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For: Mittal N, Scherrer T, Gerber AP, Janga SC. Interplay between posttranscriptional and posttranslational interactions of RNA-binding proteins. J Mol Biol 2011;409:466-79. [PMID: 21501624 DOI: 10.1016/j.jmb.2011.03.064] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/02/2011] [Accepted: 03/29/2011] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Zhang J, Yao S, Cheng X, Zhao Y, Yu W, Ren X, Ji K, Yu Q. Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora. Int J Mol Sci 2024;25:5960. [PMID: 38892149 PMCID: PMC11173211 DOI: 10.3390/ijms25115960] [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: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024]  Open
2
Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M. SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543769. [PMID: 37333139 PMCID: PMC10274648 DOI: 10.1101/2023.06.05.543769] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
3
Hao W, Wang W, Xiao X, Sun J, Wu B, Zhao Y, Pei S, Fan W, Xu D, Qin T. Genome-Wide Identification and Evolutionary Analysis of Gossypium YTH Domain-Containing RNA-Binding Protein Family and the Role of GhYTH8 in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023;12:1198. [PMID: 36904058 PMCID: PMC10006896 DOI: 10.3390/plants12051198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
4
A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. Comput Struct Biotechnol J 2022;20:3195-3207. [PMID: 35832617 PMCID: PMC9249596 DOI: 10.1016/j.csbj.2022.06.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]  Open
5
Chang K, Yuan C, Liu X. A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients. Front Oncol 2021;11:627504. [PMID: 33767995 PMCID: PMC7985171 DOI: 10.3389/fonc.2021.627504] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/27/2021] [Indexed: 11/13/2022]  Open
6
Wu J, Liu H, Lu S, Hua J, Zou B. Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice. Genome 2020;64:515-524. [PMID: 33049157 DOI: 10.1139/gen-2020-0007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
7
Sternburg EL, Karginov FV. Global Approaches in Studying RNA-Binding Protein Interaction Networks. Trends Biochem Sci 2020;45:593-603. [DOI: 10.1016/j.tibs.2020.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/24/2022]
8
Lang B, Armaos A, Tartaglia GG. RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. Nucleic Acids Res 2020;47:D601-D606. [PMID: 30445601 PMCID: PMC6324028 DOI: 10.1093/nar/gky967] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/11/2018] [Indexed: 01/15/2023]  Open
9
Cid-Samper F, Gelabert-Baldrich M, Lang B, Lorenzo-Gotor N, Ponti RD, Severijnen LAWFM, Bolognesi B, Gelpi E, Hukema RK, Botta-Orfila T, Tartaglia GG. An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome. Cell Rep 2019;25:3422-3434.e7. [PMID: 30566867 PMCID: PMC6315285 DOI: 10.1016/j.celrep.2018.11.076] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/26/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022]  Open
10
Sabalette KB, Romaniuk MA, Noé G, Cassola A, Campo VA, De Gaudenzi JG. The RNA-binding protein TcUBP1 up-regulates an RNA regulon for a cell surface-associated Trypanosoma cruzi glycoprotein and promotes parasite infectivity. J Biol Chem 2019;294:10349-10364. [PMID: 31113862 DOI: 10.1074/jbc.ra118.007123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/06/2019] [Indexed: 11/06/2022]  Open
11
MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death Differ 2019;26:2157-2178. [PMID: 30728462 DOI: 10.1038/s41418-019-0291-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/22/2023]  Open
12
Novel insights into global translational regulation through Pumilio family RNA-binding protein Puf3p revealed by ribosomal profiling. Curr Genet 2018;65:201-212. [PMID: 29951697 DOI: 10.1007/s00294-018-0862-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023]
13
Dassi E. Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins. Front Mol Biosci 2017;4:67. [PMID: 29034245 PMCID: PMC5626838 DOI: 10.3389/fmolb.2017.00067] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/20/2017] [Indexed: 12/31/2022]  Open
14
Kumachi S, Husimi Y, Nemoto N. An RNA Binding Peptide Consisting of Four Types of Amino Acid by in Vitro Selection Using cDNA Display. ACS OMEGA 2016;1:52-57. [PMID: 30023471 PMCID: PMC6044570 DOI: 10.1021/acsomega.6b00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/17/2016] [Indexed: 05/06/2023]
15
Guo C, Xue Y, Yang G, Yin S, Shi W, Cheng Y, Yan X, Fan S, Zhang H, Zeng F. Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells. Cell Biol Int 2016;40:847-60. [PMID: 26289635 DOI: 10.1002/cbin.10539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/15/2015] [Indexed: 02/05/2023]
16
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. Sci Rep 2016;6:25711. [PMID: 27161996 PMCID: PMC4861959 DOI: 10.1038/srep25711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]  Open
17
Colombrita C, Onesto E, Buratti E, de la Grange P, Gumina V, Baralle FE, Silani V, Ratti A. From transcriptomic to protein level changes in TDP-43 and FUS loss-of-function cell models. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015;1849:1398-410. [PMID: 26514432 DOI: 10.1016/j.bbagrm.2015.10.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/08/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022]
18
MicroRNA buffering and altered variance of gene expression in response to Salmonella infection. PLoS One 2014;9:e94352. [PMID: 24718561 PMCID: PMC3981782 DOI: 10.1371/journal.pone.0094352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/13/2014] [Indexed: 11/20/2022]  Open
19
Kechavarzi B, Janga SC. Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol 2014;15:R14. [PMID: 24410894 PMCID: PMC4053825 DOI: 10.1186/gb-2014-15-1-r14] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/10/2014] [Indexed: 01/10/2023]  Open
20
Bencharit S, Border MB. Where are we in the world of proteomics and bioinformatics? Expert Rev Proteomics 2013. [PMID: 23194265 DOI: 10.1586/epr.12.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
21
Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D’Onofrio M, Riva P, Quattrone A. Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. Nucleic Acids Res 2013;41:3201-16. [PMID: 23376935 PMCID: PMC3597683 DOI: 10.1093/nar/gkt017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 02/06/2023]  Open
22
Denti MA, Viero G, Provenzani A, Quattrone A, Macchi P. mRNA fate: Life and death of the mRNA in the cytoplasm. RNA Biol 2013;10:360-6. [PMID: 23466755 DOI: 10.4161/rna.23770] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
23
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3-GENES GENOMES GENETICS 2013;3:297-304. [PMID: 23390605 PMCID: PMC3564989 DOI: 10.1534/g3.112.004390] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/10/2012] [Indexed: 02/06/2023]
24
Janga SC. From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks. Brief Funct Genomics 2012;11:505-21. [PMID: 23124862 DOI: 10.1093/bfgp/els046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
25
Tebaldi T, Re A, Viero G, Pegoretti I, Passerini A, Blanzieri E, Quattrone A. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics 2012;13:220. [PMID: 22672192 PMCID: PMC3441405 DOI: 10.1186/1471-2164-13-220] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/06/2012] [Indexed: 11/10/2022]  Open
26
Joshi A, Beck Y, Michoel T. Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals. FEBS J 2012;279:3501-12. [PMID: 22436024 DOI: 10.1111/j.1742-4658.2012.08571.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Ashworth J, Wurtmann EJ, Baliga NS. Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol 2011;23:598-603. [PMID: 22209016 DOI: 10.1016/j.copbio.2011.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
28
Arvas M, Pakula T, Smit B, Rautio J, Koivistoinen H, Jouhten P, Lindfors E, Wiebe M, Penttilä M, Saloheimo M. Correlation of gene expression and protein production rate - a system wide study. BMC Genomics 2011;12:616. [PMID: 22185473 PMCID: PMC3266662 DOI: 10.1186/1471-2164-12-616] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/20/2011] [Indexed: 11/10/2022]  Open
29
Duncan CDS, Mata J. Widespread cotranslational formation of protein complexes. PLoS Genet 2011;7:e1002398. [PMID: 22144913 PMCID: PMC3228823 DOI: 10.1371/journal.pgen.1002398] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/11/2011] [Indexed: 12/28/2022]  Open
30
Joshi A, Van de Peer Y, Michoel T. Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast. Nucleic Acids Res 2011;39:9108-17. [PMID: 21840901 PMCID: PMC3241661 DOI: 10.1093/nar/gkr661] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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