Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy ASN (2016) A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 7. https://doi.org/10.1038/ncomms11706
Anvar SY, Allard G, Tseng E, Sheynkman GM, de Klerk E, Vermaat M, Yin RH, Johansson HE, Ariyurek Y, den Dunnen JT, Turner SW, ‘t Hoen PAC (2018) Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing. Genome Biol 19. https://doi.org/10.1186/s13059-018-1418-0
Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168. https://doi.org/10.1093/nar/gky066
Article CAS PubMed PubMed Central Google Scholar
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, H van Bakel, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH (2013) Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci 110. https://doi.org/10.1073/pnas.1320101110
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ (2010) Deciphering the splicing code. Nature 465:53–59. https://doi.org/10.1038/nature09000
Article CAS PubMed Google Scholar
Bentley DL (2014) Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15:163–175. https://doi.org/10.1038/nrg3662
Article CAS PubMed PubMed Central Google Scholar
Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ (2014) Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res 24:1774–1786. https://doi.org/10.1101/gr.177790.114
Article CAS PubMed PubMed Central Google Scholar
Chowdhury HA, Bhattacharyya DK, Kalita JK (2018) Differential expression analysis of RNA-seq reads: overview, taxonomy and tools. IEEE/ACM Trans Comput Biol Bioinf 1–1. https://doi.org/10.1109/tcbb.2018.2873010
Dvinge H, Bradley RK (2015) Widespread intron retention diversifies most cancer transcriptomes. Genome Med 7. https://doi.org/10.1186/s13073-015-0168-9
Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35:W297–W299. https://doi.org/10.1093/nar/gkm311
Article PubMed PubMed Central Google Scholar
Gao Y, Wang H, Zhang H, Wang Y, Chen J, Gu L, Hancock J (2018) PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq. Bioinformatics 34:1580–1582. https://doi.org/10.1093/bioinformatics/btx830
Article CAS PubMed Google Scholar
Hilgers V (2015) Alternative polyadenylation coupled to transcription initiation: insights from ELAV-mediated 3′ UTR extension. RNA Biol 12:918–921. https://doi.org/10.1080/15476286.2015.1060393
Article PubMed PubMed Central Google Scholar
Hsin J-P, Manley JL (2012) The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26:2119–2137. https://doi.org/10.1101/gad.200303.112
Article CAS PubMed PubMed Central Google Scholar
Jin Z, Lv X, Sun Y, Fan Z, Xiang G, Yao Y (2021) Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots. Environmental and experimental botany 192. https://doi.org/10.1016/j.envexpbot.2021.104645
Li H, Birol I (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191
Article CAS PubMed PubMed Central Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Article CAS PubMed PubMed Central Google Scholar
Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJL, Bomane A, Cosson B, Eyras E, Rasko JEJ, Ritchie W (2017) IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol 18. https://doi.org/10.1186/s13059-017-1184-4
Movassat M, Crabb TL, Busch A, Yao C, Reynolds DJ, Shi Y, Hertel KJ (2016) Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biol 13:646–655. https://doi.org/10.1080/15476286.2016.1191727
Article PubMed PubMed Central Google Scholar
Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG (2016) A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res 44:838–851. https://doi.org/10.1093/nar/gkv1168
Article CAS PubMed Google Scholar
Rigo F, Martinson HG (2008) Functional coupling of last-intron splicing and 3’-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage. Mol Cell Biol 28:849–862. https://doi.org/10.1128/MCB.01410-07
Article CAS PubMed Google Scholar
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–1184. https://doi.org/10.1038/nmeth.2714
Article CAS PubMed PubMed Central Google Scholar
Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192. https://doi.org/10.1093/bib/bbs017
Article CAS PubMed Google Scholar
Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, Eyras E (2018) SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol 19. https://doi.org/10.1186/s13059-018-1417-1
Ule J, Blencowe BJ (2019) Alternative Splicing Regulatory networks: functions, mechanisms, and evolution. Mol Cell 76:329–345. https://doi.org/10.1016/j.molcel.2019.09.017
Article CAS PubMed Google Scholar
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476. https://doi.org/10.1038/nature07509
Article CAS PubMed PubMed Central Google Scholar
Wong JJL, Schmitz U (2022) Intron retention: importance, challenges, and opportunities. Trends Genet 38:789–792. https://doi.org/10.1016/j.tig.2022.03.017
Article CAS PubMed Google Scholar
Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur Ab, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu S-L, Wachter A, Waugh R, Xiong L, Zhang X-N, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-Seq analysis. Genome Biol 23. https://doi.org/10.1186/s13059-022-02711-0
留言 (0)