1
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Anil AT, Pandian R, Mishra SK. Introns with branchpoint-distant 3' splice sites: Splicing mechanism and regulatory roles. Biophys Chem 2024; 314:107307. [PMID: 39173313 DOI: 10.1016/j.bpc.2024.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
The two transesterification reactions of pre-mRNA splicing require highly complex yet well-controlled rearrangements of small nuclear RNAs and proteins (snRNP) in the spliceosome. The efficiency and accuracy of these reactions are critical for gene expression, as almost all human genes pass through pre-mRNA splicing. Key parameters that determine the splicing outcome are the length of the intron, the strengths of its splicing signals and gaps between them, and the presence of splicing controlling elements. In particular, the gap between the branchpoint (BP) and the 3' splice site (ss) of introns is a major determinant of the splicing efficiency. This distance falls within a small range across the introns of an organism. The constraints exist possibly because BP and 3'ss are recognized by BP-binding proteins, U2 snRNP and U2 accessory factors (U2AF) in a coordinated manner. Furthermore, varying distances between the two signals may also affect the second transesterification reaction since the intervening RNA needs to be accurately positioned within the complex RNP machinery. Splicing such pre-mRNAs requires cis-acting elements in the RNA and many trans-acting splicing regulators. Regulated pre-mRNA splicing with BP-distant 3'ss adds another layer of control to gene expression and promotes alternative splicing.
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Affiliation(s)
- Anupa T Anil
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India
| | - Rakesh Pandian
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India
| | - Shravan Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306, Punjab, India.
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2
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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3
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Anil AT, Choudhary K, Pandian R, Gupta P, Thakran P, Singh A, Sharma M, Mishra SK. Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2. Nucleic Acids Res 2022; 50:10000-10014. [PMID: 36095128 PMCID: PMC9508853 DOI: 10.1093/nar/gkac769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/13/2022] Open
Abstract
Intron diversity facilitates regulated gene expression and alternative splicing. Spliceosomes excise introns after recognizing their splicing signals: the 5'-splice site (5'ss), branchpoint (BP) and 3'-splice site (3'ss). The latter two signals are recognized by U2 small nuclear ribonucleoprotein (snRNP) and its accessory factors (U2AFs), but longer spacings between them result in weaker splicing. Here, we show that excision of introns with a BP-distant 3'ss (e.g. rap1 intron 2) requires the ubiquitin-fold-activated splicing regulator Sde2 in Schizosaccharomyces pombe. By monitoring splicing-specific ura4 reporters in a collection of S. pombe mutants, Cay1 and Tls1 were identified as additional regulators of this process. The role of Sde2, Cay1 and Tls1 was further confirmed by increasing BP-3'ss spacings in a canonical tho5 intron. We also examined BP-distant exons spliced independently of these factors and observed that RNA secondary structures possibly bridged the gap between the two signals. These proteins may guide the 3'ss towards the spliceosome's catalytic centre by folding the RNA between the BP and 3'ss. Orthologues of Sde2, Cay1 and Tls1, although missing in the intron-poor Saccharomyces cerevisiae, are present in intron-rich eukaryotes, including humans. This type of intron-specific pre-mRNA splicing appears to have evolved for regulated gene expression and alternative splicing of key heterochromatin factors.
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Affiliation(s)
- Anupa T Anil
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Karan Choudhary
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Rakesh Pandian
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Praver Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Poonam Thakran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Arashdeep Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Shravan Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
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4
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Pan L, Tormey D, Bobon N, Baumann P. Rap1 prevents fusions between long telomeres in fission yeast. EMBO J 2022; 41:e110458. [PMID: 36059259 PMCID: PMC9574727 DOI: 10.15252/embj.2021110458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/15/2022] Open
Abstract
The conserved Rap1 protein is part of the shelterin complex that plays critical roles in chromosome end protection and telomere length regulation. Previous studies have addressed how fission yeast Rap1 contributes to telomere length maintenance, but the mechanism by which the protein inhibits end fusions has remained elusive. Here, we use a mutagenesis screen in combination with high‐throughput sequencing to identify several amino acid positions in Rap1 that have key roles in end protection. Interestingly, mutations at these sites render cells susceptible to genome instability in a conditional manner, whereby longer telomeres are prone to undergoing end fusions, while telomeres within the normal length range are sufficiently protected. The protection of long telomeres is in part dependent on their nuclear envelope attachment mediated by the Rap1–Bqt4 interaction. Our data demonstrate that long telomeres represent a challenge for the maintenance of genome integrity, thereby providing an explanation for species‐specific upper limits on telomere length.
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Affiliation(s)
- Lili Pan
- Department of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Duncan Tormey
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nadine Bobon
- Department of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Peter Baumann
- Department of Biology, Johannes Gutenberg University, Mainz, Germany.,Institute of Molecular Biology, Mainz, Germany
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5
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Zahid S, Aloe S, Sutherland JH, Holloman WK, Lue NF. Ustilago maydis telomere protein Pot1 harbors an extra N-terminal OB fold and regulates homology-directed DNA repair factors in a dichotomous and context-dependent manner. PLoS Genet 2022; 18:e1010182. [PMID: 35587917 PMCID: PMC9119445 DOI: 10.1371/journal.pgen.1010182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/02/2022] [Indexed: 01/11/2023] Open
Abstract
The telomere G-strand binding protein Pot1 plays multifaceted roles in telomere maintenance and protection. We examined the structure and activities of Pot1 in Ustilago maydis, a fungal model that recapitulates key features of mammalian telomere regulation. Compared to the well-characterized primate and fission yeast Pot1 orthologs, UmPot1 harbors an extra N-terminal OB-fold domain (OB-N), which was recently shown to be present in most metazoans. UmPot1 binds directly to Rad51 and regulates the latter's strand exchange activity. Deleting the OB-N domain, which is implicated in Rad51-binding, caused telomere shortening, suggesting that Pot1-Rad51 interaction facilitates telomere maintenance. Depleting Pot1 through transcriptional repression triggered growth arrest as well as rampant recombination, leading to multiple telomere aberrations. In addition, telomere repeat RNAs transcribed from both the G- and C-strand were dramatically up-regulated, and this was accompanied by elevated levels of telomere RNA-DNA hybrids. Telomere abnormalities of pot1-deficient cells were suppressed, and cell viability was restored by the deletion of genes encoding Rad51 or Brh2 (the BRCA2 ortholog), indicating that homology-directed repair (HDR) proteins are key mediators of telomere aberrations and cellular toxicity. Together, these observations underscore the complex physical and functional interactions between Pot1 and DNA repair factors, leading to context-dependent and dichotomous effects of HDR proteins on telomere maintenance and protection.
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Affiliation(s)
- Syed Zahid
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Sarah Aloe
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Jeanette H. Sutherland
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - William K. Holloman
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Neal F. Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, New York, United States of America
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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6
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Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
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Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
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7
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Coulon S, Vaurs M. Telomeric Transcription and Telomere Rearrangements in Quiescent Cells. J Mol Biol 2020; 432:4220-4231. [PMID: 32061930 DOI: 10.1016/j.jmb.2020.01.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Despite the condensed nature of terminal sequences, the telomeres are transcribed into a group of noncoding RNAs, including the TElomeric Repeat-containing RNA (TERRA). Since the discovery of TERRA, its evolutionary conserved function has been confirmed, and its involvement in telomere length regulation, heterochromatin establishment, and telomere recombination has been demonstrated. We previously reported that TERRA is upregulated in quiescent fission yeast cells, although the global transcription is highly reduced. Elevated telomeric transcription was also detected when telomeres detach from the nuclear periphery. These intriguing observations unveil unexpected facets of telomeric transcription in arrested cells. In this review, we present the different aspects of TERRA transcription during quiescence and discuss their implications for telomere maintenance and cell fate.
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Affiliation(s)
- Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France.
| | - Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue contre le Cancer, Marseille, F-13009, France
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8
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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: 1.3] [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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9
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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10
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Kwapisz M, Morillon A. Subtelomeric Transcription and its Regulation. J Mol Biol 2020; 432:4199-4219. [PMID: 32035903 PMCID: PMC7374410 DOI: 10.1016/j.jmb.2020.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
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Affiliation(s)
- Marta Kwapisz
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France.
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11
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Abstract
The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5' splice site (5'SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5'SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5'SS, producing a free 5' exon. Removal of the BP adenosine from the active site allows the 3'SS to bind, so that the 5' exon attacks the 3'SS to produce mature mRNA and an excised lariat intron.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Clément Charenton
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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12
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Hu Y, Bennett HW, Liu N, Moravec M, Williams JF, Azzalin CM, King MC. RNA-DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast. Genetics 2019; 213:431-447. [PMID: 31405990 PMCID: PMC6781888 DOI: 10.1534/genetics.119.302606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/09/2019] [Indexed: 11/18/2022] Open
Abstract
A subset of cancers rely on telomerase-independent mechanisms to maintain their chromosome ends. The predominant "alternative lengthening of telomeres" pathway appears dependent on homology-directed repair (HDR) to maintain telomeric DNA. However, the molecular changes needed for cells to productively engage in telomeric HDR are poorly understood. To gain new insights into this transition, we monitored the state of telomeres during serial culture of fission yeast (Schizosaccharomyces pombe) lacking the telomerase recruitment factor Ccq1. Rad52 is loaded onto critically short telomeres shortly after germination despite continued telomere erosion, suggesting that recruitment of recombination factors is not sufficient to maintain telomeres in the absence of telomerase function. Instead, survivor formation coincides with the derepression of telomeric repeat-containing RNA (TERRA). In this context, degradation of TERRA associated with the telomere in the form of R-loops drives a severe growth crisis, ultimately leading to a novel type of survivor with linear chromosomes and altered cytological telomere characteristics, including the loss of the shelterin component Rap1 (but not the TRF1/TRF2 ortholog, Taz1) from the telomere. We demonstrate that deletion of Rap1 is protective in this context, preventing the growth crisis that is otherwise triggered by degradation of telomeric R-loops in survivors with linear chromosomes. These findings suggest that upregulation of telomere-engaged TERRA, or altered recruitment of shelterin components, can support telomerase-independent telomere maintenance.
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Affiliation(s)
- Yan Hu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Henrietta W Bennett
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Na Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Martin Moravec
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), 8093, Switzerland
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes (iMM), Faculdade de Medicina da Universidade de Lisboa, 1649-028, Portugal
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520-8002
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13
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Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K. A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science 2019; 363:710-714. [PMID: 30705154 DOI: 10.1126/science.aaw5569] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 01/21/2019] [Indexed: 12/11/2022]
Abstract
During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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LARP7-like protein Pof8 regulates telomerase assembly and poly(A)+TERRA expression in fission yeast. Nat Commun 2018; 9:586. [PMID: 29422503 PMCID: PMC5805695 DOI: 10.1038/s41467-018-02874-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/05/2018] [Indexed: 02/06/2023] Open
Abstract
Telomerase is a reverse transcriptase complex that ensures stable maintenance of linear eukaryotic chromosome ends by overcoming the end replication problem, posed by the inability of replicative DNA polymerases to fully replicate linear DNA. The catalytic subunit TERT must be assembled properly with its telomerase RNA for telomerase to function, and studies in Tetrahymena have established that p65, a La-related protein 7 (LARP7) family protein, utilizes its C-terminal xRRM domain to promote assembly of the telomerase ribonucleoprotein (RNP) complex. However, LARP7-dependent telomerase complex assembly has been considered as unique to ciliates that utilize RNA polymerase III to transcribe telomerase RNA. Here we show evidence that fission yeast Schizosaccharomyces pombe utilizes the p65-related protein Pof8 and its xRRM domain to promote assembly of RNA polymerase II-encoded telomerase RNA with TERT. Furthermore, we show that Pof8 contributes to repression of the transcription of noncoding RNAs at telomeres. A functional telomerase complex requires that the catalytic TERT subunit be assembled with the template RNA TER1. Here the authors show that Pof8, a possible LARP7 family protein, is required for assembly of the telomerase complex, and repression of lncRNA transcripts at telomeres in S. pombe.
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15
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Gomez-Escobar N, Almobadel N, Alzahrani O, Feichtinger J, Planells-Palop V, Alshehri Z, Thallinger GG, Wakeman JA, McFarlane RJ. Translin and Trax differentially regulate telomere-associated transcript homeostasis. Oncotarget 2017; 7:33809-20. [PMID: 27183912 PMCID: PMC5085120 DOI: 10.18632/oncotarget.9278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
Translin and Trax proteins are highly conserved nucleic acid binding proteins that have been implicated in RNA regulation in a range of biological processes including tRNA processing, RNA interference, microRNA degradation during oncogenesis, spermatogenesis and neuronal regulation. Here, we explore the function of this paralogue pair of proteins in the fission yeast. Using transcript analysis we demonstrate a reciprocal mechanism for control of telomere-associated transcripts. Mutation of tfx1+ (Trax) elevates transcript levels from silenced sub-telomeric regions of the genome, but not other silenced regions, such as the peri-centromeric heterochromatin. In the case of some sub-telomeric transcripts, but not all, this elevation is dependent on the Trax paralogue, Tsn1 (Translin). In a reciprocal fashion, Tsn1 (Translin) serves to repress levels of transcripts (TERRAs) from the telomeric repeats, whereas Tfx1 serves to maintain these elevated levels. This reveals a novel mechanism for the regulation of telomeric transcripts. We extend this to demonstrate that human Translin and Trax also control telomere-associated transcript levels in human cells in a telomere-specific fashion.
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Affiliation(s)
- Natalia Gomez-Escobar
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Nasser Almobadel
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Othman Alzahrani
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Julia Feichtinger
- Computational Biotechnology and Bioinformatics Group, Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria.,Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Vicente Planells-Palop
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Zafer Alshehri
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Gerhard G Thallinger
- Computational Biotechnology and Bioinformatics Group, Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria.,Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Jane A Wakeman
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Ramsay J McFarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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16
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Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK. Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing. EMBO J 2017; 37:89-101. [PMID: 28947618 DOI: 10.15252/embj.201796751] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 08/11/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022] Open
Abstract
The expression of intron-containing genes in eukaryotes requires generation of protein-coding messenger RNAs (mRNAs) via RNA splicing, whereby the spliceosome removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must ensure accurate removal of highly diverse introns. We show that Sde2 is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain (referred to as Sde2-C). Precursor processing after the first di-glycine motif by the ubiquitin-specific proteases Ubp5 and Ubp15 generates a short-lived activated Sde2-C fragment with an N-terminal lysine residue, which subsequently gets incorporated into spliceosomes. Absence of Sde2 or defects in Sde2 activation both result in inefficient excision of selected introns from a subset of pre-mRNAs. Sde2 facilitates spliceosomal association of Cactin/Cay1, with a functional link between Sde2 and Cactin further supported by genetic interactions and pre-mRNA splicing assays. These findings suggest that ubiquitin-like processing of Sde2 into a short-lived activated form may function as a checkpoint to ensure proper splicing of certain pre-mRNAs in fission yeast.
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Affiliation(s)
- Poonam Thakran
- Max Planck - DST Partner Group, Department of Biological Sciences, Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Prashant Arun Pandit
- Max Planck - DST Partner Group, Department of Biological Sciences, Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Sumanjit Datta
- Max Planck - DST Partner Group, Department of Biological Sciences, Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Kiran Kumar Kolathur
- Max Planck - DST Partner Group, Department of Biological Sciences, Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Shravan Kumar Mishra
- Max Planck - DST Partner Group, Department of Biological Sciences, Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India
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17
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Zanini IMY, Soneson C, Lorenzi LE, Azzalin CM. Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. J Cell Sci 2017; 130:767-778. [PMID: 28062851 DOI: 10.1242/jcs.194068] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Cactins constitute a family of eukaryotic proteins broadly conserved from yeast to human and required for fundamental processes such as cell proliferation, genome stability maintenance, organismal development and immune response. Cactin proteins have been found to associate with the spliceosome in several model organisms, nevertheless their molecular functions await elucidation. Here we show that depletion of human cactin leads to premature sister chromatid separation, genome instability and cell proliferation arrest. Moreover, cactin is essential for efficient splicing of thousands of pre-mRNAs, and incomplete splicing of the pre-mRNA of sororin (also known as CDCA5), a cohesin-associated factor, is largely responsible for the aberrant chromatid separation in cactin-depleted cells. Lastly, cactin physically and functionally interacts with the spliceosome-associated factors DHX8 and SRRM2. We propose that cellular complexes comprising cactin, DHX8 and SRRM2 sustain precise chromosome segregation, genome stability and cell proliferation by allowing faithful splicing of specific pre-mRNAs. Our data point to novel pathways of gene expression regulation dependent on cactin, and provide an explanation for the pleiotropic dysfunctions deriving from cactin inactivation in distant eukaryotes.
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Affiliation(s)
- Isabella M Y Zanini
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Luca E Lorenzi
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
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18
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Cecchetelli AD, Hugunin J, Tannoury H, Cram EJ. CACN-1 is required in the Caenorhabditis elegans somatic gonad for proper oocyte development. Dev Biol 2016; 414:58-71. [PMID: 27046631 PMCID: PMC4875861 DOI: 10.1016/j.ydbio.2016.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 12/16/2022]
Abstract
CACN-1/Cactin is a conserved protein identified in a genome-wide screen for genes that regulate distal tip cell migration in the nematode Caenorhabditis elegans. In addition to possessing distal tip cells that migrate past their correct stopping point, animals depleted of cacn-1 are sterile. In this study, we show that CACN-1 is needed in the soma for proper germ line development and maturation. When CACN-1 is depleted, sheath cells are absent and/or abnormal. When sheath cells are absent, hermaphrodites produce sperm, but do not switch appropriately to oocyte production. When sheath cells are abnormal, some oocytes develop but are not successfully ovulated and undergo endomitotic reduplication (Emo). Our previous proteomic studies show that CACN-1 interacts with a network of splicing factors. Here, these interactors were screened using RNAi. Depletion of many of these factors led to missing or abnormal sheath cells and germ line defects, particularly absent and/or Emo oocytes. These results suggest CACN-1 is part of a protein network that influences somatic gonad development and function through alternative splicing or post-transcriptional gene regulation.
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Affiliation(s)
| | - Julie Hugunin
- Department of Biology, Northeastern University, Boston, MA 02115, United States
| | - Hiba Tannoury
- Department of Biology, Northeastern University, Boston, MA 02115, United States
| | - Erin J Cram
- Department of Biology, Northeastern University, Boston, MA 02115, United States.
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19
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Moravec M, Wischnewski H, Bah A, Hu Y, Liu N, Lafranchi L, King MC, Azzalin CM. TERRA promotes telomerase-mediated telomere elongation in Schizosaccharomyces pombe. EMBO Rep 2016; 17:999-1012. [PMID: 27154402 DOI: 10.15252/embr.201541708] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/07/2016] [Indexed: 11/09/2022] Open
Abstract
Telomerase-mediated telomere elongation provides cell populations with the ability to proliferate indefinitely. Telomerase is capable of recognizing and extending the shortest telomeres in cells; nevertheless, how this mechanism is executed remains unclear. Here, we show that, in the fission yeast Schizosaccharomyces pombe, shortened telomeres are highly transcribed into the evolutionarily conserved long noncoding RNA TERRA A fraction of TERRA produced upon telomere shortening is polyadenylated and largely devoid of telomeric repeats, and furthermore, telomerase physically interacts with this polyadenylated TERRA in vivo We also show that experimentally enhanced transcription of a manipulated telomere promotes its association with telomerase and concomitant elongation. Our data represent the first direct evidence that TERRA stimulates telomerase recruitment and activity at chromosome ends in an organism with human-like telomeres.
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Affiliation(s)
- Martin Moravec
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Amadou Bah
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Yan Hu
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Na Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Lorenzo Lafranchi
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich, Switzerland
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