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For: Schlackow M, Marguerat S, Proudfoot NJ, Bähler J, Erban R, Gullerova M. Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA 2013;19:1617-1631. [PMID: 24152550 PMCID: PMC3884648 DOI: 10.1261/rna.040675.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/17/2013] [Indexed: 05/31/2023]
Number Cited by Other Article(s)
1
Tanaka M. Transcriptional and post-transcriptional regulation of genes encoding secretory proteins in Aspergillus oryzae. Biosci Biotechnol Biochem 2024;88:381-388. [PMID: 38211972 DOI: 10.1093/bbb/zbae004] [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: 11/23/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
2
Lipińska-Zubrycka L, Grochowski M, Bähler J, Małecki M. Pervasive mRNA uridylation in fission yeast is catalysed by both Cid1 and Cid16 terminal uridyltransferases. PLoS One 2023;18:e0285576. [PMID: 37220133 DOI: 10.1371/journal.pone.0285576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]  Open
3
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
4
Nuclear mRNA maturation and mRNA export control: from trypanosomes to opisthokonts. Parasitology 2021;148:1196-1218. [PMID: 33461637 PMCID: PMC8311971 DOI: 10.1017/s0031182021000068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
5
Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019;30:248-255. [PMID: 30952021 DOI: 10.1016/j.cbd.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/24/2019] [Accepted: 03/24/2019] [Indexed: 11/21/2022]
6
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
7
Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018;28:1427-1441. [PMID: 30143597 PMCID: PMC6169888 DOI: 10.1101/gr.237826.118] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
8
Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018. [PMID: 30143597 DOI: 10.1101/gr.237826.118.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
9
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]
10
Tandem 3' UTR Patterns and Gene Expression Profiles of Marc-145 Cells During PRRSV Infection. Virol Sin 2018;33:335-344. [PMID: 30069823 DOI: 10.1007/s12250-018-0045-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]  Open
11
Zhou Z, Dang Y, Zhou M, Yuan H, Liu Y. Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation. eLife 2018;7:33569. [PMID: 29547124 PMCID: PMC5869017 DOI: 10.7554/elife.33569] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]  Open
12
Lock A, Rutherford K, Harris MA, Wood V. PomBase: The Scientific Resource for Fission Yeast. Methods Mol Biol 2018;1757:49-68. [PMID: 29761456 PMCID: PMC6440643 DOI: 10.1007/978-1-4939-7737-6_4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
13
Liu X, Freitas J, Zheng D, Oliveira MS, Hoque M, Martins T, Henriques T, Tian B, Moreira A. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA (NEW YORK, N.Y.) 2017;23:1807-1816. [PMID: 28851752 PMCID: PMC5689002 DOI: 10.1261/rna.062661.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
14
Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B. Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe. Genome Res 2017;27:1685-1695. [PMID: 28916539 PMCID: PMC5630032 DOI: 10.1101/gr.222331.117] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 08/23/2017] [Indexed: 11/25/2022]
15
Mayr C. Regulation by 3'-Untranslated Regions. Annu Rev Genet 2017;51:171-194. [PMID: 28853924 DOI: 10.1146/annurev-genet-120116-024704] [Citation(s) in RCA: 384] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
16
Lemay JF, Marguerat S, Larochelle M, Liu X, van Nues R, Hunyadkürti J, Hoque M, Tian B, Granneman S, Bähler J, Bachand F. The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection. Genes Dev 2017;30:1558-72. [PMID: 27401558 PMCID: PMC4949328 DOI: 10.1101/gad.280222.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/10/2016] [Indexed: 11/25/2022]
17
Wise JA, Nielsen O. Analysis of RNA Metabolism in Fission Yeast. Cold Spring Harb Protoc 2017;2017:2017/5/pdb.top079798. [PMID: 28461681 DOI: 10.1101/pdb.top079798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
18
Wittmann S, Renner M, Watts BR, Adams O, Huseyin M, Baejen C, El Omari K, Kilchert C, Heo DH, Kecman T, Cramer P, Grimes JM, Vasiljeva L. The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Nat Commun 2017;8:14861. [PMID: 28367989 PMCID: PMC5382271 DOI: 10.1038/ncomms14861] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/05/2017] [Indexed: 11/09/2022]  Open
19
Wang H, Li R, Zhou X, Xue L, Xu X, Liu B. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data. Sci Rep 2016;6:36388. [PMID: 27812017 PMCID: PMC5095665 DOI: 10.1038/srep36388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/14/2016] [Indexed: 12/05/2022]  Open
20
Larochelle M, Hunyadkürti J, Bachand F. Polyadenylation site selection: linking transcription and RNA processing via a conserved carboxy-terminal domain (CTD)-interacting protein. Curr Genet 2016;63:195-199. [PMID: 27582274 DOI: 10.1007/s00294-016-0645-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 12/29/2022]
21
Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 2016;12:857. [PMID: 26883383 PMCID: PMC4770384 DOI: 10.15252/msb.20156526] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
22
Geisberg JV, Moqtaderi Z. Genome-Wide Study of mRNA Isoform Half-Lives. Methods Mol Biol 2015;1358:317-23. [PMID: 26463393 DOI: 10.1007/978-1-4939-3067-8_20] [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] [Indexed: 02/23/2023]
23
Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell Mol Life Sci 2015;72:3425-39. [PMID: 26018601 DOI: 10.1007/s00018-015-1934-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/25/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
24
Zhou Y, Zhu J, Schermann G, Ohle C, Bendrin K, Sugioka-Sugiyama R, Sugiyama T, Fischer T. The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome. Nat Commun 2015;6:7050. [PMID: 25989903 PMCID: PMC4455066 DOI: 10.1038/ncomms8050] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 03/27/2015] [Indexed: 01/12/2023]  Open
25
You L, Wu J, Feng Y, Fu Y, Guo Y, Long L, Zhang H, Luan Y, Tian P, Chen L, Huang G, Huang S, Li Y, Li J, Chen C, Zhang Y, Chen S, Xu A. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. Nucleic Acids Res 2015;43:D59-D67. [PMID: 25378337 PMCID: PMC4383914 DOI: 10.1093/nar/gku1076] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/02/2014] [Accepted: 10/16/2014] [Indexed: 11/12/2022]  Open
26
Hunt AG. A rapid, simple, and inexpensive method for the preparation of strand-specific RNA-Seq libraries. Methods Mol Biol 2015;1255:195-207. [PMID: 25487215 DOI: 10.1007/978-1-4939-2175-1_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
27
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V. PomBase 2015: updates to the fission yeast database. Nucleic Acids Res 2014;43:D656-61. [PMID: 25361970 PMCID: PMC4383888 DOI: 10.1093/nar/gku1040] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
28
Castel SE, Ren J, Bhattacharjee S, Chang AY, Sánchez M, Valbuena A, Antequera F, Martienssen RA. Dicer promotes transcription termination at sites of replication stress to maintain genome stability. Cell 2014;159:572-83. [PMID: 25417108 DOI: 10.1016/j.cell.2014.09.031] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/29/2014] [Accepted: 09/17/2014] [Indexed: 12/12/2022]
29
Lemay JF, Larochelle M, Marguerat S, Atkinson S, Bähler J, Bachand F. The RNA exosome promotes transcription termination of backtracked RNA polymerase II. Nat Struct Mol Biol 2014;21:919-26. [DOI: 10.1038/nsmb.2893] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022]
30
Li XQ, Du D. Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals. BMC Evol Biol 2014;14:162. [PMID: 25052519 PMCID: PMC4360255 DOI: 10.1186/s12862-014-0162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022]  Open
31
Tanaka M, Tokuoka M, Gomi K. Effects of codon optimization on the mRNA levels of heterologous genes in filamentous fungi. Appl Microbiol Biotechnol 2014;98:3859-67. [PMID: 24682479 DOI: 10.1007/s00253-014-5609-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
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