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Kadooka C, Izumitsu K, Asai T, Hiramatsu K, Mori K, Okutsu K, Yoshizaki Y, Takamine K, Goto M, Tamaki H, Futagami T. Overexpression of the RNA-binding protein NrdA affects global gene expression and secondary metabolism in Aspergillus species. mSphere 2025; 10:e0084924. [PMID: 39853104 PMCID: PMC11852746 DOI: 10.1128/msphere.00849-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 12/16/2024] [Indexed: 01/26/2025] Open
Abstract
RNA-binding protein Nrd1 plays a role in RNA polymerase II transcription termination. In this study, we showed that the orthologous NrdA is important in global mRNA expression and secondary metabolism in Aspergillus species. We constructed an nrdA conditional expression strain using the Tet-On system in Aspergillus luchuenesis mut. kawachii. Downregulation of nrdA caused a severe growth defect, indicating that NrdA is essential for the proliferation of A. kawachii. Parallel RNA-sequencing and RNA immunoprecipitation-sequencing analysis identified potential NrdA-interacting transcripts, corresponding to 32% of the predicted protein-coding genes of A. kawachii. Subsequent gene ontology analysis suggested that overexpression of NrdA affects the production of secondary metabolites. To clarify this, we constructed Aspergillus nidulans, Aspergillus fumigatus, and Aspergillus oryzae strains overexpressing NrdA in the early developmental stage. Overexpression of NrdA reduced the production of sterigmatocystin and penicillin in A. nidulans, as well as that of helvolic acid and pyripyropene A in A. fumigatus. Moreover, it increased the production of kojic acid and reduced the production of penicillin in A. oryzae. These effects were accompanied by almost consistent changes in the mRNA levels of relevant genes. Collectively, these results suggest that NrdA is the essential RNA-binding protein, which plays a significant role in global gene expression and secondary metabolism in Aspergillus species.IMPORTANCENrd1, a component of the Nrd1-Nab3-Sen1 complex, is an essential RNA-binding protein involved in transcriptional termination in yeast. However, its role in filamentous fungi has not been studied. In this study, we characterized an orthologous NrdA in the Aspergillus species, identified potential NrdA-interacting mRNA, and investigated the effect of overexpression of NrdA on mRNA expression in Aspergillus luchuensis mut. kawachii. The results indicated that NrdA controls global gene expression involved in versatile metabolic pathways, including the secondary metabolic process, at least in the early developmental stage. We demonstrated that NrdA overexpression significantly affected the production of secondary metabolites in Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus. Our findings are of importance to the fungal research community because the secondary metabolism is an industrially and clinically important aspect for the Aspergillus species.
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Affiliation(s)
- Chihiro Kadooka
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
- Department of Biotechnology and Life Sciences, Faculty of Biotechnology and Life Sciences, Sojo University, Nishi-ku, Kumamoto, Japan
| | - Kosuke Izumitsu
- Graduate School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga, Japan
| | - Teigo Asai
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi, Japan
| | - Kentaro Hiramatsu
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Nishi-ku, Fukuoka, Japan
- Cell Innovator Co., Ltd., Higashi-ku, Fukuoka, Japan
| | - Kayu Okutsu
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Yumiko Yoshizaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Kazunori Takamine
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Masatoshi Goto
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Hisanori Tamaki
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Taiki Futagami
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Centre for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
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2
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Kuś K, Carrique L, Kecman T, Fournier M, Hassanein SS, Aydin E, Kilchert C, Grimes JM, Vasiljeva L. DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts. Nat Commun 2025; 16:10. [PMID: 39746995 PMCID: PMC11695829 DOI: 10.1038/s41467-024-55063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/29/2024] [Indexed: 01/04/2025] Open
Abstract
Precursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is established, the underlying mechanisms are not fully understood. We show that the key transcription termination factor, RNA exonuclease Xrn2 engages with Pol II forming a stable complex. Xrn2 activity is stimulated by Spt5 to ensure efficient degradation of nascent RNA leading to Pol II dislodgement from DNA. Our results support a model where Xrn2 first forms a stable complex with the elongating Pol II to achieve its full activity in degrading nascent RNA revising the current 'torpedo' model of termination, which posits that RNA degradation precedes Xrn2 engagement with Pol II. Spt5 is also a key factor that attenuates the expression of non-coding transcripts, coordinates pre-mRNA splicing and 3'-end processing. Our findings indicate that engagement with the transcribing Pol II is an essential regulatory step modulating the activity of RNA enzymes such as Xrn2, thus advancing our understanding of how RNA maturation is controlled during transcription.
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Affiliation(s)
- Krzysztof Kuś
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
| | - Loic Carrique
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marjorie Fournier
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sarah Sayed Hassanein
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Ebru Aydin
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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3
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Lopez Martinez D, Svejstrup JQ. Mechanisms of RNA Polymerase II Termination at the 3'-End of Genes. J Mol Biol 2025; 437:168735. [PMID: 39098594 DOI: 10.1016/j.jmb.2024.168735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
RNA polymerase II (RNAPII) is responsible for the synthesis of a diverse set of RNA molecules, including protein-coding messenger RNAs (mRNAs) and many short non-coding RNAs (ncRNAs). For this purpose, RNAPII relies on a multitude of factors that regulate the transcription cycle, from initiation and promoter-proximal pausing, through elongation and finally termination. RNAPII transcription termination at the end of genes ensures the release of RNAPII from the DNA template and its efficient recycling for further rounds of transcription. Termination of RNAPII is tightly coupled to 3'-end mRNA processing, which constitutes an important trigger for the subsequent transcription termination event. In this review, we discuss the current understanding of RNAPII termination mechanisms, focusing on 'canonical' termination at the 3'-end of genes. We also integrate the allosteric and 'torpedo' models into a unified model of termination, and describe the different termination factors that have been identified to date, paying special attention to the human factors and their mechanism of action at the molecular level. Indeed, in recent years the development of novel approaches in structural biology, biochemistry and cell biology have together led to a more detailed comprehension of the different mechanisms of RNAPII termination, and a better understanding of their importance in regulating gene expression, especially under cellular stress and pathological situations.
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Affiliation(s)
- David Lopez Martinez
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Q Svejstrup
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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4
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Bentley DL. Multiple Forms and Functions of Premature Termination by RNA Polymerase II. J Mol Biol 2025; 437:168743. [PMID: 39127140 PMCID: PMC11649484 DOI: 10.1016/j.jmb.2024.168743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Eukaryotic genomes are widely transcribed by RNA polymerase II (pol II) both within genes and in intergenic regions. POL II elongation complexes comprising the polymerase, the DNA template and nascent RNA transcript must be extremely processive in order to transcribe the longest genes which are over 1 megabase long and take many hours to traverse. Dedicated termination mechanisms are required to disrupt these highly stable complexes. Transcription termination occurs not only at the 3' ends of genes once a full length transcript has been made, but also within genes and in promiscuously transcribed intergenic regions. Termination at these latter positions is termed "premature" because it is not triggered in response to a specific signal that marks the 3' end of a gene, like a polyA site. One purpose of premature termination is to remove polymerases from intergenic regions where they are "not wanted" because they may interfere with transcription of overlapping genes or the progress of replication forks. Premature termination has recently been appreciated to occur at surprisingly high rates within genes where it is speculated to serve regulatory or quality control functions. In this review I summarize current understanding of the different mechanisms of premature termination and its potential functions.
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Affiliation(s)
- David L Bentley
- Dept. Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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5
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Ding DQ, Okamasa K, Yoshimura Y, Matsuda A, Yamamoto TG, Hiraoka Y, Nakayama JI. Proteins and noncoding RNAs that promote homologous chromosome recognition and pairing in fission yeast meiosis undergo condensate formation in vitro. FASEB J 2024; 38:e70163. [PMID: 39520300 DOI: 10.1096/fj.202302563rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 10/16/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024]
Abstract
Pairing of homologous chromosomes during meiosis is crucial for successful sexual reproduction. Previous studies have shown that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 locus and plays a key role in mediating robust pairing during meiosis. Several RNA-binding proteins accumulate at the sme2 and other lncRNA gene loci in conjunction with the lncRNAs transcribed from these loci. These lncRNA-protein complexes form condensates that exhibit phase separation properties on chromosomes and are necessary for robust pairing of homologous chromosomes. To further understand the mechanisms by which phase separation affects homologous chromosome pairing, we conducted an in vitro phase separation assay with the sme2 RNA-associated proteins (Smps) and RNAs. Our findings reveal that one of the Smps, Seb1, forms condensates resembling phase separation; the observed number and size of these condensates increase upon the addition of another Smp, Rhn1, and purified RNAs. Additionally, we have found that RNAs protect Smp condensates from treatment with 1,6-hexanediol. The Smp condensates containing different types of RNA display distinct FRAP profiles, and the Smp condensates containing the same type of RNA tend to fuse together more readily than those containing different types of RNAs. Collectively, these results indicate that the specific RNA species within condensates modulate their physical properties, potentially enabling the formation of regional RNA-Smp condensates with distinct characteristics that facilitate homologous chromosome pairing.
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Affiliation(s)
- Da-Qiao Ding
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Kasumi Okamasa
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Takaharu G Yamamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, Japan
- Basic Biology Program, Graduate Institute for Advanced Studies SOKENDAI, Okazaki, Japan
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6
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Aydin E, Schreiner S, Böhme J, Keil B, Weber J, Žunar B, Glatter T, Kilchert C. DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3'-end of genes and involved in the recycling of cleavage factors. Nat Commun 2024; 15:6829. [PMID: 39122693 PMCID: PMC11315920 DOI: 10.1038/s41467-024-51035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3'-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localises to cleavage bodies, which are enriched for 3'-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3'-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3'-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.
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Affiliation(s)
- Ebru Aydin
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Silke Schreiner
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Jacqueline Böhme
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Birte Keil
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Jan Weber
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Bojan Žunar
- Department of Chemistry and Biochemistry, University of Zagreb Faculty of Food Technology and Biotechnology, Zagreb, Croatia
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.
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7
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Boulanger C, Haidara N, Yague-Sanz C, Larochelle M, Jacques PÉ, Hermand D, Bachand F. Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation. Nucleic Acids Res 2024; 52:7572-7589. [PMID: 38801067 PMCID: PMC11260464 DOI: 10.1093/nar/gkae436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats that can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although CTD-associated proteins have been identified, phospho-dependent CTD interactions have remained elusive. Proximity-dependent biotinylation (PDB) has recently emerged as an alternative approach to identify protein-protein associations in the native cellular environment. In this study, we present a PDB-based map of the fission yeast RNAPII CTD interactome in living cells and identify phospho-dependent CTD interactions by using a mutant in which Ser2 was replaced by alanine in every repeat of the fission yeast CTD. This approach revealed that CTD Ser2 phosphorylation is critical for the association between RNAPII and the histone methyltransferase Set2 during transcription elongation, but is not required for 3' end processing and transcription termination. Accordingly, loss of CTD Ser2 phosphorylation causes a global increase in antisense transcription, correlating with elevated histone acetylation in gene bodies. Our findings reveal that the fundamental role of CTD Ser2 phosphorylation is to establish a chromatin-based repressive state that prevents cryptic intragenic transcription initiation.
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Affiliation(s)
- Cédric Boulanger
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Nouhou Haidara
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
| | - Marc Larochelle
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - Damien Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000, Belgium
- The Francis Crick Institute, 1 Midland Road London NW1 1AT, UK
| | - Francois Bachand
- RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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8
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Menon G, Mateo-Bonmati E, Reeck S, Maple R, Wu Z, Ietswaart R, Dean C, Howard M. Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing. Mol Cell 2024; 84:2255-2271.e9. [PMID: 38851186 DOI: 10.1016/j.molcel.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024]
Abstract
The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.
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Affiliation(s)
- Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Robert Ietswaart
- Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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9
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Chaudhuri A, Paul S, Banerjea M, Das B. Polyadenylated versions of small non-coding RNAs in Saccharomyces cerevisiae are degraded by Rrp6p/Rrp47p independent of the core nuclear exosome. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:155-186. [PMID: 38783922 PMCID: PMC11115967 DOI: 10.15698/mic2024.05.823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024]
Abstract
In Saccharomyces cerevisiae, polyadenylated forms of mature (and not precursor) small non-coding RNAs (sncRNAs) those fail to undergo proper 3'-end maturation are subject to an active degradation by Rrp6p and Rrp47p, which does not require the involvement of core exosome and TRAMP components. In agreement with this finding, Rrp6p/Rrp47p is demonstrated to exist as an exosome-independent complex, which preferentially associates with mature polyadenylated forms of these sncRNAs. Consistent with this observation, a C-terminally truncated version of Rrp6p (Rrp6p-ΔC2) lacking physical association with the core nuclear exosome supports their decay just like its full-length version. Polyadenylation is catalyzed by both the canonical and non-canonical poly(A) polymerases, Pap1p and Trf4p. Analysis of the polyadenylation profiles in WT and rrp6-Δ strains revealed that the majority of the polyadenylation sites correspond to either one to three nucleotides upstream or downstream of their mature ends and their poly(A) tails ranges from 10-15 adenylate residues. Most interestingly, the accumulated polyadenylated snRNAs are functional in the rrp6-Δ strain and are assembled into spliceosomes. Thus, Rrp6p-Rrp47p defines a core nuclear exosome-independent novel RNA turnover system in baker's yeast targeting imperfectly processed polyadenylated sncRNAs that accumulate in the absence of Rrp6p.
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Affiliation(s)
- Anusha Chaudhuri
- Present Position: Zentrum fǜr Molekulare, Medizin, Institut fǜr Kardiovaskuläre Regeneration, Haus 25B, Goethe-Universität, Theodor-Stern-Kai 7, Universitätsklinikum, 60590 Frankfurt am Main, Germany
| | - Soumita Paul
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Mayukh Banerjea
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
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10
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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11
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Esteban‐Serna S, McCaughan H, Granneman S. Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes. Mol Microbiol 2023; 120:477-489. [PMID: 37165708 PMCID: PMC10952675 DOI: 10.1111/mmi.15073] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
RNA-binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles in adaptive responses in microbes. A robust approach to examine protein-RNA interactions involves irradiating cells with UV light to form covalent adducts between RBPs and their cognate RNAs. Combined with RNA or protein purification, these procedures can provide global RBP censuses or transcriptomic maps for all target sequences of a single protein in living cells. The recent development of novel methods has quickly populated the RBP landscape in microorganisms. Here, we provide an overview of prominent UV cross-linking techniques which have been applied to investigate RNA interactomes in microbes. By assessing their advantages and caveats, this technical evaluation intends to guide the selection of appropriate methods and experimental design as well as to encourage the use of complementary UV-dependent techniques to inspect RNA-binding activity.
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Affiliation(s)
- Sofia Esteban‐Serna
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Hugh McCaughan
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Sander Granneman
- Centre for Engineering Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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12
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Duval M, Yague-Sanz C, Turowski TW, Petfalski E, Tollervey D, Bachand F. The conserved RNA-binding protein Seb1 promotes cotranscriptional ribosomal RNA processing by controlling RNA polymerase I progression. Nat Commun 2023; 14:3013. [PMID: 37230993 DOI: 10.1038/s41467-023-38826-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Transcription by RNA polymerase I (RNAPI) represents most of the transcriptional activity in eukaryotic cells and is associated with the production of mature ribosomal RNA (rRNA). As several rRNA maturation steps are coupled to RNAPI transcription, the rate of RNAPI elongation directly influences processing of nascent pre-rRNA, and changes in RNAPI transcription rate can result in alternative rRNA processing pathways in response to growth conditions and stress. However, factors and mechanisms that control RNAPI progression by influencing transcription elongation rate remain poorly understood. We show here that the conserved fission yeast RNA-binding protein Seb1 associates with the RNAPI transcription machinery and promotes RNAPI pausing states along the rDNA. The overall faster progression of RNAPI at the rDNA in Seb1-deficient cells impaired cotranscriptional pre-rRNA processing and the production of mature rRNAs. Given that Seb1 also influences pre-mRNA processing by modulating RNAPII progression, our findings unveil Seb1 as a pause-promoting factor for RNA polymerases I and II to control cotranscriptional RNA processing.
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Affiliation(s)
- Maxime Duval
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carlo Yague-Sanz
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- URPHYM-GEMO, The University of Namur, 5000, Namur, Belgium
| | - Tomasz W Turowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - François Bachand
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada.
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13
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Bag I, Chen Y, D'Orazio K, Lopez P, Wenzel S, Takagi Y, Lei EP. Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function. G3 (BETHESDA, MD.) 2022; 12:jkac152. [PMID: 35708663 PMCID: PMC9434307 DOI: 10.1093/g3journal/jkac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here, we utilized RNA-affinity pulldown coupled with mass spectrometry to identify a novel RNA-binding protein, Isha (CG4266), that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif and RNA Polymerase II C-terminal domain-interacting domain (CID). We found that Isha physically interacts with total and elongating Polymerase II and associates with chromatin at the 5' end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with the core gypsy insulator component CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor Isha that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.
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Affiliation(s)
- Indira Bag
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karole D'Orazio
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prisma Lopez
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elissa P Lei
- Corresponding author: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Zhou M, Ehsan F, Gan L, Dong A, Li Y, Liu K, Min J. Structural basis for the recognition of the S2, S5-phosphorylated RNA polymerase II CTD by the mRNA anti-terminator protein hSCAF4. FEBS Lett 2022; 596:249-259. [PMID: 34897689 DOI: 10.1002/1873-3468.14256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/05/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II serves as a binding platform for numerous enzymes and transcription factors involved in nascent RNA processing and the transcription cycle. The S2, S5-phosphorylated CTD is recognized by the transcription factor SCAF4, which functions as a transcription anti-terminator by preventing early mRNA transcript cleavage and polyadenylation. Here, we measured the binding affinities of differently modified CTD peptides by hSCAF4 and solved the complex structure of the hSCAF4-CTD-interaction domain (CID) bound to a S2, S5-quadra-phosphorylated CTD peptide. Our results revealed that the S2, S5-quadra-phosphorylated CTD peptide adopts a trans conformation and is located in a positively charged binding groove of hSCAF4-CID. Although hSCAF4-CID has almost the same binding pattern to the CTD as other CID-containing proteins, it preferentially binds to the S2, S5-phosphorylated CTD. Our findings provide insight into the regulatory mechanism of hSCAF4 in transcription termination.
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Affiliation(s)
- Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- Structural Genomics Consortium, University of Toronto, Canada
| | - Fahad Ehsan
- Structural Genomics Consortium, University of Toronto, Canada
- Department of Physiology, University of Toronto, Canada
| | - Linyao Gan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- Structural Genomics Consortium, University of Toronto, Canada
- Department of Physiology, University of Toronto, Canada
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15
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Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription. Cell Rep 2021; 36:109671. [PMID: 34496258 PMCID: PMC8441049 DOI: 10.1016/j.celrep.2021.109671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/26/2020] [Accepted: 08/13/2021] [Indexed: 12/25/2022] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the histone deacetylase activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of antisense transcription when RNA polymerase II phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, although single Hos2 and Set3 mutants have little effect, loss of Hos2 or Set3 combined with ssu72Δ results in a synergistic increase in antisense transcription globally and correlates with elevated sensitivity to genotoxic agents. We demonstrate a key role for the Ssu72/Hos2/Set3 mechanism in the suppression of cryptic antisense transcription at the 3' end of convergent genes that are most susceptible to these defects, ensuring the fidelity of gene expression within dense genomes of simple eukaryotes.
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16
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Genetic screen for suppression of transcriptional interference identifies a gain-of-function mutation in Pol2 termination factor Seb1. Proc Natl Acad Sci U S A 2021; 118:2108105118. [PMID: 34389684 DOI: 10.1073/pnas.2108105118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The system of long noncoding RNA (lncRNA)-mediated transcriptional interference that represses fission yeast phosphate homoeostasis gene pho1 provides a sensitive readout of genetic influences on cotranscriptional 3'-processing and termination and a tool for discovery of regulators of this phase of the Pol2 transcription cycle. Here, we conducted a genetic screen for relief of transcriptional interference that unveiled a mechanism by which Pol2 termination is enhanced via a gain-of-function mutation, G476S, in the RNA-binding domain of an essential termination factor, Seb1. The genetic and physical evidence for gain-of-function is compelling: 1) seb1-G476S de-represses pho1 and tgp1, both of which are subject to lncRNA-mediated transcriptional interference; 2) seb1-G476S elicits precocious lncRNA transcription termination in response to lncRNA 5'-proximal poly(A) signals; 3) seb1-G476S derepression of pho1 is effaced by loss-of-function mutations in cleavage and polyadenylation factor (CPF) subunits and termination factor Rhn1; 4) synthetic lethality of seb1-G476S with pho1 derepressive mutants rpb1-CTD-S7A and aps1∆ is rescued by CPF/Rhn1 loss-of-function alleles; and 5) seb1-G476S elicits an upstream shift in poly(A) site preference in several messenger RNA genes. A crystal structure of the Seb1-G476S RNA-binding domain indicates potential for gain of contacts from Ser476 to RNA nucleobases. To our knowledge, this is a unique instance of a gain-of-function phenotype in a eukaryal transcription termination protein.
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17
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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18
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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19
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Yague-Sanz C, Vanrobaeys Y, Fernandez R, Duval M, Larochelle M, Beaudoin J, Berro J, Labbé S, Jacques PÉ, Bachand F. Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation. Genes Dev 2020; 34:883-897. [PMID: 32499400 PMCID: PMC7328516 DOI: 10.1101/gad.337212.120] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022]
Abstract
Transcription by RNA polymerase II (RNAPII) is a dynamic process with frequent variations in the elongation rate. However, the physiological relevance of variations in RNAPII elongation kinetics has remained unclear. Here we show in yeast that a RNAPII mutant that reduces the transcription elongation rate causes widespread changes in alternative polyadenylation (APA). We unveil two mechanisms by which APA affects gene expression in the slow mutant: 3' UTR shortening and gene derepression by premature transcription termination of upstream interfering noncoding RNAs. Strikingly, the genes affected by these mechanisms are enriched for functions involved in phosphate uptake and purine synthesis, processes essential for maintenance of the intracellular nucleotide pool. As nucleotide concentration regulates transcription elongation, our findings argue that RNAPII is a sensor of nucleotide availability and that genes important for nucleotide pool maintenance have adopted regulatory mechanisms responsive to reduced rates of transcription elongation.
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Affiliation(s)
- Carlo Yague-Sanz
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Yann Vanrobaeys
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Ronan Fernandez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Maxime Duval
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Marc Larochelle
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jude Beaudoin
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Julien Berro
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Simon Labbé
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | | | - François Bachand
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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20
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Kilchert C, Kecman T, Priest E, Hester S, Aydin E, Kus K, Rossbach O, Castello A, Mohammed S, Vasiljeva L. System-wide analyses of the fission yeast poly(A) + RNA interactome reveal insights into organization and function of RNA-protein complexes. Genome Res 2020; 30:1012-1026. [PMID: 32554781 PMCID: PMC7397868 DOI: 10.1101/gr.257006.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/18/2020] [Indexed: 01/12/2023]
Abstract
Large RNA-binding complexes play a central role in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA–protein crosslinking data provide information on the organization of RNA–protein complexes. To evaluate the relative enrichment of cellular RBPs on poly(A)+ RNA, we combine poly(A)+ RNA interactome capture with a whole-cell extract normalization procedure. This approach yields estimates of in vivo RNA-binding activities that identify subunits within multiprotein complexes that directly contact RNA. As validation, we trace RNA interactions of different functional modules of the 3′ end processing machinery and reveal additional contacts. Extending our analysis to different mutants of the RNA exosome complex, we explore how substrate channeling through the complex is affected by mutation. Our data highlight the central role of the RNA helicase Mtl1 in regulation of the complex and provide insights into how different components contribute to engagement of the complex with substrate RNA. In addition, we characterize RNA-binding activities of novel RBPs that have been recurrently detected in the RNA interactomes of multiple species. We find that many of these, including cyclophilins and thioredoxins, are substoichiometric RNA interactors in vivo. Because RBPomes show very good overall agreement between species, we propose that the RNA-binding characteristics we observe in fission yeast are likely to apply to related proteins in higher eukaryotes as well.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Emily Priest
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Svenja Hester
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Ebru Aydin
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Oliver Rossbach
- Institut für Biochemie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.,Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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21
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Han Z, Jasnovidova O, Haidara N, Tudek A, Kubicek K, Libri D, Stefl R, Porrua O. Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO J 2020; 39:e101548. [PMID: 32107786 PMCID: PMC7110113 DOI: 10.15252/embj.2019101548] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/23/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Pervasive transcription is a widespread phenomenon leading to the production of a plethora of non‐coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a threat to proper gene expression that needs to be controlled. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non‐coding transcription. However, the mechanisms underlying the specific function of Sen1 at ncRNAs are poorly understood. Here, we identify a motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated carboxy‐terminal domain (CTD) of RNA polymerase II, and structurally characterize its recognition by the CTD‐interacting domain of Nrd1, an RNA‐binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1‐dependent termination strictly requires CTD recognition by the N‐terminal domain of Sen1. We provide evidence that the Sen1‐CTD interaction does not promote initial Sen1 recruitment, but rather enhances Sen1 capacity to induce the release of paused RNAPII from the DNA. Our results shed light on the network of protein–protein interactions that control termination of non‐coding transcription by Sen1.
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Affiliation(s)
- Zhong Han
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.,Université Paris-Saclay, Yvette, France
| | - Olga Jasnovidova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Nouhou Haidara
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.,Université Paris-Saclay, Yvette, France
| | - Agnieszka Tudek
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
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22
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Wu Z, Fang X, Zhu D, Dean C. Autonomous Pathway: FLOWERING LOCUS C Repression through an Antisense-Mediated Chromatin-Silencing Mechanism. PLANT PHYSIOLOGY 2020; 182:27-37. [PMID: 31740502 PMCID: PMC6945862 DOI: 10.1104/pp.19.01009] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/28/2019] [Indexed: 05/19/2023]
Abstract
The timing of flowering is vital for plant reproductive success and is therefore tightly regulated by endogenous and exogenous cues. In summer annual Arabidopsis (Arabidopsis thaliana) accessions, like Columbia-0, rapid flowering is promoted by repression of the floral repressor FLOWERING LOCUS C (FLC). This is through the activity of the autonomous pathway, a group of proteins with diverse functions including RNA 3'-end processing factors, spliceosome components, a transcription elongation factor, and chromatin modifiers. These factors function at the FLC locus linking alternative processing of an antisense long noncoding RNA, called COOLAIR, with delivery of a repressive chromatin environment that affects the transcriptional output. The transcriptional output feeds back to influence the chromatin environment, reinforcing and stabilizing that state. This review summarizes our current knowledge of the autonomous pathway and compares it with similar cotranscriptional mechanisms in other organisms.
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Affiliation(s)
- Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaofeng Fang
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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23
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Abstract
The RNA exosome is a ribonucleolytic multiprotein complex that is conserved and essential in all eukaryotes. Although we tend to speak of "the" exosome complex, it should be more correctly viewed as several different subtypes that share a common core. Subtypes of the exosome complex are present in the cytoplasm, the nucleus and the nucleolus of all eukaryotic cells, and carry out the 3'-5' processing and/or degradation of a wide range of RNA substrates.Because the substrate specificity of the exosome complex is determined by cofactors, the system is highly adaptable, and different organisms have adjusted the machinery to their specific needs. Here, we present an overview of exosome complexes and their cofactors that have been described in different eukaryotes.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany.
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24
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Sanchez AM, Garg A, Shuman S, Schwer B. Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination. Nucleic Acids Res 2019; 47:8452-8469. [PMID: 31276588 PMCID: PMC6895273 DOI: 10.1093/nar/gkz567] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/10/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here, we show that phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of the Asp1 and Aps1 IPP pyrophosphatases is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1Δ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.
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Affiliation(s)
- Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
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25
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Ding DQ, Okamasa K, Katou Y, Oya E, Nakayama JI, Chikashige Y, Shirahige K, Haraguchi T, Hiraoka Y. Chromosome-associated RNA-protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe. Nat Commun 2019; 10:5598. [PMID: 31811152 PMCID: PMC6898681 DOI: 10.1038/s41467-019-13609-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/18/2019] [Indexed: 01/07/2023] Open
Abstract
Pairing of homologous chromosomes in meiosis is essential for sexual reproduction. We have previously demonstrated that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 chromosomal loci and mediates their robust pairing in meiosis. However, the mechanisms underlying lncRNA-mediated homologous pairing have remained elusive. In this study, we identify conserved RNA-binding proteins that are required for robust pairing of homologous chromosomes. These proteins accumulate mainly at the sme2 and two other chromosomal loci together with meiosis-specific lncRNAs transcribed from these loci. Remarkably, the chromosomal accumulation of these lncRNA–protein complexes is required for robust pairing. Moreover, the lncRNA–protein complexes exhibit phase separation properties, since 1,6-hexanediol treatment reversibly disassembled these complexes and disrupted the pairing of associated loci. We propose that lncRNA–protein complexes assembled at specific chromosomal loci mediate recognition and subsequent pairing of homologous chromosomes. During meiosis, pairing of homologous chromosomes is critical for sexual reproduction. Here the authors reveal in S. pombe the role of lncRNA–protein complexes during the pairing of homologues chromosomes that assemble at specific chromosomal loci to mediate recognition of the pairs.
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Affiliation(s)
- Da-Qiao Ding
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.
| | - Kasumi Okamasa
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Yuki Katou
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Eriko Oya
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, 467-8501, Japan.,Faculty of Science and Engineering, Chuo University, Tokyo, 112-8551, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, 467-8501, Japan.,Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan. .,Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
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26
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Nakazawa N, Arakawa O, Yanagida M. Condensin locates at transcriptional termination sites in mitosis, possibly releasing mitotic transcripts. Open Biol 2019; 9:190125. [PMID: 31615333 PMCID: PMC6833218 DOI: 10.1098/rsob.190125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Condensin is an essential component of chromosome dynamics, including mitotic chromosome condensation and segregation, DNA repair, and development. Genome-wide localization of condensin is known to correlate with transcriptional activity. The functional relationship between condensin accumulation and transcription sites remains unclear, however. By constructing the auxin-inducible degron strain of condensin, herein we demonstrate that condensin does not affect transcription itself. Instead, RNA processing at transcriptional termination appears to define condensin accumulation sites during mitosis, in the fission yeast Schizosaccharomyces pombe. Combining the auxin-degron strain with the nda3 β-tubulin cold-sensitive (cs) mutant enabled us to inactivate condensin in mitotically arrested cells, without releasing the cells into anaphase. Transcriptional activation and termination were not affected by condensin's degron-mediated depletion, at heat-shock inducible genes or mitotically activated genes. On the other hand, condensin accumulation sites shifted approximately 500 bp downstream in the auxin-degron of 5′-3′ exoribonuclease Dhp1, in which transcripts became aberrantly elongated, suggesting that condensin accumulates at transcriptionally terminated DNA regions. Growth defects in mutant strains of 3′-processing ribonuclease and polyA cleavage factors were additive in condensin temperature-sensitive (ts) mutants. Considering condensin's in vitro activity to form double-stranded DNAs from unwound, single-stranded DNAs or DNA-RNA hybrids, condensin-mediated processing of mitotic transcripts at the 3′-end may be a prerequisite for faithful chromosome segregation.
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Affiliation(s)
- Norihiko Nakazawa
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
| | - Orie Arakawa
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- Okinawa Institute of Science and Technology Graduate University, G0 Cell Unit, Onna-son, Okinawa 904-0495, Japan
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27
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Wang Z, Wei L, Sheng Y, Zhang G. Yeast Synthetic Terminators: Fine Regulation of Strength through Linker Sequences. Chembiochem 2019; 20:2383-2389. [DOI: 10.1002/cbic.201900163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Zhaoxia Wang
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Linna Wei
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Yue Sheng
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
| | - Genlin Zhang
- School of Chemistry and Chemical EngineeringKey Laboratory for Green Processing of Chemical Engineering of Xinjiang BingtuanShihezi University Shihezi 832003 P. R. China
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28
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Gregersen LH, Mitter R, Ugalde AP, Nojima T, Proudfoot NJ, Agami R, Stewart A, Svejstrup JQ. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Cell 2019; 177:1797-1813.e18. [PMID: 31104839 PMCID: PMC6579486 DOI: 10.1016/j.cell.2019.04.038] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/30/2022]
Abstract
Accurate regulation of mRNA termination is required for correct gene expression. Here, we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation (polyA) sites. The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) phosphorylated on both Ser2 and Ser5 and are detected at early, alternative polyA sites. Concomitant knockout of human SCAF4 and SCAF8 results in altered polyA selection and subsequent early termination, leading to expression of truncated mRNAs and proteins lacking functional domains and is cell lethal. While SCAF4 and SCAF8 work redundantly to suppress early mRNA termination, they also have independent, non-essential functions. SCAF8 is an RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical, distal transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional termination in human cells.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro P Ugalde
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Reuven Agami
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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29
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Kamieniarz-Gdula K, Gdula MR, Panser K, Nojima T, Monks J, Wiśniewski JR, Riepsaame J, Brockdorff N, Pauli A, Proudfoot NJ. Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination. Mol Cell 2019; 74:158-172.e9. [PMID: 30819644 PMCID: PMC6458999 DOI: 10.1016/j.molcel.2019.01.027] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/07/2018] [Accepted: 01/17/2019] [Indexed: 12/02/2022]
Abstract
The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including mNET-seq, 3′ mRNA-seq, chromatin RNA-seq, and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and consequent gene downregulation. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. Human PCF11 enhances transcription termination and 3′ end processing, genome-wide PCF11 is substoichiometric to CPA complex due to autoregulation of its transcription PCF11 stimulates expression of closely spaced genes but attenuates other genes PCF11-mediated functions are conserved in vertebrates and essential in development
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Affiliation(s)
- Kinga Kamieniarz-Gdula
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Michal R Gdula
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Karin Panser
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Joan Monks
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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30
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Schmid M, Jensen TH. The Nuclear RNA Exosome and Its Cofactors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:113-132. [PMID: 31811632 DOI: 10.1007/978-3-030-31434-7_4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The RNA exosome is a highly conserved ribonuclease endowed with 3'-5' exonuclease and endonuclease activities. The multisubunit complex resides in both the nucleus and the cytoplasm, with varying compositions and activities between the two compartments. While the cytoplasmic exosome functions mostly in mRNA quality control pathways, the nuclear RNA exosome partakes in the 3'-end processing and complete decay of a wide variety of substrates, including virtually all types of noncoding (nc) RNAs. To handle these diverse tasks, the nuclear exosome engages with dedicated cofactors, some of which serve as activators by stimulating decay through oligoA addition and/or RNA helicase activities or, as adaptors, by recruiting RNA substrates through their RNA-binding capacities. Most nuclear exosome cofactors contain the essential RNA helicase Mtr4 (MTR4 in humans). However, apart from Mtr4, nuclear exosome cofactors have undergone significant evolutionary divergence. Here, we summarize biochemical and functional knowledge about the nuclear exosome and exemplify its cofactor variety by discussing the best understood model organisms-the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and human cells.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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31
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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32
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Schäfer P, Tüting C, Schönemann L, Kühn U, Treiber T, Treiber N, Ihling C, Graber A, Keller W, Meister G, Sinz A, Wahle E. Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors. RNA (NEW YORK, N.Y.) 2018; 24:1721-1737. [PMID: 30139799 PMCID: PMC6239180 DOI: 10.1261/rna.068056.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/17/2018] [Indexed: 05/05/2023]
Abstract
Cleavage factor II (CF II) is a poorly characterized component of the multiprotein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Tüting
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Lars Schönemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Ihling
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Anne Graber
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Walter Keller
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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33
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Soudet J, Gill JK, Stutz F. Noncoding transcription influences the replication initiation program through chromatin regulation. Genome Res 2018; 28:1882-1893. [PMID: 30401734 PMCID: PMC6280764 DOI: 10.1101/gr.239582.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
In eukaryotic organisms, replication initiation follows a temporal program. Among the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of widespread genomic noncoding transcription. We find that noncoding RNA transcription termination in the vicinity of autonomously replicating sequences (ARSs) shields replication initiation from transcriptional readthrough. Consistently, high natural nascent transcription correlates with low ARS efficiency and late replication timing. High readthrough transcription is also linked to increased nucleosome occupancy and high levels of H3K36me3. Moreover, forcing ARS readthrough transcription promotes these chromatin features. Finally, replication initiation defects induced by increased transcriptional readthrough are partially rescued in the absence of H3K36 methylation. Altogether, these observations indicate that natural noncoding transcription into ARSs influences replication initiation through chromatin regulation.
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Affiliation(s)
- Julien Soudet
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Jatinder Kaur Gill
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
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34
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RNA polymerase II CTD interactome with 3' processing and termination factors in fission yeast and its impact on phosphate homeostasis. Proc Natl Acad Sci U S A 2018; 115:E10652-E10661. [PMID: 30355770 DOI: 10.1073/pnas.1810711115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The carboxy-terminal domain (CTD) code encrypted within the Y1S2P3T4S5P6S7 heptad repeats of RNA polymerase II (Pol2) is deeply rooted in eukaryal biology. Key steps to deciphering the code are identifying the events in gene expression that are governed by individual "letters" and then defining a vocabulary of multiletter "words" and their meaning. Thr4 and Ser7 exert opposite effects on the fission yeast pho1 gene, expression of which is repressed under phosphate-replete conditions by transcription of an upstream flanking long noncoding RNA (lncRNA). Here we attribute the derepression of pho1 by a CTD-S7A mutation to precocious termination of lncRNA synthesis, an effect that is erased by mutations of cleavage-polyadenylation factor (CPF) subunits Ctf1, Ssu72, Ppn1, Swd22, and Dis2 and termination factor Rhn1. By contrast, a CTD-T4A mutation hyperrepresses pho1, as do CPF subunit and Rhn1 mutations, implying that T4A reduces lncRNA termination. Moreover, CTD-T4A is synthetically lethal with ppn1∆ and swd22∆, signifying that Thr4 and the Ppn1•Swd22 module play important, functionally redundant roles in promoting Pol2 termination. We find that Ppn1 and Swd22 become essential for viability when the CTD array is curtailed and that S7A overcomes the need for Ppn1•Swd22 in the short CTD context. Mutational synergies highlight redundant essential functions of (i) Ppn1•Swd22 and Rhn1, (ii) Ppn1•Swd22 and Ctf1, and (iii) Ssu72 and Dis2 phosphatases. CTD alleles Y1F, S2A, and T4A have overlapping synthetic lethalities with ppn1∆ and swd22∆, suggesting that Tyr1-Ser2-Thr4 form a three-letter CTD word that abets termination, with Rhn1 being a likely "reader" of this word.
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Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D, Rodrigue S, Tian B, Jacques PÉ, Bachand F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat Commun 2018; 9:4364. [PMID: 30341288 PMCID: PMC6195540 DOI: 10.1038/s41467-018-06546-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/30/2018] [Indexed: 11/09/2022] Open
Abstract
Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Here, we find that NNS-like transcription termination is not conserved in fission yeast. Rather, genome-wide analyses show global recruitment of mRNA 3' end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We also find that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.
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Affiliation(s)
- Marc Larochelle
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Marc-Antoine Robert
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Jean-Nicolas Hébert
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Dominick Matteau
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Pierre-Étienne Jacques
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
| | - François Bachand
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
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Kecman T, Kuś K, Heo DH, Duckett K, Birot A, Liberatori S, Mohammed S, Geis-Asteggiante L, Robinson CV, Vasiljeva L. Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination. Cell Rep 2018; 25:259-269.e5. [PMID: 30282034 PMCID: PMC6180485 DOI: 10.1016/j.celrep.2018.09.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/27/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Termination of RNA polymerase II (Pol II) transcription is a key step that is important for 3' end formation of functional mRNA, mRNA release, and Pol II recycling. Even so, the underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 is found on Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 dephosphorylation by the conserved PP1 phosphatase Dis2, which also dephosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and dephosphorylation of Pol II C-terminal domain.
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Affiliation(s)
- Tea Kecman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Krzysztof Kuś
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katie Duckett
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Department of Chemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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Atkinson SR, Marguerat S, Bitton DA, Rodríguez-López M, Rallis C, Lemay JF, Cotobal C, Malecki M, Smialowski P, Mata J, Korber P, Bachand F, Bähler J. Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast. RNA (NEW YORK, N.Y.) 2018; 24:1195-1213. [PMID: 29914874 PMCID: PMC6097657 DOI: 10.1261/rna.065524.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/14/2018] [Indexed: 05/31/2023]
Abstract
Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive noncoding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyze lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4× the previously annotated lncRNAs. The expression of most lncRNAs becomes strongly induced under the genetic and physiological perturbations, most notably during late meiosis. Most lncRNAs are cryptic and suppressed by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease, and RNAi. Double-mutant analyses reveal substantial coordination and redundancy among these pathways. We classify lncRNAs by their dominant pathway into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease, along with RNAi, dampens the expression of thousands of lncRNAs and mRNAs that become induced during meiosis. Antisense lncRNA expression mostly negatively correlates with sense mRNA expression in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. Our results highlight both similarities and differences to lncRNA regulation in budding yeast. This broad survey of the lncRNA repertoire and characteristics in S. pombe, and the interwoven regulatory pathways that target lncRNAs, provides a rich framework for their further functional analyses.
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Affiliation(s)
- Sophie R Atkinson
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Samuel Marguerat
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Danny A Bitton
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Maria Rodríguez-López
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Charalampos Rallis
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jean-François Lemay
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Cristina Cotobal
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Michal Malecki
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Pawel Smialowski
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - Juan Mata
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Philipp Korber
- LMU Munich, Biomedical Center, 82152 Planegg-Martinsried near Munich, Germany
| | - François Bachand
- Department of Biochemistry, Sherbrooke, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Jürg Bähler
- Research Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom
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Parsa JY, Boudoukha S, Burke J, Homer C, Madhani HD. Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly. Genes Dev 2018; 32:953-964. [PMID: 29967291 PMCID: PMC6075038 DOI: 10.1101/gad.310136.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/18/2018] [Indexed: 01/09/2023]
Abstract
In this study, Parsa et al. investigated the mechanisms underlying RNAi-independent heterochromatin assembly by the CTD–RRM protein Seb1 in S. pombe. They show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments, providing new insight into Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation. In Schizosaccharomyces pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNA polymerase II (RNAPII)-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
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Affiliation(s)
- Jahan-Yar Parsa
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Selim Boudoukha
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jordan Burke
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, California 94158, USA
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Watts BR, Wittmann S, Wery M, Gautier C, Kus K, Birot A, Heo DH, Kilchert C, Morillon A, Vasiljeva L. Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Nucleic Acids Res 2018; 46:5426-5440. [PMID: 29618061 PMCID: PMC6009587 DOI: 10.1093/nar/gky232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022] Open
Abstract
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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Affiliation(s)
- Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Institut für Biochemie, Heinrich-Buff-Ring 17, 35392 Gießen, Germany
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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40
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Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression. The mechanisms of heterochromatin establishment and of heterochromatin maintenance are separable and involve the ability of sequence-specific factors bound to nascent transcripts to recruit chromatin-modifying enzymes. Heterochromatin can spread along the chromatin from nucleation sites. The propensity of heterochromatin to promote its own spreading and inheritance is counteracted by inhibitory factors. Because of its importance for chromosome function, heterochromatin has key roles in the pathogenesis of various human diseases. In this Review, we discuss conserved principles of heterochromatin formation and function using selected examples from studies of a range of eukaryotes, from yeast to human, with an emphasis on insights obtained from unicellular model organisms.
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Abstract
The nuclear RNA exosome is an essential and versatile machinery that regulates maturation and degradation of a huge plethora of RNA species. The past two decades have witnessed remarkable progress in understanding the whole picture of its RNA substrates and the structural basis of its functions. In addition to the exosome itself, recent studies focusing on associated co-factors have been elucidating how the exosome is directed towards specific substrates. Moreover, it has been gradually realized that loss-of-function of exosome subunits affect multiple biological processes such as the DNA damage response, R-loop resolution, maintenance of genome integrity, RNA export, translation and cell differentiation. In this review, we summarize the current knowledge of the mechanisms of nuclear exosome-mediated RNA metabolism and discuss their physiological significance.
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Franco-Echevarría E, González-Polo N, Zorrilla S, Martínez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sánchez M, Calvo O, González B, Pérez-Cañadillas JM. The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Nucleic Acids Res 2017; 45:10293-10305. [PMID: 28973465 PMCID: PMC5737872 DOI: 10.1093/nar/gkx685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022] Open
Abstract
Transcription termination of non-coding RNAs is regulated in yeast by a complex of three RNA binding proteins: Nrd1, Nab3 and Sen1. Nrd1 is central in this process by interacting with Rbp1 of RNA polymerase II, Trf4 of TRAMP and GUAA/G terminator sequences. We lack structural data for the last of these binding events. We determined the structures of Nrd1 RNA binding domain and its complexes with three GUAA-containing RNAs, characterized RNA binding energetics and tested rationally designed mutants in vivo. The Nrd1 structure shows an RRM domain fused with a second α/β domain that we name split domain (SD), because it is formed by two non-consecutive segments at each side of the RRM. The GUAA interacts with both domains and with a pocket of water molecules, trapped between the two stacking adenines and the SD. Comprehensive binding studies demonstrate for the first time that Nrd1 has a slight preference for GUAA over GUAG and genetic and functional studies suggest that Nrd1 RNA binding domain might play further roles in non-coding RNAs transcription termination.
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Affiliation(s)
- Elsa Franco-Echevarría
- Departament of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Silvia Zorrilla
- Department of Cellular and Molecular Biology, Biological Research Center, CSIC
| | - Santiago Martínez-Lumbreras
- Department of Chemistry, King's College London.,Department of Biological Physical Chemistry, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | - Clara M Santiveri
- Spectroscopy and Nuclear Magnetic Resonance Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre
| | - Ramón Campos-Olivas
- Spectroscopy and Nuclear Magnetic Resonance Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca
| | - Beatriz González
- Departament of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | - José Manuel Pérez-Cañadillas
- Department of Biological Physical Chemistry, Institute of Physical-Chemistry "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
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