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For: Burlacu E, Lackmann F, Aguilar LC, Belikov S, Nues RV, Trahan C, Hector RD, Dominelli-Whiteley N, Cockroft SL, Wieslander L, Oeffinger M, Granneman S. High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast. Nat Commun 2017;8:714. [PMID: 28959008 DOI: 10.1038/s41467-017-00761-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/26/2017] [Indexed: 11/25/2022]  Open
Number Cited by Other Article(s)
1
Mitterer V, Hamze H, Kunowska N, Stelzl U, Henras A, Hurt E. The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis. Nucleic Acids Res 2024;52:1975-1987. [PMID: 38113283 PMCID: PMC10899779 DOI: 10.1093/nar/gkad1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]  Open
2
Fernández-Fernández J, Martín-Villanueva S, Perez-Fernandez J, de la Cruz J. The Role of Ribosomal Proteins eL15 and eL36 in the Early Steps of Yeast 60S Ribosomal Subunit Assembly. J Mol Biol 2023;435:168321. [PMID: 37865285 DOI: 10.1016/j.jmb.2023.168321] [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] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
3
Sanghai ZA, Piwowarczyk R, Broeck AV, Klinge S. A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation. Nat Struct Mol Biol 2023;30:594-599. [PMID: 37037974 DOI: 10.1038/s41594-023-00947-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/24/2023] [Indexed: 04/12/2023]
4
Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023;42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023]  Open
5
Khreiss A, Capeyrou R, Lebaron S, Albert B, Bohnsack K, Bohnsack M, Henry Y, Henras A, Humbert O. The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome. Nucleic Acids Res 2023;51:744-764. [PMID: 36610750 PMCID: PMC9881158 DOI: 10.1093/nar/gkac1196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]  Open
6
Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP. Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Nat Struct Mol Biol 2022;29:1228-1238. [PMID: 36482249 PMCID: PMC10680166 DOI: 10.1038/s41594-022-00874-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
7
Liu X, Huang H, Karbstein K. Using DMS-MaPseq to Uncover the Roles of DEAD-box Proteins in Ribosome Assembly. Methods 2022;204:249-257. [PMID: 35550176 PMCID: PMC10152975 DOI: 10.1016/j.ymeth.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 12/20/2022]  Open
8
Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 40S Subunit. Acta Naturae 2022;14:14-30. [PMID: 35441050 PMCID: PMC9013438 DOI: 10.32607/actanaturae.11540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/02/2022] [Indexed: 11/29/2022]  Open
9
Mitterer V, Pertschy B. RNA folding and functions of RNA helicases in ribosome biogenesis. RNA Biol 2022;19:781-810. [PMID: 35678541 PMCID: PMC9196750 DOI: 10.1080/15476286.2022.2079890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022]  Open
10
Corsaro D. Insights into Microsporidia Evolution from Early Diverging Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022;114:71-90. [PMID: 35543999 DOI: 10.1007/978-3-030-93306-7_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
11
Pöll G, Pilsl M, Griesenbeck J, Tschochner H, Milkereit P. Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. PLoS One 2021;16:e0252497. [PMID: 34813592 PMCID: PMC8610266 DOI: 10.1371/journal.pone.0252497] [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: 05/14/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022]  Open
12
Jaafar M, Contreras J, Dominique C, Martín-Villanueva S, Capeyrou R, Vitali P, Rodríguez-Galán O, Velasco C, Humbert O, Watkins NJ, Villalobo E, Bohnsack KE, Bohnsack MT, Henry Y, Merhi RA, de la Cruz J, Henras AK. Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast. Nat Commun 2021;12:6153. [PMID: 34686656 PMCID: PMC8536666 DOI: 10.1038/s41467-021-26207-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/22/2021] [Indexed: 12/15/2022]  Open
13
Aquino GRR, Hackert P, Krogh N, Pan KT, Jaafar M, Henras AK, Nielsen H, Urlaub H, Bohnsack KE, Bohnsack MT. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly. Nat Commun 2021;12:6152. [PMID: 34686661 PMCID: PMC8536713 DOI: 10.1038/s41467-021-26208-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/22/2021] [Indexed: 02/07/2023]  Open
14
Knüppel R, Fenk M, Jüttner M, Ferreira-Cerca S. In Vivo RNA Chemical Footprinting Analysis in Archaea. Methods Mol Biol 2021;2106:193-208. [PMID: 31889259 DOI: 10.1007/978-1-0716-0231-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
15
Marangio P, Law KYT, Sanguinetti G, Granneman S. diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data. Genome Biol 2021;22:165. [PMID: 34044851 PMCID: PMC8157727 DOI: 10.1186/s13059-021-02379-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/10/2021] [Indexed: 11/21/2022]  Open
16
Zhang W, Tian W, Gao Z, Wang G, Zhao H. Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint. Int J Mol Sci 2020;21:ijms21176395. [PMID: 32899108 PMCID: PMC7504139 DOI: 10.3390/ijms21176395] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023]  Open
17
Ramos-Sáenz A, González-Álvarez D, Rodríguez-Galán O, Rodríguez-Gil A, Gaspar SG, Villalobo E, Dosil M, de la Cruz J. Pol5 is an essential ribosome biogenesis factor required for 60S ribosomal subunit maturation in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2019;25:1561-1575. [PMID: 31413149 PMCID: PMC6795146 DOI: 10.1261/rna.072116.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
18
Pillon MC, Lo YH, Stanley RE. IT'S 2 for the price of 1: Multifaceted ITS2 processing machines in RNA and DNA maintenance. DNA Repair (Amst) 2019;81:102653. [PMID: 31324529 PMCID: PMC6764878 DOI: 10.1016/j.dnarep.2019.102653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
19
Palm D, Streit D, Shanmugam T, Weis BL, Ruprecht M, Simm S, Schleiff E. Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. Nucleic Acids Res 2019;47:1880-1895. [PMID: 30576513 PMCID: PMC6393314 DOI: 10.1093/nar/gky1261] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022]  Open
20
Espinar-Marchena F, Rodríguez-Galán O, Fernández-Fernández J, Linnemann J, de la Cruz J. Ribosomal protein L14 contributes to the early assembly of 60S ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Res 2019;46:4715-4732. [PMID: 29788267 PMCID: PMC5961077 DOI: 10.1093/nar/gky123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]  Open
21
Strobel EJ, Yu AM, Lucks JB. High-throughput determination of RNA structures. Nat Rev Genet 2019;19:615-634. [PMID: 30054568 DOI: 10.1038/s41576-018-0034-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
22
Lackmann F, Belikov S, Burlacu E, Granneman S, Wieslander L. Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements. Nucleic Acids Res 2019;46:3692-3706. [PMID: 29373706 PMCID: PMC5909432 DOI: 10.1093/nar/gky036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/15/2018] [Indexed: 01/25/2023]  Open
23
Co-Assembly of 40S and 60S Ribosomal Proteins in Early Steps of Eukaryotic Ribosome Assembly. Int J Mol Sci 2019;20:ijms20112806. [PMID: 31181743 PMCID: PMC6600400 DOI: 10.3390/ijms20112806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/28/2019] [Accepted: 06/06/2019] [Indexed: 01/21/2023]  Open
24
Chaker-Margot M, Klinge S. Assembly and early maturation of large subunit precursors. RNA (NEW YORK, N.Y.) 2019;25:465-471. [PMID: 30670483 PMCID: PMC6426289 DOI: 10.1261/rna.069799.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
25
Choudhary K, Lai YH, Tran EJ, Aviran S. dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome Biol 2019;20:40. [PMID: 30791935 PMCID: PMC6385470 DOI: 10.1186/s13059-019-1641-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/24/2019] [Indexed: 12/16/2022]  Open
26
RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes. Nat Commun 2018;9:5383. [PMID: 30568249 PMCID: PMC6300602 DOI: 10.1038/s41467-018-07783-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 11/28/2018] [Indexed: 01/31/2023]  Open
27
Mailler E, Paillart JC, Marquet R, Smyth RP, Vivet-Boudou V. The evolution of RNA structural probing methods: From gels to next-generation sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018;10:e1518. [PMID: 30485688 DOI: 10.1002/wrna.1518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/13/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023]
28
Joret C, Capeyrou R, Belhabich-Baumas K, Plisson-Chastang C, Ghandour R, Humbert O, Fribourg S, Leulliot N, Lebaron S, Henras AK, Henry Y. The Npa1p complex chaperones the assembly of the earliest eukaryotic large ribosomal subunit precursor. PLoS Genet 2018;14:e1007597. [PMID: 30169518 PMCID: PMC6136799 DOI: 10.1371/journal.pgen.1007597] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 09/13/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022]  Open
29
Wang D, McAteer SP, Wawszczyk AB, Russell CD, Tahoun A, Elmi A, Cockroft SL, Tollervey D, Granneman S, Tree JJ, Gally DL. An RNA-dependent mechanism for transient expression of bacterial translocation filaments. Nucleic Acids Res 2018;46:3366-3381. [PMID: 29432565 PMCID: PMC5909449 DOI: 10.1093/nar/gky096] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/28/2018] [Accepted: 02/06/2018] [Indexed: 12/31/2022]  Open
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