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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [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: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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2
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Izquierdo-Pujol J, Puertas MC, Martinez-Picado J, Morón-López S. Targeting Viral Transcription for HIV Cure Strategies. Microorganisms 2024; 12:752. [PMID: 38674696 PMCID: PMC11052381 DOI: 10.3390/microorganisms12040752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Combination antiretroviral therapy (ART) suppresses viral replication to undetectable levels, reduces mortality and morbidity, and improves the quality of life of people living with HIV (PWH). However, ART cannot cure HIV infection because it is unable to eliminate latently infected cells. HIV latency may be regulated by different HIV transcription mechanisms, such as blocks to initiation, elongation, and post-transcriptional processes. Several latency-reversing (LRA) and -promoting agents (LPA) have been investigated in clinical trials aiming to eliminate or reduce the HIV reservoir. However, none of these trials has shown a conclusive impact on the HIV reservoir. Here, we review the cellular and viral factors that regulate HIV-1 transcription, the potential pharmacological targets and genetic and epigenetic editing techniques that have been or might be evaluated to disrupt HIV-1 latency, the role of miRNA in post-transcriptional regulation of HIV-1, and the differences between the mechanisms regulating HIV-1 and HIV-2 expression.
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Affiliation(s)
- Jon Izquierdo-Pujol
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
| | - Maria C. Puertas
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
| | - Javier Martinez-Picado
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
- Department of Infectious Diseases and Immunity, School of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Sara Morón-López
- IrsiCaixa, 08916 Badalona, Spain; (J.I.-P.); (M.C.P.); (J.M.-P.)
- Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- CIBERINFEC, 28029 Madrid, Spain
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Abstract
Formation of the 3' end of a eukaryotic mRNA is a key step in the production of a mature transcript. This process is mediated by a number of protein factors that cleave the pre-mRNA, add a poly(A) tail, and regulate transcription by protein dephosphorylation. Cleavage and polyadenylation specificity factor (CPSF) in humans, or cleavage and polyadenylation factor (CPF) in yeast, coordinates these enzymatic activities with each other, with RNA recognition, and with transcription. The site of pre-mRNA cleavage can strongly influence the translation, stability, and localization of the mRNA. Hence, cleavage site selection is highly regulated. The length of the poly(A) tail is also controlled to ensure that every transcript has a similar tail when it is exported from the nucleus. In this review, we summarize new mechanistic insights into mRNA 3'-end processing obtained through structural studies and biochemical reconstitution and outline outstanding questions in the field.
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Affiliation(s)
- Vytautė Boreikaitė
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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4
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RBBP6 activates the pre-mRNA 3' end processing machinery in humans. Genes Dev 2022; 36:210-224. [PMID: 35177536 PMCID: PMC8887125 DOI: 10.1101/gad.349223.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
Abstract
In this study, Boreikaite et al. reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. 3′ end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3′ end of the mature transcript, which is important for mRNA localization, translation, and stability. Cleavage must therefore be tightly regulated. Here, we reconstituted specific and efficient 3′ endonuclease activity of human CPSF with purified proteins. This required the seven-subunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm), and, importantly, the multidomain protein RBBP6. Unlike its yeast homolog Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to humans. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in mRNA processing.
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Current understanding of CREPT and p15RS, carboxy-terminal domain (CTD)-interacting proteins, in human cancers. Oncogene 2020; 40:705-716. [PMID: 33239754 DOI: 10.1038/s41388-020-01544-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 10/21/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
CREPT and p15RS, also named RPRD1B and RPRD1A, are RPRD (regulation of nuclear pre-mRNA-domain-containing) proteins containing C-terminal domain (CTD)-interacting domain (CID), which mediates the binding to the CTD of Rpb1, the largest subunit of RNA polymerase II (RNAPII). CREPT and p15RS are highly conserved, with a common yeast orthologue Rtt103. Intriguingly, human CREPT and p15RS possess opposite functions in the regulation of cell proliferation and tumorigenesis. While p15RS inhibits cell proliferation, CREPT promotes cell cycle and tumor growth. Aberrant expression of both CREPT and p15RS was found in numerous types of cancers. At the molecular level, both CREPT and p15RS were reported to regulate gene transcription by interacting with RNAPII. However, CREPT also exerts a key function in the processes linked to DNA damage repairs. In this review, we summarized the recent studies regarding the biological roles of CREPT and p15RS, as well as the molecular mechanisms underlying their activities. Fully revealing the mechanisms of CREPT and p15RS functions will not only provide new insights into understanding gene transcription and maintenance of DNA stability in tumors, but also promote new approach development for tumor diagnosis and therapy.
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6
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Zhou Z, Gong Q, Lin Z, Wang Y, Li M, Wang L, Ding H, Li P. Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. Front Oncol 2020; 10:577636. [PMID: 33072610 PMCID: PMC7544984 DOI: 10.3389/fonc.2020.577636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Ser/Arg-rich (SR) proteins are RNA-binding proteins known as constitutive and alternative splicing (AS) regulators that regulate multiple aspects of the gene expression program. Ser/Arg-rich splicing factor 3 (SRSF3) is the smallest member of the SR protein family, and its level is controlled by multiple factors and involves complex mechanisms in eukaryote cells, whereas the aberrant expression of SRSF3 is associated with many human diseases, including cancer. Here, we review state-of-the-art research on SRSF3 in terms of its function, expression, and misregulation in human cancers. We emphasize the negative consequences of the overexpression of the SRSF3 oncogene in cancers, the pathways underlying SRSF3-mediated transformation, and implications of potential anticancer drugs by downregulation of SRSF3 expression for cancer therapy. Cumulative research on SRSF3 provides critical insight into its essential part in maintaining cellular processes, offering potential new targets for anti-cancer therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Qi Gong
- Departments of Pediatrics, Second Clinical Medical College of Qingdao University, Qingdao, China
| | - Zhijuan Lin
- Key Laboratory for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Mengkun Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongfei Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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7
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Yeo IC, Devarenne TP. Screening for potential nuclear substrates for the plant cell death suppressor kinase Adi3 using peptide microarrays. PLoS One 2020; 15:e0234011. [PMID: 32484825 PMCID: PMC7266335 DOI: 10.1371/journal.pone.0234011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
The tomato AGC protein kinase Adi3 is a Ser/Thr kinase that functions as a negative regulator of programmed cell death through cell death suppression (CDS) activity in the nucleus. In this study, to understand the mechanism of Adi3 CDS, peptide microarrays containing random Ser- and Thr-peptide phosphorylation substrates were used to screen for downstream phosphorylation substrates. In the microarray phosphorylation assay, Adi3 showed promiscuous kinase activity more toward Ser-peptides compared to Thr-peptides, and a preference for aromatic and cyclic amino acids on both Ser- and Thr-peptides was seen. The 63 highest phosphorylated peptide sequences from the Ser-peptide microarray were selected as queries for a BLAST search against the tomato proteome. As a result, 294 candidate nuclear Adi3 substrates were selected and categorized based on their functions. Many of these proteins were classified as DNA/RNA polymerases or regulators involved in transcription and translation events. The list of potential Adi3 substrates was narrowed to eleven and four candidates were tested for phosphorylation by Adi3. Two of these candidates, RNA polymerase II 2nd largest subunit (RPB2) and the pathogen defense related transcription factor Pti5, were confirmed as Adi3 phosphorylation substrates by in vitro kinase assays. Using a mutational approach two residues, Thr675 and Thr676, were identified as Adi3 phosphorylation sites on RPB2. This study provides the foundation for understanding Adi3 CDS mechanisms in the nucleus as well as other cellular functions.
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Affiliation(s)
- In-Cheol Yeo
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Timothy P. Devarenne
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
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8
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Kindgren P, Ivanov M, Marquardt S. Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis. Nucleic Acids Res 2020; 48:2332-2347. [PMID: 31863587 PMCID: PMC7049701 DOI: 10.1093/nar/gkz1189] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 01/12/2023] Open
Abstract
Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal RNAPII stalling in predisposing genes for transcriptional activation during plant-environment interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.
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Affiliation(s)
- Peter Kindgren
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
| | - Maxim Ivanov
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
| | - Sebastian Marquardt
- University of Copenhagen, Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Frederiksberg, Denmark
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9
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Wang X, Hennig T, Whisnant AW, Erhard F, Prusty BK, Friedel CC, Forouzmand E, Hu W, Erber L, Chen Y, Sandri-Goldin RM, Dölken L, Shi Y. Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27. Nat Commun 2020; 11:293. [PMID: 31941886 PMCID: PMC6962326 DOI: 10.1038/s41467-019-14109-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
Infection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes. However, the underlying mechanisms remain unclear. Here, we demonstrate that the HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essential mRNA 3' processing factor CPSF. It thereby induces the assembly of a dead-end 3' processing complex, blocking mRNA 3' cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3' processing for viral and a subset of host transcripts. Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced host shutoff and identify CPSF as an important factor that mediates regulation of transcription termination. These findings have broad implications for understanding the regulation of transcription termination by other viruses, cellular stress and cancer.
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Affiliation(s)
- Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Bhupesh K Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Elmira Forouzmand
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Computer Science, University of California, Irvine, Irvine, CA, 92697, USA
| | - William Hu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota, Saint Paul, MN, 55018, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota, Saint Paul, MN, 55018, USA
| | - Rozanne M Sandri-Goldin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany.
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA.
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Bauer DLV, Tellier M, Martínez-Alonso M, Nojima T, Proudfoot NJ, Murphy S, Fodor E. Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription. Cell Rep 2019; 23:2119-2129.e3. [PMID: 29768209 PMCID: PMC5972227 DOI: 10.1016/j.celrep.2018.04.047] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/03/2018] [Accepted: 04/11/2018] [Indexed: 12/24/2022] Open
Abstract
Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases. Defective Pol II termination occurs independently of the ability of the viral NS1 protein to interfere with host mRNA processing. Instead, this termination defect is a common effect of diverse cellular stresses and underlies the production of previously reported downstream-of-gene transcripts (DoGs). Our work has implications for understanding not only host-virus interactions but also fundamental aspects of mammalian transcription. Influenza virus infection dysregulates host transcription Viral infection depletes Pol II from gene bodies downstream of the TSS Virus-induced stress leads to a catastrophic failure of Pol II termination Defective termination does not require viral NS1: host CPSF30 interaction
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Affiliation(s)
- David L V Bauer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Mónica Martínez-Alonso
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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11
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Distinct Functions of the Cap-Binding Complex in Stimulation of Nuclear mRNA Export. Mol Cell Biol 2019; 39:MCB.00540-18. [PMID: 30745412 DOI: 10.1128/mcb.00540-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
Cap-binding complex (CBC) associates cotranscriptionally with the cap structure at the 5' end of nascent mRNA to protect it from exonucleolytic degradation. Here, we show that CBC promotes the targeting of an mRNA export adaptor, Yra1 (forming transcription export [TREX] complex with THO and Sub2), to the active genes and enhances mRNA export in Saccharomyces cerevisiae Likewise, recruitment of Npl3 (an hnRNP involved in mRNA export via formation of export-competent ribonuclear protein complex [RNP]) to the active genes is facilitated by CBC. Thus, CBC enhances targeting of the export factors and promotes mRNA export. Such function of CBC is not mediated via THO and Sub2 of TREX, cleavage and polyadenylation factors, or Sus1 (that regulates mRNA export via transcription export 2 [TREX-2]). However, CBC promotes splicing of SUS1 mRNA and, consequently, Sus1 protein level and mRNA export via TREX-2. Collectively, our results support the hypothesis that CBC promotes recruitment of Yra1 and Npl3 to the active genes, independently of THO, Sub2, or cleavage and polyadenylation factors, and enhances mRNA export via TREX and RNP, respectively, in addition to its role in facilitating SUS1 mRNA splicing to increase mRNA export through TREX-2, revealing distinct stimulatory functions of CBC in mRNA export.
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12
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Ji D, Manavski N, Meurer J, Zhang L, Chi W. Regulated chloroplast transcription termination. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:69-77. [PMID: 30414934 DOI: 10.1016/j.bbabio.2018.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 11/16/2022]
Abstract
Transcription termination by the RNA polymerase (RNAP) is a fundamental step of gene expression that involves the release of the nascent transcript and dissociation of the RNAP from the DNA template. However, the functional importance of termination extends beyond the mere definition of the gene borders. Chloroplasts originate from cyanobacteria and possess their own gene expression system. Plastids have a unique hybrid transcription system consisting of two different types of RNAPs of dissimilar phylogenetic origin together with several additional nuclear encoded components. Although the basic components involved in chloroplast transcription have been identified, little attention has been paid to the chloroplast transcription termination. Recent identification and functional characterization of novel factors in regulating transcription termination in Arabidopsis chloroplasts via genetic and biochemical approaches have provided insights into the mechanisms and significance of transcription termination in chloroplast gene expression. This review provides an overview of the current knowledge of the transcription termination in chloroplasts.
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Affiliation(s)
- Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Nikolay Manavski
- Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moleculaire des Plantes, 12 rue du General Zimmer, 67084 Strasbourg, France
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Planegg-Martinsried, Germany
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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13
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Sonkar A, Lyngdoh DL, Shukla R, Shukla H, Tripathi T, Ahmed S. Point mutation A394E in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. Int J Biol Macromol 2018; 119:785-791. [PMID: 30076928 DOI: 10.1016/j.ijbiomac.2018.07.193] [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: 06/29/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 12/01/2022]
Abstract
Accurate chromosomal segregation is crucial for the maintenance of genomic integrity. Rna14 is a major component of the yeast pre-mRNA 3'-end processing factor, the cleavage factor IA complex, and is involved in cleavage and polyadenylation of mRNA in the nucleus. Rna14 is also essential for the maintenance of genomic integrity in fission yeast Schizosaccharomyces pombe. In the present study, we report that a non-homologous mutation, A394E that is present in the central intrinsic disordered region of Rna14 leads to chromosomal instability in fission yeast. This mutation was shown to disrupt chromosome segregation and 3'-end maturation, and also affects the pre-mRNA splicing in vivo at non-permissive temperatures. We observed that a significant part of Rna14 is intrinsically disordered, that includes the N- and C-terminal of Rna14, as well as the central region containing the HAT repeats and the mutation within amino acid residues 372-435. These regions are crucial for the function of Rna14 as they are involved in the interaction of Rna14 with other proteins.
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Affiliation(s)
- Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Denzelle Lee Lyngdoh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
| | - Shakil Ahmed
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Lucknow 226031, India.
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14
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McKinlay A, Podicheti R, Wendte JM, Cocklin R, Rusch DB. RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis. RNA Biol 2017; 15:269-279. [PMID: 29199514 DOI: 10.1080/15476286.2017.1409930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3' boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.
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Affiliation(s)
- Anastasia McKinlay
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ram Podicheti
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA.,c School of Informatics and Computing, Indiana University , Bloomington , IN , USA
| | - Jered M Wendte
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ross Cocklin
- a Department of Biology , Indiana University , Bloomington , Indiana , USA.,d Howard Hughes Medical Institute, Indiana University , Bloomington , Indiana
| | - Douglas B Rusch
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA
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15
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Garavís M, González-Polo N, Allepuz-Fuster P, Louro JA, Fernández-Tornero C, Calvo O. Sub1 contacts the RNA polymerase II stalk to modulate mRNA synthesis. Nucleic Acids Res 2017; 45:2458-2471. [PMID: 27924005 PMCID: PMC5389574 DOI: 10.1093/nar/gkw1206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
Biogenesis of messenger RNA is critically influenced by the phosphorylation state of the carboxy-terminal domain (CTD) in the largest RNA polymerase II (RNAPII) subunit. Several kinases and phosphatases are required to maintain proper CTD phosphorylation levels and, additionally, several other proteins modulate them, including Rpb4/7 and Sub1. The Rpb4/7 heterodimer, constituting the RNAPII stalk, promote phosphatase functions and Sub1 globally influences CTD phosphorylation, though its mechanism remains mostly unknown. Here, we show that Sub1 physically interacts with the RNAPII stalk domain, Rpb4/7, likely through its C-terminal region, and associates with Fcp1. While Rpb4 is not required for Sub1 interaction with RNAPII complex, a fully functional heterodimer is required for Sub1 association to promoters. We also demonstrate that a complete CTD is necessary for proper association of Sub1 to chromatin and to the RNAPII. Finally, genetic data show a functional relationship between Sub1 and the RNAPII clamp domain. Altogether, our results indicate that Sub1, Rpb4/7 and Fcp1 interaction modulates CTD phosphorylation. In addition, Sub1 interaction with Rpb4/7 can also modulate transcription start site selection and transcription elongation rate likely by influencing the clamp function.
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Affiliation(s)
- Miguel Garavís
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Noelia González-Polo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Jaime Alegrio Louro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Olga Calvo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
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16
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Al-Husini N, Sharifi A, Mousavi SA, Chitsaz H, Ansari A. Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast. Sci Rep 2017; 7:6894. [PMID: 28761171 PMCID: PMC5537279 DOI: 10.1038/s41598-017-07062-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/26/2017] [Indexed: 11/14/2022] Open
Abstract
In budding yeast, the 3′ end processing of mRNA and the coupled termination of transcription by RNAPII requires the CF IA complex. We have earlier demonstrated a role for the Clp1 subunit of this complex in termination and promoter-associated transcription of CHA1. To assess the generality of the observed function of Clp1 in transcription, we tested the effect of Clp1 on transcription on a genomewide scale using the Global Run-On-Seq (GRO-Seq) approach. GRO-Seq analysis showed the polymerase reading through the termination signal in the downstream region of highly transcribed genes in a temperature-sensitive mutant of Clp1 at elevated temperature. No such terminator readthrough was observed in the mutant at the permissive temperature. The poly(A)-independent termination of transcription of snoRNAs, however, remained unaffected in the absence of Clp1 activity. These results strongly suggest a role for Clp1 in poly(A)-coupled termination of transcription. Furthermore, the density of antisense transcribing polymerase upstream of the promoter region exhibited an increase in the absence of Clp1 activity, thus implicating Clp1 in promoter directionality. The overall conclusion of these results is that Clp1 plays a general role in poly(A)-coupled termination of RNAPII transcription and in enhancing promoter directionality in budding yeast.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, 48202, USA
| | - Ali Sharifi
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Seyed Ahmad Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamidreza Chitsaz
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, 48202, USA.
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17
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Wittmann S, Renner M, Watts BR, Adams O, Huseyin M, Baejen C, El Omari K, Kilchert C, Heo DH, Kecman T, Cramer P, Grimes JM, Vasiljeva L. The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Nat Commun 2017; 8:14861. [PMID: 28367989 PMCID: PMC5382271 DOI: 10.1038/ncomms14861] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/05/2017] [Indexed: 11/09/2022] Open
Abstract
Termination of RNA polymerase II (Pol II) transcription is an important step in the transcription cycle, which involves the dislodgement of polymerase from DNA, leading to release of a functional transcript. Recent studies have identified the key players required for this process and showed that a common feature of these proteins is a conserved domain that interacts with the phosphorylated C-terminus of Pol II (CTD-interacting domain, CID). However, the mechanism by which transcription termination is achieved is not understood. Using genome-wide methods, here we show that the fission yeast CID-protein Seb1 is essential for termination of protein-coding and non-coding genes through interaction with S2-phosphorylated Pol II and nascent RNA. Furthermore, we present the crystal structures of the Seb1 CTD- and RNA-binding modules. Unexpectedly, the latter reveals an intertwined two-domain arrangement of a canonical RRM and second domain. These results provide important insights into the mechanism underlying eukaryotic transcription termination.
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Affiliation(s)
- Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Max Renner
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Oliver Adams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Miles Huseyin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Carlo Baejen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Kamel El Omari
- Diamond Light Source Ltd, Harwell Science &Innovation Campus, Didcot OX11 0DE, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Diamond Light Source Ltd, Harwell Science &Innovation Campus, Didcot OX11 0DE, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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18
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Richard P, Vethantham V, Manley JL. Roles of Sumoylation in mRNA Processing and Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:15-33. [PMID: 28197904 DOI: 10.1007/978-3-319-50044-7_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUMO has gained prominence as a regulator in a number of cellular processes. The roles of sumoylation in RNA metabolism, however, while considerable, remain less well understood. In this chapter we have assembled data from proteomic analyses, localization studies and key functional studies to extend SUMO's role to the area of mRNA processing and metabolism. Proteomic analyses have identified multiple putative sumoylation targets in complexes functioning in almost all aspects of mRNA metabolism, including capping, splicing and polyadenylation of mRNA precursors. Possible regulatory roles for SUMO have emerged in pre-mRNA 3' processing, where SUMO influences the functions of polyadenylation factors and activity of the entire complex. SUMO is also involved in regulating RNA editing and RNA binding by hnRNP proteins, and recent reports have suggested the involvement of the SUMO pathway in mRNA export. Together, these reports suggest that SUMO is involved in regulation of many aspects of mRNA metabolism and hold the promise for exciting future studies.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | | | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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19
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Hot1 factor recruits co-activator Sub1 and elongation complex Spt4/5 to osmostress genes. Biochem J 2016; 473:3065-79. [DOI: 10.1042/bcj20160463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Hyperosmotic stress response involves the adaptative mechanisms needed for cell survival. Under high osmolarity conditions, many stress response genes are activated by several unrelated transcription factors that are controlled by the Hog1 kinase. Osmostress transcription factor Hot1 regulates the expression of several genes involved in glycerol biosynthesis, and the presence of this transcription factor in their promoters is essential for RNApol II recruitment. The physical association between Hog1 and Hot1 activates this transcription factor and directs the RNA polymerase II localization at these promoters. We, herein, demonstrate that physical and genetic interactions exist between Hot1 and several proteins involved in transcriptional and posttranscriptional processes: for example, transcription co-activator Sub1 and elongation complex Spt4/5. The results presented in this work demonstrate that Hot1 enrichment is not detected through the coding regions of its target genes and rule out a direct role in transcription elongation. Instead, other data presented herein indicate a key function of the Hot1 transcription factor in the recruitment of these proteins to the promoter or the 5′-coding region of the genes under its control.
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20
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Abstract
Chromatin is a highly dynamic structure that imparts structural organization to the genome and regulates the gene expression underneath. The decade long research in deciphering the significance of epigenetics in maintaining cellular integrity has embarked the focus on chromatin remodeling enzymes. These drivers have been categorized as readers, writers and erasers with each having significance of their own. Largely, on the basis of structure, ATP dependent chromatin remodelers have been grouped into 4 families; SWI/SNF, ISWI, IN080 and CHD. It is still unclear to what degree these enzymes are swayed by local DNA sequences when shifting a nucleosome to different positions. The ability of regulating active and repressive transcriptional state via open and close chromatin architecture has been well studied however, the significance of chromatin remodelers in regulating transcription at each step i.e. initiation, elongation and termination require further attention. The authors have highlighted the significance and role of different chromatin remodelers in transcription, DNA repair and histone variant deposition.
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Affiliation(s)
- Monica Tyagi
- a Kusuma School of Biological Sciences, Indian Institute of Technology Delhi Hauz Khas , New Delhi , India
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21
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Rienzo M, Casamassimi A. Integrator complex and transcription regulation: Recent findings and pathophysiology. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:1269-80. [PMID: 27427483 DOI: 10.1016/j.bbagrm.2016.07.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022]
Abstract
In the last decade, a novel molecular complex has been added to the RNA polymerase II-mediated transcription machinery as one of the major components. This multiprotein complex, named Integrator, plays a pivotal role in the regulation of most RNA Polymerase II-dependent genes. This complex consists of at least 14 different subunits. However, studies investigating its structure and composition are still lacking. Although it was originally discovered as a complex implicated in the 3'-end formation of noncoding small nuclear RNAs, recent studies indicate additional roles for Integrator in transcription regulation, for example during transcription pause-release and elongation of polymerase, in the biogenesis of transcripts derived from enhancers, as well as in DNA and RNA metabolism for some of its components. Noteworthy, several subunits have been emerging to play roles during development and differentiation; more importantly, their alterations are likely to be involved in several human pathologies, including cancer and lung diseases.
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Affiliation(s)
- Monica Rienzo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy
| | - Amelia Casamassimi
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.
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22
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Ogorodnikov A, Kargapolova Y, Danckwardt S. Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Pflugers Arch 2016; 468:993-1012. [PMID: 27220521 PMCID: PMC4893057 DOI: 10.1007/s00424-016-1828-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
The human transcriptome is highly dynamic, with each cell type, tissue, and organ system expressing an ensemble of transcript isoforms that give rise to considerable diversity. Apart from alternative splicing affecting the "body" of the transcripts, extensive transcriptome diversification occurs at the 3' end. Transcripts differing at the 3' end can have profound physiological effects by encoding proteins with distinct functions or regulatory properties or by affecting the mRNA fate via the inclusion or exclusion of regulatory elements (such as miRNA or protein binding sites). Importantly, the dynamic regulation at the 3' end is associated with various (patho)physiological processes, including the immune regulation but also tumorigenesis. Here, we recapitulate the mechanisms of constitutive mRNA 3' end processing and review the current understanding of the dynamically regulated diversity at the transcriptome 3' end. We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.
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Affiliation(s)
- Anton Ogorodnikov
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany.
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23
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Harlen KM, Trotta KL, Smith EE, Mosaheb MM, Fuchs SM, Churchman LS. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue. Cell Rep 2016; 15:2147-2158. [PMID: 27239037 DOI: 10.1016/j.celrep.2016.05.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/22/2016] [Accepted: 04/26/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD) and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7), we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3' end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3' splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.
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Affiliation(s)
- Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kristine L Trotta
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Erin E Smith
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, MA 02155, USA
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24
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Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins. Gene 2016; 587:107-19. [PMID: 27154819 DOI: 10.1016/j.gene.2016.04.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 04/30/2016] [Indexed: 01/04/2023]
Abstract
Alternative pre-mRNA splicing provides a source of vast protein diversity by removing non-coding sequences (introns) and accurately linking different exonic regions in the correct reading frame. The regulation of alternative splicing is essential for various cellular functions in both pathological and physiological conditions. In eukaryotic cells, this process is commonly used to increase proteomic diversity and to control gene expression either co- or post-transcriptionally. Alternative splicing occurs within a megadalton-sized, multi-component machine consisting of RNA and proteins; during the splicing process, this complex undergoes dynamic changes via RNA-RNA, protein-protein and RNA-protein interactions. Co-transcriptional splicing functionally integrates the transcriptional machinery, thereby enabling the two processes to influence one another, whereas post-transcriptional splicing facilitates the coupling of RNA splicing with post-splicing events. This review addresses the structural aspects of spliceosomes and the mechanistic implications of their stepwise assembly on the regulation of pre-mRNA splicing. Moreover, the role of phosphorylation-based, signal-induced changes in the regulation of the splicing process is demonstrated.
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25
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Wu X, Ji G, Li QQ. Computational analysis of plant polyadenylation signals. Methods Mol Biol 2015; 1255:3-11. [PMID: 25487199 DOI: 10.1007/978-1-4939-2175-1_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Messenger RNA polyadenylation in eukaryotes marks the end of a transcript, and the process is associated with transcription termination. Increasing evidence reveals the potential of gene expression regulation through alternative polyadenylation. The site of poly(A) addition is defined by poly(A) signals reside in the transcribed pre-mRNA. To gain further insight into poly(A) signals and their functions in defining alternative polyadenylation sites that lie within different genomic regions, SignalSleuth2 was developed to extract and analyze cis-elements from a set of data with known poly(A) sites. After obtaining the sequences surrounding the poly(A) sites, exhaustive search of short sequence motifs in specified range of nucleotide sequences are performed, variable motif sizes and rank the detected motifs based on their occurrence frequencies are tallied. It also has new functions including Position-Specific Scoring Matrix (PSSM) scores calculation and multiple scanning modes. This program is powerful in revealing underline sequence motifs surrounding any target regions in a given dataset.
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Affiliation(s)
- Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
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26
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Huang Y, Yao X, Wang G. 'Mediator-ing' messenger RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:257-69. [PMID: 25515410 DOI: 10.1002/wrna.1273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/29/2014] [Accepted: 10/17/2014] [Indexed: 12/27/2022]
Abstract
Pre-messenger RNA (mRNA) processing, generally including capping, mRNA splicing, and cleavage-polyadenylation, is physically and functionally associated with transcription. The reciprocal coupling between transcription and mRNA processing ensures the efficient and regulated gene expression and editing. Multiple transcription factors/cofactors and mRNA processing factors are involved in the coupling process. This review focuses on several classic examples and recent advances that enlarge our understanding of how the transcriptional factors or cofactors, especially the Mediator complex, contribute to the RNA Pol II elongation, mRNA splicing, and polyadenylation.
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Affiliation(s)
- Yan Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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27
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Stadelmayer B, Micas G, Gamot A, Martin P, Malirat N, Koval S, Raffel R, Sobhian B, Severac D, Rialle S, Parrinello H, Cuvier O, Benkirane M. Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat Commun 2014; 5:5531. [PMID: 25410209 PMCID: PMC4263189 DOI: 10.1038/ncomms6531] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/10/2014] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. Here, we show that negative elongation factor (NELF) interacts with Integrator complex subunits (INTScom), RNAPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated INTScom subunits. Interestingly, in addition to controlling RNAPII pause-release INTS11 catalytic subunit of the INTScom is required for RNAPII processivity. Finally, INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3' box sequence required for small nuclear RNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle. RNA polymerase II (RNAPII) pausing at transcriptional start sites is an important element of gene transcription regulation. Here, the authors implicate the Integrator complex as a regulator of RNAPII pause-release and completion of mRNA synthesis at a subset of the negative elongation factor target genes.
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Affiliation(s)
- Bernd Stadelmayer
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
| | - Gaël Micas
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Adrien Gamot
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Pascal Martin
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France
| | - Nathalie Malirat
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Slavik Koval
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Raoul Raffel
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Bijan Sobhian
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | | | | | | | - Olivier Cuvier
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [3] IGF, MGX-Montpellier GenomiX, France
| | - Monsef Benkirane
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
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Abstract
The spliceosomal factor TRAP150 is essential for pre-mRNA splicing in vivo and, when overexpressed, it enhances splicing efficiency. In this study, we found that TRAP150 interacted with the cleavage and polyadenylation specificity factor (CPSF) and co-fractionated with CPSF and RNA polymerase II. Moreover, TRAP150 preferentially associated with the U1 small ribonucleoprotein (snRNP). However, our data do not support a role for TRAP150 in alternative 5′ splice site or exon selection or in alternative polyadenylation. Because U1 snRNP participates in premature cleavage and polyadenylation (PCPA), we tested whether TRAP150 is a cofactor in the control of PCPA. Although TRAP150 depletion had no significant effect on PCPA, overexpression of TRAP150 forced activation of a cryptic 3′ splice site, yielding spliced PCPA transcripts. Mechanistic studies showed that TRAP150-activated splicing occurred in composite but not authentic terminal exons, and such an activity was enhanced by debilitation of U1 snRNP or interference with transcription elongation or termination. Together, these results indicate that TRAP150 provides an additional layer of PCPA regulation, through which it may increase the diversity of abortive RNA transcripts under conditions of compromised gene expression.
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Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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29
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Schaughency P, Merran J, Corden JL. Genome-wide mapping of yeast RNA polymerase II termination. PLoS Genet 2014; 10:e1004632. [PMID: 25299594 PMCID: PMC4191890 DOI: 10.1371/journal.pgen.1004632] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/21/2014] [Indexed: 12/22/2022] Open
Abstract
Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts. Transcription termination is an important regulatory event for both non-coding and coding transcripts. Using high-throughput sequencing, we have mapped RNA Polymerase II's position in the genome after depletion of termination factors from the nucleus. We found that depletion of Ysh1 and Sen1 cause build up of polymerase directly downstream of coding and non-coding genes, respectively. Depletion of Nrd1 causes an increase in polymerase that is distributed up to 1,000 bases downstream of non-coding genes. The depletion of Nrd1 helped us to identify more than 250 unique termination regions for non-coding RNAs. Within this set of newly identified non-coding termination regions, we are further able to classify them based on sequence motif similarities, suggesting a functional role for different terminator motifs. The role of these factors in transcriptional termination of coding and/or non-coding transcripts can be inferred from the effect of polymerase's position downstream of given termination sites. This method of depletion and sequencing can be used to further elucidate other factors whose importance to transcription has yet to be determined.
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Affiliation(s)
- Paul Schaughency
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jonathan Merran
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jeffry L. Corden
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
- * E-mail:
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30
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Abstract
What has been will be again, what has been done will be done again; there is nothing new under the sun. -Ecclesiastes 1:9 (New International Version) Posttranscriptional regulation of gene expression has an important role in defining the phenotypic characteristics of an organism. Well-defined steps in mRNA metabolism that occur in the nucleus-capping, splicing, and polyadenylation-are mechanistically linked to the process of transcription. Recent evidence suggests another link between RNA polymerase II (Pol II) and a posttranscriptional process that occurs in the cytoplasm-mRNA decay. This conclusion appears to represent a conundrum. How could mRNA synthesis in the nucleus and mRNA decay in the cytoplasm be mechanistically linked? After a brief overview of mRNA processing, we will review the recent evidence for transcription-coupled mRNA decay and the possible involvement of Snf1, the Saccharomyces cerevisiae ortholog of AMP-activated protein kinase, in this process.
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31
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Lenstra TL, Tudek A, Clauder S, Xu Z, Pachis ST, van Leenen D, Kemmeren P, Steinmetz LM, Libri D, Holstege FCP. The role of Ctk1 kinase in termination of small non-coding RNAs. PLoS One 2013; 8:e80495. [PMID: 24324601 PMCID: PMC3851182 DOI: 10.1371/journal.pone.0080495] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is influenced by the phosphorylation status of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II). Late termination of mRNAs is performed by the CPF/CF complex, the recruitment of which is dependent on CTD-Ser2 phosphorylation (Ser2P). Early termination of shorter cryptic unstable transcripts (CUTs) and small nucleolar/nuclear RNAs (sno/snRNAs) is performed by the Nrd1-Nab3-Sen1 (NNS) complex that binds phosphorylated CTD-Ser5 (Ser5P) via the CTD-interacting domain (CID) of Nrd1p. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1p are more similar to those derived from alterations in the Ser5P-dependent NNS pathway, than from loss of CTD-Ser2P binding factors. Tiling array analysis of ctk1Δ cells reveals readthrough at snoRNAs, at many cryptic unstable transcripts (CUTs) and stable uncharacterized transcripts (SUTs), but only at some mRNAs. Despite the suggested predominant role in termination of mRNAs, we observed that a CTK1 deletion or a Pol II CTD mutant lacking all Ser2 positions does not result in a global mRNA termination defect. Rather, termination defects in these strains are widely observed at NNS-dependent genes. These results indicate that Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.
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Affiliation(s)
- Tineke L. Lenstra
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Agnieszka Tudek
- LEA Laboratory of Nuclear RNA Metabolism, Centre de de Génétique Moléculaire, C.N.R.S.-UPR3404, Gif sur Yvette, France
| | - Sandra Clauder
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Zhenyu Xu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Spyridon T. Pachis
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lars M. Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Domenico Libri
- LEA Laboratory of Nuclear RNA Metabolism, Centre de de Génétique Moléculaire, C.N.R.S.-UPR3404, Gif sur Yvette, France
- * E-mail: (DL); (FCPH)
| | - Frank C. P. Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail: (DL); (FCPH)
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32
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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33
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Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M. The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem 2013; 288:36676-90. [PMID: 24196955 DOI: 10.1074/jbc.m113.508267] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase II (RNApII) C-terminal domain (CTD)-interacting domain (CID) proteins are involved in two distinct RNApII termination pathways and recognize different phosphorylated forms of CTD. To investigate the role of differential CTD-CID interactions in the choice of termination pathway, we altered the CTD-binding specificity of Nrd1 by domain swapping. Nrd1 with the CID from Rtt103 (Nrd1(CID(Rtt103))) causes read-through transcription at many genes, but can also trigger termination where multiple Nrd1/Nab3-binding sites and the Ser(P)-2 CTD co-exist. Therefore, CTD-CID interactions target specific termination complexes to help choose an RNApII termination pathway. Interactions of Nrd1 with both CTD and nascent transcripts contribute to efficient termination by the Nrd1 complex. Surprisingly, replacing the Nrd1 CID with that from Rtt103 reduces binding to Rrp6/Trf4, and RNA transcripts terminated by Nrd1(CID(Rtt103)) are predominantly processed by core exosome. Thus, the Nrd1 CID couples Ser(P)-5 CTD not only to termination, but also to RNA processing by the nuclear exosome.
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Affiliation(s)
- Dong-hyuk Heo
- From the Center for RNA Research, Institute for Basic Science and
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34
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Thomas MP, Lieberman J. Live or let die: posttranscriptional gene regulation in cell stress and cell death. Immunol Rev 2013; 253:237-52. [PMID: 23550650 DOI: 10.1111/imr.12052] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Studies of the regulation of gene expression historically focused on transcription. However, during stress and apoptosis, profound gene expression changes occur more rapidly and globally than is possible by regulating transcription. Posttranscriptional changes in mRNA processing and translation in response to diverse stresses shut down most protein translation to conserve energy and lead to rapid remodeling of the proteome to promote repair. Pre-mRNA splicing and mRNA stability are fundamentally altered under some stress conditions. Stress pathways coordinate a cytoprotective repair response, while simultaneously initiating signaling that can ultimately trigger cell death. How the cell mediates the decision between repair and apoptosis is largely not understood. In some stresses, microRNAs may tip the balance. Here, we review what is known about posttranscriptional gene regulation during stress, focusing on what is still unknown and how new technologies might be used to understand what changes are most physiologically important in different forms of stress and death.
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Affiliation(s)
- Marshall P Thomas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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35
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Ni T, Yang Y, Hafez D, Yang W, Kiesewetter K, Wakabayashi Y, Ohler U, Peng W, Zhu J. Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. BMC Genomics 2013; 14:615. [PMID: 24025092 PMCID: PMC3848854 DOI: 10.1186/1471-2164-14-615] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/10/2013] [Indexed: 11/10/2022] Open
Abstract
Background Polyadenylation is a key regulatory step in eukaryotic gene expression and one of the major contributors of transcriptome diversity. Aberrant polyadenylation often associates with expression defects and leads to human diseases. Results To better understand global polyadenylation regulation, we have developed a polyadenylation sequencing (PA-seq) approach. By profiling polyadenylation events in 13 human tissues, we found that alternative cleavage and polyadenylation (APA) is prevalent in both protein-coding and noncoding genes. In addition, APA usage, similar to gene expression profiling, exhibits tissue-specific signatures and is sufficient for determining tissue origin. A 3′ untranslated region shortening index (USI) was further developed for genes with tandem APA sites. Strikingly, the results showed that different tissues exhibit distinct patterns of shortening and/or lengthening of 3′ untranslated regions, suggesting the intimate involvement of APA in establishing tissue or cell identity. Conclusions This study provides a comprehensive resource to uncover regulated polyadenylation events in human tissues and to characterize the underlying regulatory mechanism.
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Affiliation(s)
- Ting Ni
- National Heart Lung Blood Institute, National Institutes of Health, Genetics and Development Biology Center, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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36
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Affiliation(s)
- Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich,
Germany
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry,
Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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37
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Natarajan M, Schiralli Lester GM, Lee C, Missra A, Wasserman GA, Steffen M, Gilmour DS, Henderson AJ. Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription. J Biol Chem 2013; 288:25995-26003. [PMID: 23884411 DOI: 10.1074/jbc.m113.496489] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A barrier to eradicating HIV infection is targeting and eliminating latently infected cells. Events that contribute to HIV transcriptional latency include repressive chromatin structure, transcriptional interference, the inability of Tat to recruit positive transcription factor b, and poor processivity of RNA polymerase II (RNAP II). In this study, we investigated mechanisms by which negative elongation factor (NELF) establishes and maintains HIV latency. Negative elongation factor (NELF) induces RNAP II promoter proximal pausing and limits provirus expression in HIV-infected primary CD4(+) T cells. Decreasing NELF expression overcomes RNAP II pausing to enhance HIV transcription elongation in infected primary T cells, demonstrating the importance of pausing in repressing HIV transcription. We also show that RNAP II pausing is coupled to premature transcription termination and chromatin remodeling. NELF interacts with Pcf11, a transcription termination factor, and diminishing Pcf11 in primary CD4(+) T cells induces HIV transcription elongation. In addition, we identify NCoR1-GPS2-HDAC3 as a NELF-interacting corepressor complex that is associated with repressed HIV long terminal repeats. We propose a model in which NELF recruits Pcf11 and NCoR1-GPS2-HDAC3 to paused RNAP II, reinforcing repression of HIV transcription and establishing a critical checkpoint for HIV transcription and latency.
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Affiliation(s)
- Malini Natarajan
- From the Immunology and Infectious Diseases, Integrated Biosciences Graduate Program, Penn State University, University Park, Pennsylvania 16802,; the Departments of Medicine and Infectious Diseases
| | | | - Chanhyo Lee
- the Departments of Medicine and Infectious Diseases
| | - Anamika Missra
- the Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802
| | | | - Martin Steffen
- Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts 02118 and
| | - David S Gilmour
- the Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802
| | - Andrew J Henderson
- the Departments of Medicine and Infectious Diseases,; Microbiology, and.
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38
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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39
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RNA polymerase II mutations conferring defects in poly(A) site cleavage and termination in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2013; 3:167-80. [PMID: 23390594 PMCID: PMC3564978 DOI: 10.1534/g3.112.004531] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/27/2012] [Indexed: 01/06/2023]
Abstract
Transcription termination by RNA polymerase (Pol) II is an essential but poorly understood process. In eukaryotic nuclei, the 3′ ends of mRNAs are generated by cleavage and polyadenylation, and the same sequence elements that specify that process are required for downstream release of the polymerase from the DNA. Although Pol II is known to bind proteins required for both events, few studies have focused on Pol II mutations as a means to uncover the mechanisms that couple polyadenylation and termination. We performed a genetic screen in the yeast Saccharomyces cerevisiae to isolate mutations in the N-terminal half of Rpb2, the second largest Pol II subunit, that conferred either a decreased or increased response to a well-characterized poly(A) site. Most of the mutant alleles encoded substitutions affecting either surface residues or conserved active site amino acids at positions important for termination by other RNA polymerases. Reverse transcription polymerase chain reaction experiments revealed that transcript cleavage at the poly(A) site was impaired in both classes of increased readthrough mutants. Transcription into downstream sequences beyond where termination normally occurs was also probed. Although most of the tested readthrough mutants showed a reduction in termination concomitant with the reduced poly(A) usage, these processes were uncoupled in at least one mutant strain. Several rpb2 alleles were found to be similar or identical to published mutants associated with defective TFIIF function. Tests of these and additional mutations known to impair Rpb2−TFIIF interactions revealed similar decreased readthrough phenotypes, suggesting that TFIIF may have a role in 3′ end formation and termination.
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40
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Anamika K, Gyenis À, Tora L. How to stop: the mysterious links among RNA polymerase II occupancy 3' of genes, mRNA 3' processing and termination. Transcription 2012; 4:7-12. [PMID: 23131668 DOI: 10.4161/trns.22300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic genes are transcribed by RNA polymerase II (RNAP II) through cycles of initiation, elongation and termination. Termination remains the least understood stage of transcription. Here we discuss the role of RNAP II occupancy downstream of the 3'ends of genes and its links with termination and mRNA 3' processing.
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Affiliation(s)
- Krishanpal Anamika
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch Cedex, France
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41
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Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Nat Struct Mol Biol 2012; 19:1011-7. [PMID: 22961381 PMCID: PMC3711404 DOI: 10.1038/nsmb.2381] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 08/02/2012] [Indexed: 11/16/2022]
Abstract
Recent studies showed that Rai1 is a crucial component of the mRNA 5′-end capping quality control mechanism in yeast. The yeast genome encodes a weak homolog of Rai1, Ydr370C, but little is known about this protein. Here we report the crystal structures of Kluyveromyces lactis Ydr370C and the first biochemical and functional studies on this protein. The overall structure of Ydr370C is similar to Rai1. Ydr370C has robust decapping activity on RNAs with unmethylated caps but it has no detectable pyrophosphohydrolase activity. Unexpectedly, Ydr370C also possesses distributive, 5′-3′ exoribonuclease activity, and we propose the name Dxo1 for this novel eukaryotic enzyme with both decapping and exonuclease activities. Studies in yeast where both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process.
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42
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Sugiyama T, Sugioka-Sugiyama R, Hada K, Niwa R. Rhn1, a nuclear protein, is required for suppression of meiotic mRNAs in mitotically dividing fission yeast. PLoS One 2012; 7:e42962. [PMID: 22912768 PMCID: PMC3422304 DOI: 10.1371/journal.pone.0042962] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/16/2012] [Indexed: 12/23/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, many meiotic mRNAs are transcribed during mitosis and meiosis and selectively eliminated in mitotic cells. However, this pathway for mRNA decay, called the determinant of selective removal (DSR)-Mmi1 system, targets only some of the numerous meiotic mRNAs that are transcribed in mitotic cells. Here we describe Rhn1, a nuclear protein involved in meiotic mRNA suppression in vegetative fission yeast. Rhn1 is homologous to budding yeast Rtt103 and localizes to one or a few discrete nuclear dots in growing vegetative cells. Rhn1 colocalizes with a pre-mRNA 3′-end processing factor, Pcf11, and with the 5′–3′ exoribonuclease, Dhp1; moreover, Rhn1 coimmunoprecipitates with Pcf11. Loss of rhn1 results in elevated sensitivity to high temperature, to thiabendazole (TBZ), and to UV. Interestingly, meiotic mRNAs—including moa1+, mcp5+, and mug96+—accumulate in mitotic rhn1Δ cells. Accumulation of meiotic mRNAs also occurs in strains lacking Lsk1, a kinase that phosphorylates serine 2 (Ser-2) in the C-terminal domain (CTD) of RNA polymerase II (Pol II), and in strains lacking Sen1, an ATP-dependent 5′–3′ RNA/DNA helicase: notably, both Lsk1 and Sen1 have been implicated in termination of Pol II-dependent transcription. Furthermore, RNAi knockdown of cids-2, a Caenorhabditis elegans ortholog of rhn1+, leads to elevated expression of a germline-specific gene, pgl-1, in somatic cells. These results indicate that Rhn1 contributes to the suppression of meiotic mRNAs in vegetative fission yeast and that the mechanism by which Rhn1 downregulates germline-specific transcripts may be conserved in unicellular and multicellular organisms.
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Affiliation(s)
- Tomoyasu Sugiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Fukumitsu H, Soumiya H, Furukawa S. Knockdown of pre-mRNA cleavage factor Im 25 kDa promotes neurite outgrowth. Biochem Biophys Res Commun 2012; 425:848-53. [PMID: 22898046 DOI: 10.1016/j.bbrc.2012.07.164] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 07/31/2012] [Indexed: 01/16/2023]
Abstract
Mammalian precursor mRNA (pre-mRNA) cleavage factor I (CFIm) plays important roles in the selection of poly(A) sites in a 3'-untranslated region (3'-UTR), producing mRNAs with variable 3' ends. Because 3'-UTRs often contain cis elements that impact stability or localization of mRNA or translation, alternative polyadenylation diversifies utilization of primary transcripts in mammalian cells. However, the physiological role of CFIm remains unclear. CFIm acts as a heterodimer comprising a 25kDa subunit (CFIm25) and one of the three large subunits-CFIm59, CFIm68, or CFIm72. CFIm25 binds directly to RNA and introduces and anchors the larger subunit. To examine the physiological roles of CFIm, we knocked down the CFIm25 gene in neuronal cells using RNA interference. Knockdown of CFIm25 increased the number of primary dendrites of developing hippocampal neurons and promoted nerve growth factor (NGF)-induced neurite extension from rat pheochromocytoma PC12 cells without affecting the morphology of proliferating PC12 cells. On the other hand, CFIm25 knockdown did not influence constitutively active or dominantly negative RhoA suppression or promotion of NGF-induced neurite extension from PC12 cells, respectively. Taken together, our results indicate that endogenous CFIm may promote neuritogenesis in developing neurons by coordinating events upstream of NGF-induced RhoA inactivation.
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Affiliation(s)
- Hidefumi Fukumitsu
- Laboratory of Molecular Biology, Department of Biofunctional Analysis, Gifu Pharmaceutical University, Daigakunishi 1-25-4, Gifu 501 1196, Japan.
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Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes. Mol Cell Biol 2012; 32:3428-37. [PMID: 22733996 DOI: 10.1128/mcb.00247-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fcp1 dephosphorylates the C-terminal domain of the largest subunit of RNA polymerase II (Pol II) to recycle it into a form that can initiate a new round of transcription. Previously, we identified Drosophila Fcp1 as an important factor in optimal Hsp70 mRNA accumulation after heat shock. Here, we examine the role of Fcp1 in transcription of heat shock genes in vivo. We demonstrate that Fcp1 localizes to active sites of transcription including the induced Hsp70 gene. The reduced Hsp70 mRNA accumulation seen by RNA interference (RNAi) depletion of Fcp1 in S2 cells is a result of a loss of Pol II in the coding region of highly transcribed heat shock-induced genes: Hsp70, Hsp26, and Hsp83. Moreover, Fcp1 depletion dramatically increases phosphorylation of the non-chromatin-bound Pol II. Reexpression of either wild-type or catalytically dead versions of Fcp1 demonstrates that both the reduced Pol II levels on heat shock genes and the increased levels of phosphorylated free Pol II are dependent on the catalytic activity of Fcp1. Our results indicate that Fcp1 is required to maintain the pool of initiation-competent unphosphorylated Pol II, and this function is particularly important for the highly transcribed heat shock genes.
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RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts. PLoS One 2012; 7:e38769. [PMID: 22701709 PMCID: PMC3372504 DOI: 10.1371/journal.pone.0038769] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 05/13/2012] [Indexed: 11/19/2022] Open
Abstract
Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding of Pol II downstream of the 3′ end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all expressed genes we observed Pol II occupancy downstream of the EAGs suggesting that Pol II pausing 3′ from the transcription units is a rather common phenomenon. Downstream of EAGs Pol II transcripts can also be detected by global run-on and sequencing, suggesting the presence of functionally active Pol II. Based on Pol II occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts undergo polyA tail addition [poly(A)+], Pol II occupancy downstream of the EAGs can be detected up to 4–6 kb. Inhibition of polyadenylation significantly increased Pol II occupancy downstream of EAGs at poly(A)+ genes, but not at the EAGs of core histone genes. The differential genome-wide Pol II occupancy profiles 3′ of the EAGs have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be independent of the phosphorylation status of the C-terminal domain of the large subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3′ end processing mechanisms and consequent Pol II transcription termination processes.
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Mechanisms of HIV Transcriptional Regulation and Their Contribution to Latency. Mol Biol Int 2012; 2012:614120. [PMID: 22701796 PMCID: PMC3371693 DOI: 10.1155/2012/614120] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/09/2012] [Indexed: 12/26/2022] Open
Abstract
Long-lived latent HIV-infected cells lead to the rebound of virus replication following antiretroviral treatment interruption and present a major barrier to eliminating HIV infection. These latent reservoirs, which include quiescent memory T cells and tissue-resident macrophages, represent a subset of cells with decreased or inactive proviral transcription. HIV proviral transcription is regulated at multiple levels including transcription initiation, polymerase recruitment, transcription elongation, and chromatin organization. How these biochemical processes are coordinated and their potential role in repressing HIV transcription along with establishing and maintaining latency are reviewed.
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Gummalla M, Maeda RK, Castro Alvarez JJ, Gyurkovics H, Singari S, Edwards KA, Karch F, Bender W. abd-A regulation by the iab-8 noncoding RNA. PLoS Genet 2012; 8:e1002720. [PMID: 22654672 PMCID: PMC3359974 DOI: 10.1371/journal.pgen.1002720] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 04/03/2012] [Indexed: 12/29/2022] Open
Abstract
The homeotic genes in Drosophila melanogaster are aligned on the chromosome in the order of the body segments that they affect. The genes affecting the more posterior segments repress the more anterior genes. This posterior dominance rule must be qualified in the case of abdominal-A (abd-A) repression by Abdominal-B (Abd-B). Animals lacking Abd-B show ectopic expression of abd-A in the epidermis of the eighth abdominal segment, but not in the central nervous system. Repression in these neuronal cells is accomplished by a 92 kb noncoding RNA. This “iab-8 RNA” produces a micro RNA to repress abd-A, but also has a second, redundant repression mechanism that acts only “in cis.” Transcriptional interference with the abd-A promoter is the most likely mechanism. Although long, noncoding RNAs have been found in many organisms, it has been difficult to assign to them any molecular function. The homeotic gene clusters in the fruit fly, Drosophila melanogaster, contain many such noncoding RNAs. We have characterized one such noncoding RNA, a 92 kb transcription unit from within the bithorax complex. This transcript, called the iab-8 ncRNA, is made in the cells of the central nervous system in the eighth abdominal segment, along with the homeotic transcription factor Abdominal-B. Another homeotic transcription factor, abdominal-A, is repressed in these cells. It has generally been assumed that abdominal-A repression in these cells is mediated by the Abdominal-B protein. However, here we show that it is not Abdominal-B that represses abdominal-A, but the iab-8 ncRNA. This repression is accomplished by two redundant mechanisms; the iab-8 precursor produces a micro RNA, which targets the abdominal-A mRNA, and iab-8 transcription interferes with the abdominal-A promoter, which lies just downstream of the iab-8 ncRNA poly(A) site.
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Affiliation(s)
- Maheshwar Gummalla
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Robert K. Maeda
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | | | - Swetha Singari
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - Kevin A. Edwards
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - François Karch
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- * E-mail: (FK); (WB)
| | - Welcome Bender
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (FK); (WB)
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Zhang DW, Rodríguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ. Emerging Views on the CTD Code. GENETICS RESEARCH INTERNATIONAL 2012; 2012:347214. [PMID: 22567385 PMCID: PMC3335543 DOI: 10.1155/2012/347214] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/03/2011] [Indexed: 12/21/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the "CTD code" hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. Here, we highlight the role of CTD modifications in directing transcription initiation, elongation, and termination. We examine the major readers, writers, and erasers of the CTD code and examine the relevance of describing patterns of posttranslational modifications as a "code." Finally, we discuss major questions regarding the function of the newly discovered CTD modifications and the fundamental insights into transcription regulation that will necessarily emerge upon addressing those challenges.
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Affiliation(s)
- David W. Zhang
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Juan B. Rodríguez-Molina
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Joshua R. Tietjen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Corey M. Nemec
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Aseem Z. Ansari
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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Proshkin SA, Shematorova EK, Souslova EA, Proshkina GM, Shpakovski GV. A minor isoform of the human RNA polymerase II subunit hRPB11 (POLR2J) interacts with several components of the translation initiation factor eIF3. BIOCHEMISTRY (MOSCOW) 2012; 76:976-80. [PMID: 22022972 DOI: 10.1134/s0006297911080141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Using the yeast two-hybrid (YTH) system we have uncovered interaction of the hRPB11cα minor isoform of Homo sapiens RNA polymerase II hRPB11 (POLR2J) subunit with three different subunits of the human translation initiation factor eIF3 (hEIF3): eIF3a, eIF3i, and eIF3m. One variant of eIF3m identified in the study is the product of translation of alternatively spliced mRNA. We have named a novel isoform of this subunit eIF3mβ. By means of the YTH system we also have shown that the new eIF3mβ isoform interacts with the eIF3a subunit. Whereas previously described subunit eIF3mα (GA17) has clear cytoplasmic localization, the novel eIF3mβ isoform is detected predominantly in the cell nucleus. The discovered interactions of the hRPB11cα isoform with several hEIF3 subunits demonstrate a new type coordination between transcription and the following (downstream) stages of gene expression (such as mRNA transport from nucleus to the active ribosomes in cytoplasm) in Homo sapiens and point out the possibility of existence of nuclear hEIF3 subcomplexes.
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Affiliation(s)
- S A Proshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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50
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García-Oliver E, García-Molinero V, Rodríguez-Navarro S. mRNA export and gene expression: the SAGA-TREX-2 connection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:555-65. [PMID: 22178374 DOI: 10.1016/j.bbagrm.2011.11.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 01/07/2023]
Abstract
In the gene expression field, different steps have been traditionally viewed as discrete and unconnected events. Nowadays, genetic and functional studies support the model of a coupled network of physical and functional connections to carry out mRNA biogenesis. Gene expression is a coordinated process that comprises different linked steps like transcription, RNA processing, export to the cytoplasm, translation and degradation of mRNAs. Its regulation is essential for cellular survival and can occur at many different levels. Transcription is the central function that occurs in the nucleus, and RNAPII plays an essential role in mRNA biogenesis. During transcription, nascent mRNA is associated with the mRNA-binding proteins involved in processing and export of the mRNA particle. Cells have developed a network of multi-protein complexes whose functions regulate the different factors involved both temporally and spatially. This coupling mechanism acts as a quality control to solve some of the organization problems of gene expression in vivo, where all the factors implicated ensure that mRNAs are ready to be exported and translated. In this review, we focus on the functional coupling of gene transcription and mRNA export, and place particular emphasis on the relationship between the NPC-associated complex, TREX2, and the transcription co-activator, SAGA. We have pinpointed the experimental evidence for Sus1's roles in transcription initiation, transcription elongation and mRNA export. In addition, we have reviewed other NPC-related processes such as gene gating to the nuclear envelope, the chromatin structure and the cellular context in which these processes take place. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Encar García-Oliver
- Centro de Investigación Príncipe Felipe (CIPF), Gene Expression coupled with RNA Transport Laboratory, Valencia, Spain
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