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability. Trends Genet 2023; 39:858-872. [PMID: 37481442 PMCID: PMC10592469 DOI: 10.1016/j.tig.2023.06.008] [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: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Transcription elongation requires elaborate coordination between the transcriptional machinery and chromatin regulatory factors to successfully produce RNA while preserving the epigenetic landscape. Recent structural and genomic studies have highlighted that suppressor of Ty 6 (Spt6), a conserved histone chaperone and transcription elongation factor, sits at the crux of the transcription elongation process. Other recent studies have revealed that Spt6 also promotes DNA replication and genome integrity. Here, we review recent studies of Spt6 that have provided new insights into the mechanisms by which Spt6 controls transcription and have revealed the breadth of Spt6 functions in eukaryotic cells.
Collapse
Affiliation(s)
- Catherine L W Miller
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA
| | - James L Warner
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
4
|
Hegazy YA, Cloutier SC, Utturkar SM, Das S, Tran E. The genomic region of the 3' untranslated region (3'UTR) of PHO84, rather than the antisense RNA, promotes gene repression. Nucleic Acids Res 2023; 51:7900-7913. [PMID: 37462073 PMCID: PMC10450162 DOI: 10.1093/nar/gkad579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/20/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023] Open
Abstract
PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense pairs in a dbp2Δ strain and found over 700 sense/antisense pairs, including PHO84, to be positively correlated, contrasting the prevailing model. To define what mechanism regulates the PHO84 gene and how this regulation could have been originally attributed to repression by the antisense transcript, we conducted a series of molecular biology and genetics experiments. We now report that the 3' untranslated region (3'UTR) of PHO84 plays a repressive role in sense expression, an activity not linked to the antisense transcripts. Moreover, we provide results of a genetic screen for 3'UTR-dependent repression of PHO84 and show that the vast majority of identified factors are linked to negative regulation. Finally, we show that the PHO84 promoter and terminator form gene loops which correlate with transcriptional repression, and that the RNA-binding protein, Tho1, increases this looping and the 3'UTR-dependent repression. Our results negate the current model for antisense non-coding transcripts of PHO84 and suggest that many of these transcripts are byproducts of open chromatin.
Collapse
Affiliation(s)
- Youssef A Hegazy
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Sara C Cloutier
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Sagar M Utturkar
- Purdue University Institute for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street West Lafayette, IN 47907-2064, USA
| | - Subhadeep Das
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
- Purdue University Institute for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street West Lafayette, IN 47907-2064, USA
| |
Collapse
|
5
|
Kasiliauskaite A, Kubicek K, Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R. Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res 2022; 50:5961-5973. [PMID: 35640611 PMCID: PMC9177984 DOI: 10.1093/nar/gkac451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (Pol II) and acts as a histone chaperone, which promotes the reassembly of nucleosomes following the passage of Pol II. The precise mechanism of nucleosome reassembly mediated by Spt6 remains unclear. In this study, we used a hybrid approach combining cryo-electron microscopy and small-angle X-ray scattering to visualize the architecture of Spt6 from Saccharomyces cerevisiae. The reconstructed overall architecture of Spt6 reveals not only the core of Spt6, but also its flexible N- and C-termini, which are critical for Spt6's function. We found that the acidic N-terminal region of Spt6 prevents the binding of Spt6 not only to the Pol II CTD and Pol II CTD-linker, but also to pre-formed intact nucleosomes and nucleosomal DNA. The N-terminal region of Spt6 self-associates with the tSH2 domain and the core of Spt6 and thus controls binding to Pol II and nucleosomes. Furthermore, we found that Spt6 promotes the assembly of nucleosomes in vitro. These data indicate that the cooperation between the intrinsically disordered and structured regions of Spt6 regulates nucleosome and Pol II CTD binding, and also nucleosome assembly.
Collapse
Affiliation(s)
- Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Tomas Klumpler
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Martina Zanova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - David Zapletal
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Eliska Koutna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| |
Collapse
|
6
|
Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
Collapse
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
7
|
Liu C, Zhang W, Xing W. Diverse and conserved roles of the protein Ssu72 in eukaryotes: from yeast to higher organisms. Curr Genet 2020; 67:195-206. [PMID: 33244642 DOI: 10.1007/s00294-020-01132-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
Gene transcription is a complex biological process that involves a set of factors, enzymes and nucleotides. Ssu72 plays a crucial role in every step of gene transcription. RNA polymerase II (RNAPII) occupies an important position in the synthesis of mRNAs. The largest subunit of RNAPII, Rpb1, harbors its C-terminal domain (CTD), which participates in the initiation, elongation and termination of transcription. The CTD consists of heptad repeats of the consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and is highly conserved among different species. The CTD is flexible in structure and undergoes conformational changes in response to serine phosphorylation and proline isomerization, which are regulated by specific kinases/phosphatases and isomerases, respectively. Ssu72 is a CTD phosphatase with catalytic activity against phosphorylated Ser5 and Ser7. The isomerization of Pro6 affects the binding of Ssu72 to its substrate. Ssu72 can also indirectly change the phosphorylation status of Ser2. In addition, Ssu72 is a member of the 3'-end cleavage and polyadenylation factor (CPF) complex. Together with other CPF components, Ssu72 regulates the 3'-end processing of premature mRNA. Recent studies have revealed other roles of Ssu72, including its roles in balancing phosphate homeostasis and controlling chromosome behaviors, which should be further explored. In conclusion, the protein Ssu72 is an enzyme worthy of attention, not confined to its role in gene transcription.
Collapse
Affiliation(s)
- Changfu Liu
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Weihao Zhang
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Wenge Xing
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| |
Collapse
|
8
|
Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
Collapse
Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
9
|
Ólafsson G, Thorpe PH. Polo kinase recruitment via the constitutive centromere-associated network at the kinetochore elevates centromeric RNA. PLoS Genet 2020; 16:e1008990. [PMID: 32810142 PMCID: PMC7455000 DOI: 10.1371/journal.pgen.1008990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/28/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
The kinetochore, a multi-protein complex assembled on centromeres, is essential to segregate chromosomes during cell division. Deficiencies in kinetochore function can lead to chromosomal instability and aneuploidy-a hallmark of cancer cells. Kinetochore function is controlled by recruitment of regulatory proteins, many of which have been documented, however their function often remains uncharacterized and many are yet to be identified. To identify candidates of kinetochore regulation we used a proteome-wide protein association strategy in budding yeast and detected many proteins that are involved in post-translational modifications such as kinases, phosphatases and histone modifiers. We focused on the Polo-like kinase, Cdc5, and interrogated which cellular components were sensitive to constitutive Cdc5 localization. The kinetochore is particularly sensitive to constitutive Cdc5 kinase activity. Targeting Cdc5 to different kinetochore subcomplexes produced diverse phenotypes, consistent with multiple distinct functions at the kinetochore. We show that targeting Cdc5 to the inner kinetochore, the constitutive centromere-associated network (CCAN), increases the levels of centromeric RNA via an SPT4 dependent mechanism.
Collapse
Affiliation(s)
- Guðjón Ólafsson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| |
Collapse
|
10
|
Bobkov GOM, Huang A, van den Berg SJW, Mitra S, Anselm E, Lazou V, Schunter S, Feederle R, Imhof A, Lusser A, Jansen LET, Heun P. Spt6 is a maintenance factor for centromeric CENP-A. Nat Commun 2020; 11:2919. [PMID: 32522980 PMCID: PMC7287101 DOI: 10.1038/s41467-020-16695-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Replication and transcription of genomic DNA requires partial disassembly of nucleosomes to allow progression of polymerases. This presents both an opportunity to remodel the underlying chromatin and a danger of losing epigenetic information. Centromeric transcription is required for stable incorporation of the centromere-specific histone dCENP-A in M/G1 phase, which depends on the eviction of previously deposited H3/H3.3-placeholder nucleosomes. Here we demonstrate that the histone chaperone and transcription elongation factor Spt6 spatially and temporarily coincides with centromeric transcription and prevents the loss of old CENP-A nucleosomes in both Drosophila and human cells. Spt6 binds directly to dCENP-A and dCENP-A mutants carrying phosphomimetic residues alleviate this association. Retention of phosphomimetic dCENP-A mutants is reduced relative to wildtype, while non-phosphorylatable dCENP-A retention is increased and accumulates at the centromere. We conclude that Spt6 acts as a conserved CENP-A maintenance factor that ensures long-term stability of epigenetic centromere identity during transcription-mediated chromatin remodeling.
Collapse
Affiliation(s)
- Georg O M Bobkov
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Anming Huang
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Sebastiaan J W van den Berg
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sreyoshi Mitra
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Eduard Anselm
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Vasiliki Lazou
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Sarah Schunter
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, LMU, Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
| | - Axel Imhof
- BioMedical Center and Center for Integrated Protein Sciences Munich, Ludwig-Maximilians-University of Munich, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK.
| |
Collapse
|
11
|
Trotta E. RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. J Biol Chem 2019; 294:12349-12358. [PMID: 31235518 PMCID: PMC6699833 DOI: 10.1074/jbc.ra119.008529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/19/2019] [Indexed: 07/24/2023] Open
Abstract
In yeast (Saccharomyces cerevisiae), the synthesis of tRNAs by RNA polymerase III (RNAP III) down-regulates the transcription of the nearby RNAP II-transcribed genes by a mechanism that is poorly understood. To clarify the basis of this tRNA gene-mediated (TGM) silencing, here, conducting a bioinformatics analysis of available ChIP-chip and ChIP-sequencing genomic data from yeast, we investigated whether the RNAP III transcriptional machinery can recruit protein factors required for RNAP II transcription. An analysis of 46 genome-wide protein-density profiles revealed that 12 factors normally implicated in RNAP II-mediated gene transcription are more enriched at tRNA than at mRNA loci. These 12 factors typically have RNA-binding properties, participate in the termination stage of the RNAP II transcription, and preferentially localize to the tRNA loci by a mechanism that apparently is based on the RNAP III transcription level. The factors included two kinases of RNAP II (Bur1 and Ctk1), a histone demethylase (Jhd2), and a mutated form of a nucleosome-remodeling factor (Spt6) that have never been reported to be recruited to tRNA loci. Moreover, we show that the expression levels of RNAP II-transcribed genes downstream of tRNA loci correlate with the distance from the tRNA gene by a mechanism that depends on their orientation. These results are consistent with the notion that pre-tRNAs recruit RNAP II-associated factors, thereby reducing the availability of these factors for RNAP II transcription and contributing, at least in part, to the TGM-silencing mechanism.
Collapse
Affiliation(s)
- Edoardo Trotta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche (CNR), Roma 00133, Italy.
| |
Collapse
|
12
|
Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide in Saccharomyces cerevisiae. Genetics 2018; 209:743-756. [PMID: 29695490 DOI: 10.1534/genetics.118.300943] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
Histone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier for DNA-dependent processes. Here, we have examined the role of two highly conserved yeast (Saccharomyces cerevisiae) histone chaperones, facilitates chromatin transcription (FACT) and Spt6, in regulating transcription. We show that the H3 tail contributes to the recruitment of FACT to coding sequences in a manner dependent on acetylation. We found that deleting a H3 histone acetyltransferase Gcn5 or mutating lysines on the H3 tail impairs FACT recruitment at ADH1 and ARG1 genes. However, deleting the H4 tail or mutating the H4 lysines failed to dampen FACT occupancy in coding regions. Additionally, we show that FACT depletion reduces RNA polymerase II (Pol II) occupancy genome-wide. Spt6 depletion leads to a reduction in Pol II occupancy toward the 3'-end, in a manner dependent on the gene length. Severe transcription and histone-eviction defects were also observed in a strain that was impaired for Spt6 recruitment (spt6Δ202) and depleted of FACT. Importantly, the severity of the defect strongly correlated with wild-type Pol II occupancies at these genes, indicating critical roles for Spt6 and Spt16 in promoting high-level transcription. Collectively, our results show that both FACT and Spt6 are important for transcription globally and may participate during different stages of transcription.
Collapse
|
13
|
Hennig T, Michalski M, Rutkowski AJ, Djakovic L, Whisnant AW, Friedl MS, Jha BA, Baptista MAP, L'Hernault A, Erhard F, Dölken L, Friedel CC. HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. PLoS Pathog 2018; 14:e1006954. [PMID: 29579120 PMCID: PMC5886697 DOI: 10.1371/journal.ppat.1006954] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/05/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways but with similar consequences. In contrast to previous reports, we found that inhibition of Ca2+ signaling by BAPTA-AM did not specifically inhibit DoG transcription but globally impaired transcription. Most importantly, HSV-1-induced DoTT, but not stress-induced DoG transcription, was accompanied by a strong increase in open chromatin downstream of the affected poly(A) sites. In its extent and kinetics, downstream open chromatin essentially matched the poly(A) read-through transcription. We show that this does not cause but rather requires DoTT as well as high levels of transcription into the genomic regions downstream of genes. This raises intriguing new questions regarding the role of histone repositioning in the wake of RNA Polymerase II passage downstream of impaired poly(A) site recognition. Recently, we reported that productive herpes simplex virus 1 (HSV-1) infection leads to disruption of transcription termination (DoTT) of most but not all cellular genes. This results in extensive transcription beyond poly(A) sites and into downstream genes. Subsequently, cellular stress responses were found to trigger transcription downstream of genes (DoG) for >10% of protein-coding genes. Here, we directly compared the two phenomena in HSV-1 infection, salt and heat stress and observed significant overlaps between the affected genes. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways with similar consequences. In addition, we show that inhibition of calcium signaling does not specifically inhibit stress-induced DoG transcription but globally impairs RNA polymerase I, II and III transcription. Finally, HSV-1-induced DoTT, but not stress-induced DoG transcription, was accompanied by a strong increase in chromatin accessibility downstream of affected poly(A) sites. In its kinetics and extent, this essentially matched poly(A) read-through transcription but does not cause but rather requires DoTT. We hypothesize that this results from impaired histone repositioning when RNA Polymerase II enters downstream intergenic regions of genes affected by DoTT.
Collapse
Affiliation(s)
- Thomas Hennig
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Andrzej J Rutkowski
- Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lara Djakovic
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Adam W Whisnant
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marie-Sophie Friedl
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Bhaskar Anand Jha
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marisa A P Baptista
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Anne L'Hernault
- Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Florian Erhard
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.,Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| |
Collapse
|
14
|
Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell 2017; 68:913-925.e3. [PMID: 29220656 DOI: 10.1016/j.molcel.2017.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/21/2017] [Accepted: 11/15/2017] [Indexed: 12/28/2022]
Abstract
The RNA polymerase II largest subunit C-terminal domain consists of repeated YSPTSPS heptapeptides. The role of tyrosine-1 (Tyr1) remains incompletely understood, as, for example, mutating all Tyr1 residues to Phe (Y1F) is lethal in vertebrates but a related mutant has only a mild phenotype in S. pombe. Here we show that Y1F substitution in budding yeast resulted in a strong slow-growth phenotype. The Y1F strain was also hypersensitive to several different cellular stresses that involve MAP kinase signaling. These phenotypes were all linked to transcriptional changes, and we also identified genetic and biochemical interactions between Tyr1 and both transcription initiation and termination factors. Further studies uncovered defects related to MAP kinase I (Slt2) pathways, and we provide evidence that Slt2 phosphorylates Tyr1 in vitro and in vivo. Our study has thus identified Slt2 as a Tyr1 kinase, and in doing so provided links between stress response activation and Tyr1 phosphorylation.
Collapse
Affiliation(s)
- Nathan Yurko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
15
|
Gómez-Herreros F, Margaritis T, Rodríguez-Galán O, Pelechano V, Begley V, Millán-Zambrano G, Morillo-Huesca M, Muñoz-Centeno MC, Pérez-Ortín JE, de la Cruz J, Holstege FCP, Chávez S. The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation. Nucleic Acids Res 2017. [PMID: 28637236 PMCID: PMC5737610 DOI: 10.1093/nar/gkx529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.
Collapse
Affiliation(s)
- Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Thanasis Margaritis
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Vicent Pelechano
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Gonzalo Millán-Zambrano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Macarena Morillo-Huesca
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| |
Collapse
|
16
|
Yurko NM, Manley JL. The RNA polymerase II CTD "orphan" residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7. Transcription 2017; 9:30-40. [PMID: 28771071 DOI: 10.1080/21541264.2017.1338176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of a unique repeated heptad sequence of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. An important function of the CTD is to couple transcription with RNA processing reactions that occur during the initiation, elongation, and termination phases of transcription. During this transcription cycle, the CTD is subject to extensive modification, primarily phosphorylation, on its non-proline residues. Reversible phosphorylation of Ser2 and Ser5 is well known to play important and general functions during transcription in all eukaryotes. More recent studies have enhanced our understanding of Tyr1, Thr4, and Ser7, and what have been previously characterized as unknown or specialized functions for these residues has changed to a more fine-detailed map of transcriptional regulation that highlights similarities as well as significant differences between organisms. Here, we review recent findings on the function and modification of these three residues, which further illustrate the importance of the CTD in precisely modulating gene expression.
Collapse
Affiliation(s)
- Nathan M Yurko
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| | - James L Manley
- a Department of Biological Sciences , Columbia University , New York , NY , USA
| |
Collapse
|
17
|
Sdano MA, Fulcher JM, Palani S, Chandrasekharan MB, Parnell TJ, Whitby FG, Formosa T, Hill CP. A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. eLife 2017; 6:28723. [PMID: 28826505 PMCID: PMC5599234 DOI: 10.7554/elife.28723] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/11/2017] [Indexed: 01/01/2023] Open
Abstract
We determined that the tandem SH2 domain of S. cerevisiae Spt6 binds the linker region of the RNA polymerase II subunit Rpb1 rather than the expected sites in its heptad repeat domain. The 4 nM binding affinity requires phosphorylation at Rpb1 S1493 and either T1471 or Y1473. Crystal structures showed that pT1471 binds the canonical SH2 pY site while pS1493 binds an unanticipated pocket 70 Å distant. Remarkably, the pT1471 phosphate occupies the phosphate-binding site of a canonical pY complex, while Y1473 occupies the position of a canonical pY side chain, with the combination of pT and Y mimicking a pY moiety. Biochemical data and modeling indicate that pY1473 can form an equivalent interaction, and we find that pT1471/pS1493 and pY1473/pS1493 combinations occur in vivo. ChIP-seq and genetic analyses demonstrate the importance of these interactions for recruitment of Spt6 to sites of transcription and for the maintenance of repressive chromatin.
Collapse
Affiliation(s)
- Matthew A Sdano
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - James M Fulcher
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Timothy J Parnell
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| |
Collapse
|
18
|
The pol II CTD: new twists in the tail. Nat Struct Mol Biol 2016; 23:771-7. [DOI: 10.1038/nsmb.3285] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022]
|
19
|
Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to Coding Regions Promotes Transcription Genome Wide. PLoS One 2016; 11:e0148897. [PMID: 26848854 PMCID: PMC4744024 DOI: 10.1371/journal.pone.0148897] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/25/2016] [Indexed: 12/03/2022] Open
Abstract
Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions.
Collapse
|
20
|
Zhou H, Liu Q, Shi T, Yu Y, Lu H. Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation. Yeast 2015; 32:643-55. [DOI: 10.1002/yea.3085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Qi Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing Technology; Shanghai 200237 People's Republic of China
| |
Collapse
|
21
|
Spain MM, Ansari SA, Pathak R, Palumbo MJ, Morse RH, Govind CK. The RSC complex localizes to coding sequences to regulate Pol II and histone occupancy. Mol Cell 2014; 56:653-66. [PMID: 25457164 DOI: 10.1016/j.molcel.2014.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/26/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022]
Abstract
ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions.
Collapse
Affiliation(s)
- Marla M Spain
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Suraiya A Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, NY State Department of Health, Albany, NY 12208, USA
| | - Rakesh Pathak
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Michael J Palumbo
- Laboratory of Molecular Genetics, Wadsworth Center, NY State Department of Health, Albany, NY 12208, USA
| | - Randall H Morse
- Laboratory of Molecular Genetics, Wadsworth Center, NY State Department of Health, Albany, NY 12208, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.
| |
Collapse
|