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For: Graber JH, Salisbury J, Hutchins LN, Blumenthal T. C. elegans sequences that control trans-splicing and operon pre-mRNA processing. RNA 2007;13:1409-26. [PMID: 17630324 PMCID: PMC1950753 DOI: 10.1261/rna.596707] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 05/17/2007] [Indexed: 05/04/2023]
Number Cited by Other Article(s)
1
Knoebel E, Brinck A, Nonet ML. Parameters that influence bipartite reporter system expression in Caenorhabditis elegans. Genetics 2025:iyaf076. [PMID: 40341369 DOI: 10.1093/genetics/iyaf076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/08/2025] [Indexed: 05/10/2025]  Open
2
Gao P, Zhao Y, Xu G, Zhong Y, Sun C. Unique features of conventional and nonconventional introns in Euglena gracilis. BMC Genomics 2024;25:595. [PMID: 38872102 PMCID: PMC11170887 DOI: 10.1186/s12864-024-10495-9] [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: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]  Open
3
Cassart C, Yague-Sanz C, Bauer F, Ponsard P, Stubbe FX, Migeot V, Wery M, Morillon A, Palladino F, Robert V, Hermand D. RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans. SCIENCE ADVANCES 2020;6:6/50/eabc1450. [PMID: 33298437 PMCID: PMC7725455 DOI: 10.1126/sciadv.abc1450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
4
Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. PLoS Negl Trop Dis 2020;14:e0008869. [PMID: 33196647 PMCID: PMC7704054 DOI: 10.1371/journal.pntd.0008869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/30/2020] [Accepted: 10/09/2020] [Indexed: 01/01/2023]  Open
5
Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020;215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023]  Open
6
Nelson C, Ambros V. Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity. Development 2019;146:dev172031. [PMID: 30770392 PMCID: PMC6432665 DOI: 10.1242/dev.172031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
7
Yague-Sanz C, Hermand D. SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data. Gigascience 2018;7:5052207. [PMID: 30010768 PMCID: PMC6055573 DOI: 10.1093/gigascience/giy084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 07/01/2018] [Indexed: 11/13/2022]  Open
8
Garrido-Lecca A, Saldi T, Blumenthal T. Localization of RNAPII and 3' end formation factor CstF subunits on C. elegans genes and operons. Transcription 2016;7:96-110. [PMID: 27124504 DOI: 10.1080/21541264.2016.1168509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
9
Pettitt J, Philippe L, Sarkar D, Johnston C, Gothe HJ, Massie D, Connolly B, Müller B. Operons are a conserved feature of nematode genomes. Genetics 2014;197:1201-11. [PMID: 24931407 PMCID: PMC4125394 DOI: 10.1534/genetics.114.162875] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/06/2014] [Indexed: 01/09/2023]  Open
10
DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast. Genome Res 2013;23:1690-703. [PMID: 23788651 PMCID: PMC3787265 DOI: 10.1101/gr.144964.112] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
11
Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
12
Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011;3:385-96. [PMID: 22012871 DOI: 10.1002/wrna.116] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
13
Laing R, Hunt M, Protasio AV, Saunders G, Mungall K, Laing S, Jackson F, Quail M, Beech R, Berriman M, Gilleard JS. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One 2011;6:e23216. [PMID: 21858033 PMCID: PMC3156134 DOI: 10.1371/journal.pone.0023216] [Citation(s) in RCA: 21] [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: 05/24/2011] [Accepted: 07/12/2011] [Indexed: 11/30/2022]  Open
14
Grishkevich V, Hashimshony T, Yanai I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Res 2011;21:707-17. [PMID: 21367940 PMCID: PMC3083087 DOI: 10.1101/gr.113381.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 02/17/2011] [Indexed: 02/01/2023]
15
Divergence in enzyme regulation between Caenorhabditis elegans and human tyrosine hydroxylase, the key enzyme in the synthesis of dopamine. Biochem J 2011;434:133-41. [DOI: 10.1042/bj20101561] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
16
Lasda EL, Blumenthal T. Trans-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011;2:417-34. [PMID: 21957027 DOI: 10.1002/wrna.71] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
17
Morton JJ, Blumenthal T. RNA Processing in C. elegans. Methods Cell Biol 2011;106:187-217. [DOI: 10.1016/b978-0-12-544172-8.00007-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
18
The evolution of spliced leader trans-splicing in nematodes. Biochem Soc Trans 2010;38:1125-30. [DOI: 10.1042/bst0381125] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
19
Lasda EL, Allen MA, Blumenthal T. Polycistronic pre-mRNA processing in vitro: snRNP and pre-mRNA role reversal in trans-splicing. Genes Dev 2010;24:1645-58. [PMID: 20624853 DOI: 10.1101/gad.1940010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
20
RNA polymerase II C-terminal domain phosphorylation patterns in Caenorhabditis elegans operons, polycistronic gene clusters with only one promoter. Mol Cell Biol 2010;30:3887-93. [PMID: 20498277 DOI: 10.1128/mcb.00325-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
21
Derelle R, Momose T, Manuel M, Da Silva C, Wincker P, Houliston E. Convergent origins and rapid evolution of spliced leader trans-splicing in metazoa: insights from the ctenophora and hydrozoa. RNA (NEW YORK, N.Y.) 2010;16:696-707. [PMID: 20142326 PMCID: PMC2844618 DOI: 10.1261/rna.1975210] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/23/2009] [Indexed: 05/20/2023]
22
Lee LW, Lo HW, Lo SJ. Vectors for co-expression of two genes in Caenorhabditis elegans. Gene 2010;455:16-21. [PMID: 20149852 DOI: 10.1016/j.gene.2010.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 11/19/2022]
23
Sleumer MC, Mah AK, Baillie DL, Jones SJM. Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res 2010;38:2990-3004. [PMID: 20100800 PMCID: PMC2875031 DOI: 10.1093/nar/gkq003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
24
Liu C, Oliveira A, Chauhan C, Ghedin E, Unnasch TR. Functional analysis of putative operons in Brugia malayi. Int J Parasitol 2010;40:63-71. [PMID: 19631652 PMCID: PMC2813416 DOI: 10.1016/j.ijpara.2009.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/06/2009] [Accepted: 07/07/2009] [Indexed: 11/21/2022]
25
Shapiro JA. Revisiting the Central Dogma in the 21st Century. Ann N Y Acad Sci 2009;1178:6-28. [DOI: 10.1111/j.1749-6632.2009.04990.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
26
Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, Vidal M. Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Res 2009;19:2334-42. [PMID: 19801531 DOI: 10.1101/gr.098640.109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
27
Liu C, Chauhan C, Katholi CR, Unnasch TR. The splice leader addition domain represents an essential conserved motif for heterologous gene expression in B. malayi. Mol Biochem Parasitol 2009;166:15-21. [PMID: 19428668 PMCID: PMC2680783 DOI: 10.1016/j.molbiopara.2009.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 11/28/2022]
28
Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Krüger N, Sonnenburg S, Rätsch G. mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res 2009;19:2133-43. [PMID: 19564452 DOI: 10.1101/gr.090597.108] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
29
Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A 2009;106 Suppl 1:9963-70. [PMID: 19528647 DOI: 10.1073/pnas.0901004106] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
30
Hutchins LN, Murphy SM, Singh P, Graber JH. Position-dependent motif characterization using non-negative matrix factorization. ACTA ACUST UNITED AC 2008;24:2684-90. [PMID: 18852176 PMCID: PMC2639279 DOI: 10.1093/bioinformatics/btn526] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
31
Sonnenburg S, Zien A, Philips P, Rätsch G. POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors. Bioinformatics 2008;24:i6-14. [PMID: 18586746 PMCID: PMC2718648 DOI: 10.1093/bioinformatics/btn170] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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