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For: Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP. Extensive alternative polyadenylation during zebrafish development. Genome Res 2012;22:2054-66. [PMID: 22722342 PMCID: PMC3460199 DOI: 10.1101/gr.139733.112] [Citation(s) in RCA: 248] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Number Cited by Other Article(s)
51
Agarwal V, Lopez-Darwin S, Kelley DR, Shendure J. The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nat Commun 2021;12:5101. [PMID: 34429411 PMCID: PMC8385098 DOI: 10.1038/s41467-021-25388-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023]  Open
52
He Y, Yu H, Zhao H, Zhu H, Zhang Q, Wang A, Shen Y, Xu X, Li J. Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella). BMC Genomics 2021;22:620. [PMID: 34399686 PMCID: PMC8369720 DOI: 10.1186/s12864-021-07924-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/06/2021] [Indexed: 01/23/2023]  Open
53
Van Essen D, Alcaraz AJG, Miller JGP, Jones PD, Doering JA, Wiseman S. The brominated flame retardant, TBCO, impairs oocyte maturation in zebrafish (Danio rerio). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021;238:105929. [PMID: 34375885 DOI: 10.1016/j.aquatox.2021.105929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/15/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
54
Meng X, Kuang K, Zhang Y, Guan K, Liu B, Zhou X. Alternative polyadenylation events differ dramatically between Tongcheng and Large White pigs in response to PRRSV infection. Anim Genet 2021;52:744-748. [PMID: 34309053 DOI: 10.1111/age.13125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/01/2022]
55
Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021;121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
56
Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. BMC Genomics 2021;22:476. [PMID: 34174817 PMCID: PMC8234626 DOI: 10.1186/s12864-021-07781-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022]  Open
57
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. Blood Adv 2021;5:1310-1323. [PMID: 33656539 DOI: 10.1182/bloodadvances.2020002090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 01/19/2021] [Indexed: 11/20/2022]  Open
58
Mitschka S, Fansler MM, Mayr C. Generation of 3'UTR knockout cell lines by CRISPR/Cas9-mediated genome editing. Methods Enzymol 2021;655:427-457. [PMID: 34183132 DOI: 10.1016/bs.mie.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
59
Buchumenski I, Holler K, Appelbaum L, Eisenberg E, Junker JP, Levanon EY. Systematic identification of A-to-I RNA editing in zebrafish development and adult organs. Nucleic Acids Res 2021;49:4325-4337. [PMID: 33872356 PMCID: PMC8096273 DOI: 10.1093/nar/gkab247] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022]  Open
60
Gourain V, Armant O, Lübke L, Diotel N, Rastegar S, Strähle U. Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. Front Neurosci 2021;15:671249. [PMID: 34054419 PMCID: PMC8162057 DOI: 10.3389/fnins.2021.671249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022]  Open
61
Nascimento-Oliveira JI, Fantinatti BEA, Wolf IR, Cardoso AL, Ramos E, Rieder N, de Oliveira R, Martins C. Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. BMC Genomics 2021;22:344. [PMID: 33980143 PMCID: PMC8117508 DOI: 10.1186/s12864-021-07651-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022]  Open
62
Bhat P, Burkard TR, Herzog VA, Pauli A, Ameres SL. Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets. Methods Enzymol 2021;655:205-223. [PMID: 34183122 DOI: 10.1016/bs.mie.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
63
Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data. Methods Enzymol 2021;655:225-243. [PMID: 34183123 DOI: 10.1016/bs.mie.2021.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
64
Wright K, de Silva K, Plain KM, Purdie AC, Blair TA, Duggin IG, Britton WJ, Oehlers SH. Mycobacterial infection-induced miR-206 inhibits protective neutrophil recruitment via the CXCL12/CXCR4 signalling axis. PLoS Pathog 2021;17:e1009186. [PMID: 33826679 PMCID: PMC8055004 DOI: 10.1371/journal.ppat.1009186] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/19/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022]  Open
65
Lee S, Wei L, Zhang B, Goering R, Majumdar S, Wen J, Taliaferro JM, Lai EC. ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing. PLoS Genet 2021;17:e1009439. [PMID: 33826609 PMCID: PMC8055025 DOI: 10.1371/journal.pgen.1009439] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]  Open
66
Function analysis and molecular characterization of cyclin A in ovary development of oriental river prawn, Macrobrachium nipponense. Gene 2021;788:145583. [PMID: 33753150 DOI: 10.1016/j.gene.2021.145583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/26/2020] [Accepted: 03/12/2021] [Indexed: 11/24/2022]
67
Luu I, Ikert H, Craig PM. Chronic exposure to anthropogenic and climate related stressors alters transcriptional responses in the liver of zebrafish (Danio rerio) across multiple generations. Comp Biochem Physiol C Toxicol Pharmacol 2021;240:108918. [PMID: 33141083 DOI: 10.1016/j.cbpc.2020.108918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/09/2020] [Accepted: 10/18/2020] [Indexed: 01/04/2023]
68
Jin W, Zhu Q, Yang Y, Yang W, Wang D, Yang J, Niu X, Yu D, Gong J. Animal-APAdb: a comprehensive animal alternative polyadenylation database. Nucleic Acids Res 2021;49:D47-D54. [PMID: 32986825 PMCID: PMC7779049 DOI: 10.1093/nar/gkaa778] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022]  Open
69
Zygotic Genome Activation: Critical Prelude to the Most Important Time of Your Life. Methods Mol Biol 2021;2218:319-329. [PMID: 33606242 DOI: 10.1007/978-1-0716-0970-5_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
70
Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m6A Readers Function Redundantly during Zebrafish Development. Cell Rep 2020;33:108598. [PMID: 33378672 PMCID: PMC11407899 DOI: 10.1016/j.celrep.2020.108598] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/09/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]  Open
71
Dicks S, Jürgensen L, Leuschner F, Hassel D, Andrieux G, Boerries M. Cardiac Regeneration and Tumor Growth-What Do They Have in Common? Front Genet 2020;11:586658. [PMID: 33362851 PMCID: PMC7756072 DOI: 10.3389/fgene.2020.586658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/04/2020] [Indexed: 11/13/2022]  Open
72
Alternative Polyadenylation: a new frontier in post transcriptional regulation. Biomark Res 2020;8:67. [PMID: 33292571 PMCID: PMC7690165 DOI: 10.1186/s40364-020-00249-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]  Open
73
Liyanage TD, Nikapitiya C, Lee J, De Zoysa M. Molecular insight into regulation of miRNAs in the spleen of zebrafish (Danio rerio) upon pathogenic Streptococcus parauberis infection. FISH & SHELLFISH IMMUNOLOGY 2020;106:898-909. [PMID: 32889099 DOI: 10.1016/j.fsi.2020.08.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
74
Wei L, Lee S, Majumdar S, Zhang B, Sanfilippo P, Joseph B, Miura P, Soller M, Lai EC. Overlapping Activities of ELAV/Hu Family RNA Binding Proteins Specify the Extended Neuronal 3' UTR Landscape in Drosophila. Mol Cell 2020;80:140-155.e6. [PMID: 33007254 DOI: 10.1016/j.molcel.2020.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022]
75
Carrasco J, Rauer M, Hummel B, Grzejda D, Alfonso-Gonzalez C, Lee Y, Wang Q, Puchalska M, Mittler G, Hilgers V. ELAV and FNE Determine Neuronal Transcript Signatures through EXon-Activated Rescue. Mol Cell 2020;80:156-163.e6. [PMID: 33007255 DOI: 10.1016/j.molcel.2020.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
76
Bae B, Gruner HN, Lynch M, Feng T, So K, Oliver D, Mastick GS, Yan W, Pieraut S, Miura P. Elimination of Calm1 long 3'-UTR mRNA isoform by CRISPR-Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice. RNA (NEW YORK, N.Y.) 2020;26:1414-1430. [PMID: 32522888 PMCID: PMC7491327 DOI: 10.1261/rna.076430.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 05/04/2023]
77
Levin M, Zalts H, Mostov N, Hashimshony T, Yanai I. Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms. Nucleic Acids Res 2020;48:5926-5938. [PMID: 32421815 PMCID: PMC7293032 DOI: 10.1093/nar/gkaa359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023]  Open
78
Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. eLife 2020;9:55792. [PMID: 32831172 PMCID: PMC7486121 DOI: 10.7554/elife.55792] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]  Open
79
Liu Y, Zhu Z, Ho IHT, Shi Y, Li J, Wang X, Chan MTV, Cheng CHK. Genetic Deletion of miR-430 Disrupts Maternal-Zygotic Transition and Embryonic Body Plan. Front Genet 2020;11:853. [PMID: 32849832 PMCID: PMC7417628 DOI: 10.3389/fgene.2020.00853] [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: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022]  Open
80
Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells. Int J Mol Sci 2020;21:ijms21155549. [PMID: 32756402 PMCID: PMC7432238 DOI: 10.3390/ijms21155549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]  Open
81
Zhang Z, So K, Peterson R, Bauer M, Ng H, Zhang Y, Kim JH, Kidd T, Miura P. Elav-Mediated Exon Skipping and Alternative Polyadenylation of the Dscam1 Gene Are Required for Axon Outgrowth. Cell Rep 2020;27:3808-3817.e7. [PMID: 31242415 PMCID: PMC7092717 DOI: 10.1016/j.celrep.2019.05.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 04/18/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022]  Open
82
Ren C, Deng K, Wang Z, Deng M, Fan Y, Zhang Y, Ma J, Wang S, Liu Z, Wang F. Reinterpreting sheep muscle strand-specific RNA sequencing data showing extensive 3'UTR extensions. Anim Genet 2020;51:788-798. [PMID: 32696483 DOI: 10.1111/age.12987] [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: 10/15/2019] [Revised: 05/16/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022]
83
miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data. Cells 2020;9:cells9081752. [PMID: 32707870 PMCID: PMC7465656 DOI: 10.3390/cells9081752] [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: 06/25/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/04/2022]  Open
84
Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020;10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022]  Open
85
Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, Yu H, Wei Y, Wu Q, Zhang Y. Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 2020;15:e0234696. [PMID: 32544193 PMCID: PMC7297374 DOI: 10.1371/journal.pone.0234696] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/02/2020] [Indexed: 12/19/2022]  Open
86
Bradshaw WJ, Valenzano DR. Extreme genomic volatility characterizes the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes. Proc Biol Sci 2020;287:20200489. [PMID: 32396805 PMCID: PMC7287348 DOI: 10.1098/rspb.2020.0489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]  Open
87
Characterization and Functional Analysis of Polyadenylation Sites in Fast and Slow Muscles. BIOMED RESEARCH INTERNATIONAL 2020;2020:2626584. [PMID: 32258109 PMCID: PMC7102456 DOI: 10.1155/2020/2626584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/01/2019] [Accepted: 01/16/2020] [Indexed: 12/05/2022]
88
Yang F, Wang W, Cetinbas M, Sadreyev RI, Blower MD. Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation. RNA (NEW YORK, N.Y.) 2020;26:324-344. [PMID: 31896558 PMCID: PMC7025505 DOI: 10.1261/rna.073247.119] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/30/2019] [Indexed: 05/10/2023]
89
Zhu S, Ye W, Ye L, Fu H, Ye C, Xiao X, Ji Y, Lin W, Ji G, Wu X. PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants. PLANT PHYSIOLOGY 2020;182:228-242. [PMID: 31767692 PMCID: PMC6945835 DOI: 10.1104/pp.19.00943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/18/2019] [Indexed: 05/23/2023]
90
Ikert H, Craig PM. Chronic exposure to venlafaxine and increased water temperature reversibly alters microRNA in zebrafish gonads (Danio rerio). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019;33:100634. [PMID: 31715506 DOI: 10.1016/j.cbd.2019.100634] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/09/2019] [Accepted: 10/12/2019] [Indexed: 01/28/2023]
91
Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M. Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res 2019;47:2560-2573. [PMID: 30590745 PMCID: PMC6411841 DOI: 10.1093/nar/gky1270] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023]  Open
92
Yu Z, Lin J, Li QQ. Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation. THE PLANT CELL 2019;31:2332-2352. [PMID: 31427469 PMCID: PMC6790095 DOI: 10.1105/tpc.18.00545] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/15/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
93
Shui Y, Liu GF, Xu ZH, Zhu GY. Exploring potential proteins associated with cyclin B 3'UTR in Procambarus clarkii oocytes. Biochem Biophys Res Commun 2019;517:458-462. [PMID: 31376940 DOI: 10.1016/j.bbrc.2019.07.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
94
Arefeen A, Liu J, Xiao X, Jiang T. TAPAS: tool for alternative polyadenylation site analysis. Bioinformatics 2019;34:2521-2529. [PMID: 30052912 DOI: 10.1093/bioinformatics/bty110] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023]  Open
95
Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences. G3-GENES GENOMES GENETICS 2019;9:2749-2760. [PMID: 31239292 PMCID: PMC6686930 DOI: 10.1534/g3.119.400196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
96
Sarropoulou E, Kaitetzidou E, Papandroulakis N, Tsalafouta A, Pavlidis M. Inventory of European Sea Bass (Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development. Front Genet 2019;10:657. [PMID: 31404269 PMCID: PMC6670005 DOI: 10.3389/fgene.2019.00657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 01/25/2023]  Open
97
Chen M, Ji G, Fu H, Lin Q, Ye C, Ye W, Su Y, Wu X. A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. Brief Bioinform 2019;21:1261-1276. [PMID: 31267126 DOI: 10.1093/bib/bbz068] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]  Open
98
Ye C, Long Y, Ji G, Li QQ, Wu X. APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data. Bioinformatics 2019;34:1841-1849. [PMID: 29360928 DOI: 10.1093/bioinformatics/bty029] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/17/2018] [Indexed: 12/28/2022]  Open
99
Zhou X, Zhang Y, Michal JJ, Qu L, Zhang S, Wildung MR, Du W, Pouchnik DJ, Zhao H, Xia Y, Shi H, Ji G, Davis JF, Smith GD, Griswold MD, Harland RM, Jiang Z. Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis. Cell Mol Life Sci 2019;76:2185-2198. [PMID: 30729254 PMCID: PMC6597005 DOI: 10.1007/s00018-019-03036-1] [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: 04/26/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 12/27/2022]
100
Cao J, Ye C, Hao G, Dabney-Smith C, Hunt AG, Li QQ. Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress. FRONTIERS IN PLANT SCIENCE 2019;10:589. [PMID: 31134121 PMCID: PMC6523994 DOI: 10.3389/fpls.2019.00589] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/23/2019] [Indexed: 05/15/2023]
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