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For: Zhang L, Lin J, Ye K. Structural and functional analysis of the U3 snoRNA binding protein Rrp9. RNA 2013;19:701-711. [PMID: 23509373 PMCID: PMC3677284 DOI: 10.1261/rna.037580.112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/06/2013] [Indexed: 06/01/2023]
Number Cited by Other Article(s)
1
Lin R, Elmir E, Reynolds MJ, Johnson AW. In vitro characterization of the yeast DEAH/RHA RNA helicase Dhr1. J Biol Chem 2025;301:108366. [PMID: 40024476 PMCID: PMC11994318 DOI: 10.1016/j.jbc.2025.108366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 01/31/2025] [Accepted: 02/12/2025] [Indexed: 03/04/2025]  Open
2
Karan A, Rivas E. All-at-once RNA folding with 3D motif prediction framed by evolutionary information. RESEARCH SQUARE 2025:rs.3.rs-5664139. [PMID: 40195991 PMCID: PMC11974997 DOI: 10.21203/rs.3.rs-5664139/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
3
Song Z, Bae B, Schnabl S, Yuan F, De Zoysa T, Akinyi MV, Le Roux CA, Choquet K, Whipple AJ, Van Nostrand EL. Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP. Genome Biol 2025;26:39. [PMID: 40001124 PMCID: PMC11863803 DOI: 10.1186/s13059-025-03508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/13/2025] [Indexed: 02/27/2025]  Open
4
Karan A, Rivas E. All-at-once RNA folding with 3D motif prediction framed by evolutionary information. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.17.628809. [PMID: 39764046 PMCID: PMC11702757 DOI: 10.1101/2024.12.17.628809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2025]
5
Chen W, Zhang L, Zhong G, Liu S, Sun Y, Zhang J, Liu Z, Wang L. Regulation of microglia inflammation and oligodendrocyte demyelination by Engeletin via the TLR4/RRP9/NF-κB pathway after spinal cord injury. Pharmacol Res 2024;209:107448. [PMID: 39395773 DOI: 10.1016/j.phrs.2024.107448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/19/2024] [Accepted: 10/01/2024] [Indexed: 10/14/2024]
6
Aikio E, Koivukoski S, Kallio E, Sadeesh N, Niskanen EA, Latonen L. Complementary analysis of proteome-wide proteomics reveals changes in RNA binding protein-profiles during prostate cancer progression. Cancer Rep (Hoboken) 2023;6:e1886. [PMID: 37591798 PMCID: PMC10598248 DOI: 10.1002/cnr2.1886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/19/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023]  Open
7
Kumar S, Shuaib M, AlAsmari AF, Alqahtani F, Gupta S. GNL3 and PA2G4 as Prognostic Biomarkers in Prostate Cancer. Cancers (Basel) 2023;15:2723. [PMID: 37345060 PMCID: PMC10216705 DOI: 10.3390/cancers15102723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/23/2023]  Open
8
Zhang Z, Yu H, Yao W, Zhu N, Miao R, Liu Z, Song X, Xue C, Cai C, Cheng M, Lin K, Qi D. RRP9 promotes gemcitabine resistance in pancreatic cancer via activating AKT signaling pathway. Cell Commun Signal 2022;20:188. [PMID: 36434608 PMCID: PMC9700947 DOI: 10.1186/s12964-022-00974-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]  Open
9
Du MG, Liu F, Chang Y, Tong S, Liu W, Chen YJ, Xie P. Neddylation modification of the U3 snoRNA-binding protein RRP9 by Smurf1 promotes tumorigenesis. J Biol Chem 2021;297:101307. [PMID: 34662580 PMCID: PMC8569593 DOI: 10.1016/j.jbc.2021.101307] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/29/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]  Open
10
Streit D, Shanmugam T, Garbelyanski A, Simm S, Schleiff E. The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited. PLANTS (BASEL, SWITZERLAND) 2020;9:E1016. [PMID: 32806552 PMCID: PMC7464842 DOI: 10.3390/plants9081016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
11
Clerget G, Bourguignon-Igel V, Marmier-Gourrier N, Rolland N, Wacheul L, Manival X, Charron C, Kufel J, Méreau A, Senty-Ségault V, Tollervey D, Lafontaine DLJ, Branlant C, Rederstorff M. Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA. Nucleic Acids Res 2020;48:3848-3868. [PMID: 31996908 PMCID: PMC7144924 DOI: 10.1093/nar/gkaa066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/24/2023]  Open
12
Ribosome assembly coming into focus. Nat Rev Mol Cell Biol 2019;20:116-131. [PMID: 30467428 DOI: 10.1038/s41580-018-0078-y] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
13
Francisco-Velilla R, Azman EB, Martinez-Salas E. Impact of RNA-Protein Interaction Modes on Translation Control: The Versatile Multidomain Protein Gemin5. Bioessays 2019;41:e1800241. [PMID: 30919488 DOI: 10.1002/bies.201800241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/04/2019] [Indexed: 12/12/2022]
14
Rippin M, Borchhardt N, Karsten U, Becker B. Cold Acclimation Improves the Desiccation Stress Resilience of Polar Strains of Klebsormidium (Streptophyta). Front Microbiol 2019;10:1730. [PMID: 31447802 PMCID: PMC6691101 DOI: 10.3389/fmicb.2019.01730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022]  Open
15
Dudnakova T, Dunn-Davies H, Peters R, Tollervey D. Mapping targets for small nucleolar RNAs in yeast. Wellcome Open Res 2018;3:120. [PMID: 30345388 PMCID: PMC6171561 DOI: 10.12688/wellcomeopenres.14735.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 12/15/2022]  Open
16
Dudnakova T, Dunn-Davies H, Peters R, Tollervey D. Mapping targets for small nucleolar RNAs in yeast. Wellcome Open Res 2018;3:120. [PMID: 30345388 PMCID: PMC6171561 DOI: 10.12688/wellcomeopenres.14735.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 02/15/2024]  Open
17
Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. Curr Opin Struct Biol 2018;49:85-93. [PMID: 29414516 DOI: 10.1016/j.sbi.2018.01.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
18
Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S. The complete structure of the small-subunit processome. Nat Struct Mol Biol 2017;24:944-953. [PMID: 28945246 DOI: 10.1038/nsmb.3472] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023]
19
Rothé B, Manival X, Rolland N, Charron C, Senty-Ségault V, Branlant C, Charpentier B. Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly. Nucleic Acids Res 2017;45:7455-7473. [PMID: 28505348 PMCID: PMC5499572 DOI: 10.1093/nar/gkx424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/02/2017] [Indexed: 01/23/2023]  Open
20
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. eLife 2017;6. [PMID: 28244370 PMCID: PMC5354517 DOI: 10.7554/elife.22086] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/26/2017] [Indexed: 12/12/2022]  Open
21
Chaker-Margot M, Barandun J, Hunziker M, Klinge S. Architecture of the yeast small subunit processome. Science 2016;355:science.aal1880. [PMID: 27980088 DOI: 10.1126/science.aal1880] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
22
Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI. Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. BMC Genomics 2016;17:691. [PMID: 27576499 PMCID: PMC5006418 DOI: 10.1186/s12864-016-2934-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/12/2016] [Indexed: 01/08/2023]  Open
23
Zhang C, Sun Q, Chen R, Chen X, Lin J, Ye K. Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits. Nucleic Acids Res 2016;44:7475-86. [PMID: 27330138 PMCID: PMC5009746 DOI: 10.1093/nar/gkw562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/10/2016] [Indexed: 12/28/2022]  Open
24
Chen S, Blank MF, Iyer A, Huang B, Wang L, Grummt I, Voit R. SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing. Nat Commun 2016;7:10734. [PMID: 26867678 PMCID: PMC4754350 DOI: 10.1038/ncomms10734] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023]  Open
25
Zheng S, Lan P, Liu X, Ye K. Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. J Biol Chem 2014;289:22692-22703. [PMID: 24990943 DOI: 10.1074/jbc.m114.584490] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
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