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For: Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 2012;22:1616-25. [PMID: 22955974 DOI: 10.1101/gr.134445.111] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
101
Tellier M, Maudlin I, Murphy S. Transcription and splicing: A two-way street. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020;11:e1593. [PMID: 32128990 DOI: 10.1002/wrna.1593] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
102
Zhao S, Ye Z, Stanton R. Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols. RNA (NEW YORK, N.Y.) 2020;26:903-909. [PMID: 32284352 PMCID: PMC7373998 DOI: 10.1261/rna.074922.120] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
103
Lee D, Zhang J, Liu J, Gerstein M. Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput Biol 2020;16:e1008006. [PMID: 32584815 PMCID: PMC7343189 DOI: 10.1371/journal.pcbi.1008006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022]  Open
104
Ding J, Adiconis X, Simmons SK, Kowalczyk MS, Hession CC, Marjanovic ND, Hughes TK, Wadsworth MH, Burks T, Nguyen LT, Kwon JYH, Barak B, Ge W, Kedaigle AJ, Carroll S, Li S, Hacohen N, Rozenblatt-Rosen O, Shalek AK, Villani AC, Regev A, Levin JZ. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods. Nat Biotechnol 2020;38:737-746. [PMID: 32341560 PMCID: PMC7289686 DOI: 10.1038/s41587-020-0465-8] [Citation(s) in RCA: 537] [Impact Index Per Article: 107.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/24/2020] [Indexed: 01/06/2023]
105
Abou Alezz M, Celli L, Belotti G, Lisa A, Bione S. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front Genet 2020;11:488. [PMID: 32499820 PMCID: PMC7242645 DOI: 10.3389/fgene.2020.00488] [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: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022]  Open
106
Thillainadesan G, Xiao H, Holla S, Dhakshnamoorthy J, Jenkins LMM, Wheeler D, Grewal SIS. Conserved protein Pir2ARS2 mediates gene repression through cryptic introns in lncRNAs. Nat Commun 2020;11:2412. [PMID: 32415063 PMCID: PMC7229227 DOI: 10.1038/s41467-020-16280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023]  Open
107
Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, Zhang QC, Shen X. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature 2020;580:147-150. [PMID: 32238924 PMCID: PMC12018070 DOI: 10.1038/s41586-020-2105-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/09/2020] [Indexed: 12/21/2022]
108
Botto AEC, Muñoz JC, Giono LE, Nieto-Moreno N, Cuenca C, Kornblihtt AR, Muñoz MJ. Reciprocal regulation between alternative splicing and the DNA damage response. Genet Mol Biol 2020;43:e20190111. [PMID: 32236390 PMCID: PMC7197977 DOI: 10.1590/1678-4685-gmb-2019-0111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/16/2019] [Indexed: 12/16/2022]  Open
109
Drexler HL, Choquet K, Churchman LS. Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores. Mol Cell 2020;77:985-998.e8. [PMID: 31839405 PMCID: PMC7060811 DOI: 10.1016/j.molcel.2019.11.017] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
110
Tan JY, Biasini A, Young RS, Marques AC. Splicing of enhancer-associated lincRNAs contributes to enhancer activity. Life Sci Alliance 2020;3:3/4/e202000663. [PMID: 32086317 PMCID: PMC7035876 DOI: 10.26508/lsa.202000663] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022]  Open
111
Sun X, Wang Z, Hall JM, Perez-Cervantes C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PLoS Comput Biol 2020;16:e1007119. [PMID: 32040509 PMCID: PMC7034927 DOI: 10.1371/journal.pcbi.1007119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 02/21/2020] [Accepted: 01/14/2020] [Indexed: 01/22/2023]  Open
112
Li S, Wang Y, Zhao Y, Zhao X, Chen X, Gong Z. Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs. MOLECULAR PLANT 2020;13:266-277. [PMID: 31759129 PMCID: PMC8034514 DOI: 10.1016/j.molp.2019.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
113
Zhu D, Mao F, Tian Y, Lin X, Gu L, Gu H, Qu LJ, Wu Y, Wu Z. The Features and Regulation of Co-transcriptional Splicing in Arabidopsis. MOLECULAR PLANT 2020;13:278-294. [PMID: 31760161 DOI: 10.1016/j.molp.2019.11.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/29/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
114
Pendergraff H, Schmidt S, Vikeså J, Weile C, Øverup C, W. Lindholm M, Koch T. Nuclear and Cytoplasmatic Quantification of Unconjugated, Label-Free Locked Nucleic Acid Oligonucleotides. Nucleic Acid Ther 2020;30:4-13. [PMID: 31618108 PMCID: PMC6987631 DOI: 10.1089/nat.2019.0810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022]  Open
115
Auboeuf D. Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces. Life (Basel) 2020;10:life10020007. [PMID: 31973071 PMCID: PMC7175370 DOI: 10.3390/life10020007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/11/2022]  Open
116
Price AJ, Hwang T, Tao R, Burke EE, Rajpurohit A, Shin JH, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR. Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation. Genome Res 2020;30:1-11. [PMID: 31852722 PMCID: PMC6961577 DOI: 10.1101/gr.250217.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022]
117
Yin Y, Shen X. Identification of cis-Elements for RNA Subcellular Localization Through REL-seq. Methods Mol Biol 2020;2161:143-160. [PMID: 32681511 DOI: 10.1007/978-1-0716-0680-3_11] [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: 12/14/2022]
118
Wang J, Chen S, Jiang N, Li N, Wang X, Li Z, Li X, Liu H, Li L, Yang Y, Ni T, Yu C, Ma J, Zheng B, Ren G. Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana. Nucleic Acids Res 2019;47:7886-7900. [PMID: 31216029 PMCID: PMC6736097 DOI: 10.1093/nar/gkz526] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 12/23/2022]  Open
119
Mora Gallardo C, Sánchez de Diego A, Gutiérrez Hernández J, Talavera-Gutiérrez A, Fischer T, Martínez-A C, van Wely KHM. Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing. Nucleic Acids Res 2019;47:5381-5394. [PMID: 30931476 PMCID: PMC6547428 DOI: 10.1093/nar/gkz235] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022]  Open
120
Lemaire S, Fontrodona N, Aubé F, Claude JB, Polvèche H, Modolo L, Bourgeois CF, Mortreux F, Auboeuf D. Characterizing the interplay between gene nucleotide composition bias and splicing. Genome Biol 2019;20:259. [PMID: 31783898 PMCID: PMC6883713 DOI: 10.1186/s13059-019-1869-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022]  Open
121
Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019;21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 467] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
122
Jabre I, Reddy ASN, Kalyna M, Chaudhary S, Khokhar W, Byrne LJ, Wilson CM, Syed NH. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Res 2019;47:2716-2726. [PMID: 30793202 PMCID: PMC6451118 DOI: 10.1093/nar/gkz121] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/15/2022]  Open
123
Xu B, Shi Y, Wu Y, Meng Y, Jin Y. Role of RNA secondary structures in regulating Dscam alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019;1862:194381. [DOI: 10.1016/j.bbagrm.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
124
Maudlin IE, Beggs JD. Spt5 modulates cotranscriptional spliceosome assembly in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2019;25:1298-1310. [PMID: 31289129 PMCID: PMC6800482 DOI: 10.1261/rna.070425.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
125
Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Front Genet 2019;10:709. [PMID: 31475029 PMCID: PMC6706457 DOI: 10.3389/fgene.2019.00709] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023]  Open
126
A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia. Noncoding RNA Res 2019;4:96-108. [PMID: 31891018 PMCID: PMC6926186 DOI: 10.1016/j.ncrna.2019.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/09/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022]  Open
127
Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019;11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
128
Shenasa H, Hertel KJ. Combinatorial regulation of alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019;1862:194392. [PMID: 31276857 DOI: 10.1016/j.bbagrm.2019.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/23/2022]
129
Overexpressed long noncoding RNA CRNDE with distinct alternatively spliced isoforms in multiple cancers. Front Med 2019;13:330-343. [PMID: 29808251 DOI: 10.1007/s11684-017-0557-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/30/2017] [Indexed: 12/22/2022]
130
Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D, Wilson SA. Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Mol Cell 2019;75:310-323.e8. [PMID: 31104896 PMCID: PMC6675937 DOI: 10.1016/j.molcel.2019.04.034] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 02/25/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
131
Zuckerman B, Ulitsky I. Predictive models of subcellular localization of long RNAs. RNA (NEW YORK, N.Y.) 2019;25:557-572. [PMID: 30745363 PMCID: PMC6467007 DOI: 10.1261/rna.068288.118] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/07/2019] [Indexed: 05/14/2023]
132
Xiao S, Cao S, Huang Q, Xia L, Deng M, Yang M, Jia G, Liu X, Shi J, Wang W, Li Y, Liu S, Zhu H, Tan K, Luo Q, Zhong M, He C, Xia L. The RNA N6-methyladenosine modification landscape of human fetal tissues. Nat Cell Biol 2019;21:651-661. [PMID: 31036937 DOI: 10.1038/s41556-019-0315-4] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/15/2019] [Indexed: 12/14/2022]
133
Bunch H, Choe H, Kim J, Jo DS, Jeon S, Lee S, Cho DH, Kang K. P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes. Front Genet 2019;10:342. [PMID: 31068966 PMCID: PMC6491683 DOI: 10.3389/fgene.2019.00342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/29/2019] [Indexed: 01/16/2023]  Open
134
Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019;10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
135
Nozawa RS, Gilbert N. RNA: Nuclear Glue for Folding the Genome. Trends Cell Biol 2019;29:201-211. [DOI: 10.1016/j.tcb.2018.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 12/10/2018] [Accepted: 12/14/2018] [Indexed: 12/20/2022]
136
Ragan C, Goodall GJ, Shirokikh NE, Preiss T. Insights into the biogenesis and potential functions of exonic circular RNA. Sci Rep 2019;9:2048. [PMID: 30765711 PMCID: PMC6376117 DOI: 10.1038/s41598-018-37037-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 12/03/2018] [Indexed: 01/16/2023]  Open
137
Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun 2019;10:521. [PMID: 30705266 PMCID: PMC6355915 DOI: 10.1038/s41467-019-08381-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023]  Open
138
Krchňáková Z, Thakur PK, Krausová M, Bieberstein N, Haberman N, Müller-McNicoll M, Staněk D. Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins. Nucleic Acids Res 2019;47:911-928. [PMID: 30445574 PMCID: PMC6344860 DOI: 10.1093/nar/gky1147] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]  Open
139
Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019;84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
140
Godoy Herz MA, Kornblihtt AR. Alternative Splicing and Transcription Elongation in Plants. FRONTIERS IN PLANT SCIENCE 2019;10:309. [PMID: 30972082 PMCID: PMC6443983 DOI: 10.3389/fpls.2019.00309] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
141
ncRNA Editing: Functional Characterization and Computational Resources. Methods Mol Biol 2019;1912:133-174. [PMID: 30635893 DOI: 10.1007/978-1-4939-8982-9_6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
142
Guigo R, de Hoon M. Recent advances in functional genome analysis. F1000Res 2018;7. [PMID: 30613379 PMCID: PMC6305211 DOI: 10.12688/f1000research.15274.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 12/12/2022]  Open
143
Yazarlou F, Modarressi MH, Mowla SJ, Oskooei VK, Motevaseli E, Tooli LF, Nekoohesh L, Eghbali M, Ghafouri-Fard S, Afsharpad M. Urinary exosomal expression of long non-coding RNAs as diagnostic marker in bladder cancer. Cancer Manag Res 2018;10:6357-6365. [PMID: 30568497 PMCID: PMC6267766 DOI: 10.2147/cmar.s186108] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
144
Li B, Ma L, Zhang C, Zhou Z, Yuan H, Jiang H, Pan Y, Tan Q. Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate. Mol Genet Genomic Med 2018;6:1157-1167. [PMID: 30411541 PMCID: PMC6305670 DOI: 10.1002/mgg3.497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/03/2018] [Accepted: 10/02/2018] [Indexed: 01/10/2023]  Open
145
Hansen MMK, Desai RV, Simpson ML, Weinberger LS. Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability. Cell Syst 2018;7:384-397.e6. [PMID: 30243562 PMCID: PMC6202163 DOI: 10.1016/j.cels.2018.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
146
Palazzo AF, Lee ES. Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs. Front Genet 2018;9:440. [PMID: 30386371 PMCID: PMC6199362 DOI: 10.3389/fgene.2018.00440] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/26/2022]  Open
147
Chen W, Feng P, Ding H, Lin H. Classifying Included and Excluded Exons in Exon Skipping Event Using Histone Modifications. Front Genet 2018;9:433. [PMID: 30327665 PMCID: PMC6174203 DOI: 10.3389/fgene.2018.00433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]  Open
148
Biamonti G, Maita L, Montecucco A. The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism. Front Oncol 2018;8:408. [PMID: 30319972 PMCID: PMC6168629 DOI: 10.3389/fonc.2018.00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022]  Open
149
Martinez NM, Gilbert WV. Pre-mRNA modifications and their role in nuclear processing. QUANTITATIVE BIOLOGY 2018;6:210-227. [PMID: 30533247 DOI: 10.1007/s40484-018-0147-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
150
Wang Y, Wang Z, Liu T, Gong S, Zhang W. Effects of flanking regions on HDV cotranscriptional folding kinetics. RNA (NEW YORK, N.Y.) 2018;24:1229-1240. [PMID: 29954950 PMCID: PMC6097654 DOI: 10.1261/rna.065961.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/25/2018] [Indexed: 05/20/2023]
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