Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Science China Life Sciences

Volumn 57, Issue 1, 2014, Pages 22-35

  Yang, YuCheng ^a   Umetsu, Jumpei ^a,b   Lu, Zhi John ^a  

^a TSINGHUA UNIVERSITY   (China)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

non coding RNA; RNA binding protein; RNA structure; Saccharomyces cerevisiae; UTR

Indexed keywords

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

FUNGAL RNA; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTOME;

ARTICLE; FUNGAL GENOME; GENETICS; METABOLISM; PROTEIN BINDING; RNA PROCESSING; SACCHAROMYCES CEREVISIAE;

GENOME, FUNGAL; PROTEIN BINDING; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTOME;

EID: 84891901081     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-013-4583-0     Document Type: Article

References (56)

1. Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet, 2007, 8: 533-543.
2. Moore MJ. From birth to death: the complex lives of eukaryotic mRNAs. Science, 2005, 309: 1514-1518.
3. Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol, 2007, 8: 479-490.
4. Kedde M, Strasser MJ, Boldajipour B, Oude Vrielink JA, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Orom UA, Lund AH, Perrakis A, Raz E, Agami R. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell, 2007, 131: 1273-1286.
5. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol, 2008, 6: e255.
6. Jamonnak N, Creamer TJ, Darby MM, Schaughency P, Wheelan SJ, Corden JL. Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA, 2011, 17: 2011-2025.
7. Granneman S, Petfalski E, Swiatkowska A, Tollervey D. Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking. EMBO J, 2010, 29: 2026-2036.
8. 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: 9108-9117.
9. Lukong KE, Chang KW, Khandjian EW, Richard S. RNA-binding proteins in human genetic disease. Trends Genet, 2008, 24: 416-425.
10. Iwakiri J, Tateishi H, Chakraborty A, Patil P, Kenmochi N. Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition. Nucleic Acids Res, 2012, 40: 3299-3306.
11. Valley CT, Porter DF, Qiu C, Campbell ZT, Hall TM, Wickens M. Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site. Proc Natl Acad Sci USA, 2012, 109: 6054-6059.
12. Oberstrass FC, Lee A, Stefl R, Janis M, Chanfreau G, Allain FH. Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol, 2006, 13: 160-167.
13. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. Hits-clip yields genome-wide insights into brain alternative RNA processing. Nature, 2008, 456: 464-469.
14. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr., Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 2010, 141: 129-141.
15. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol, 2010, 17: 909-915.
16. Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Site identification in high-throughput RNA-protein interaction data. Bioinformatics, 2012, 28: 3013-3020.
17. Zhang C, Darnell RB. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechol, 2011, 29: 607-614.
18. Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. Paralyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol, 2011, 12: R79.
19. Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol, 2013, 14: R13.
20. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 2009, 10: R25.
21. Quinlan AR, Hall IM. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 2010, 26: 841-842.
22. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 2008, 320: 1344-1349.
23. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. The structure of the eukaryotic ribosome at 3. 0 Å resolution. Science, 2011, 334: 1524-1529.
24. Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res, 2003, 31: 3450-3460.
25. Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J. tRNAdb 2009: Compilation of tRNA sequences and tRNA genes. Nucleic Acids Res, 2009, 37: D159-162.
26. Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 2009, 25: 1974-1975.
27. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA, 2002, 99: 5860-5865.
28. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protocols, 2012, 7: 562-578.
29. Gruber AR, Findeiss S, Washietl S, Hofacker IL, Stadler PF. Rnaz 2. 0: Improved noncoding RNA detection. In: Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, 2010. 69-79.
30. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007, 35: W345-349.
31. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res, 2011, 39: D146-151.
32. Rabani M, Kertesz M, Segal E. Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci USA, 2008, 105: 14885-14890.
33. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature, 2010, 467: 103-107.
34. Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K. Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol, 2007, 5: 25.
35. Karaduman R, Fabrizio P, Hartmuth K, Urlaub H, Luhrmann R. RNA structure and RNA-protein interactions in purified yeast U6 snRNPs. J Mol Biol, 2006, 356: 1248-1262.
36. Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hill R, Hansen KC, Hesselberth JR, Zhao R. Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. Nucleic Acids Res, 2013, 41: 3805-3818.
37. Esakova O, Krasilnikov AS. Of proteins and RNA: the RNase P/MRP family. RNA, 2010, 16: 1725-1747.
38. Davila Lopez M, Rosenblad MA, Samuelsson T. Conserved and variable domains of RNase MRP RNA. RNA Biol, 2009, 6: 208-220.
39. Esakova O, Perederina A, Quan C, Schmitt ME, Krasilnikov AS. Footprinting analysis demonstrates extensive similarity between eukaryotic RNase P and RNase MRP holoenzymes. RNA, 2008, 14: 1558-1567.
40. Melnikov S, Ben-Shem A, Garreau de Loubresse N, Jenner L, Yusupova G, Yusupov M. One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol, 2012, 19: 560-567.
41. Wilson DN, Doudna Cate JH. The structure and function of the eu karyotic ribosome. Cold Spring Harbor Perspect Biol, 2012, 4, pii: a011536.
42. Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N. Atomic structures of the eukaryotic ribosome. Trends Biochem Sci, 2012, 37: 189-198.
43. Ben-Shem A, Jenner L, Yusupova G, Yusupov M. Crystal structure of the eukaryotic ribosome. Science, 2010, 330: 1203-1209.
44. Leshin JA, Heselpoth R, Belew AT, Dinman J. High throughput structural analysis of yeast ribosomes using hSHAPE. RNA Biol, 2011, 8: 478-487.
45. Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol, 2012, 19: 900-905.
46. Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell, 2012, 149: 202-213.
47. Waas WF, Druzina Z, Hanan M, Schimmel P. Role of a tRNA base modification and its precursors in frameshifting in eukaryotes. J Biol Chem, 2007, 282: 26026-26034.
48. Persson BC. Modification of tRNA as a regulatory device. Mol Microbiol, 1993, 8: 1011-1016.
49. Alexander RW, Eargle J, Luthey-Schulten Z. Experimental and computational determination of tRNA dynamics. FEBS Lett, 2010, 584: 376-386.
50. Olivier C, Poirier G, Gendron P, Boisgontier A, Major F, Chartrand P. Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol Cell Biol, 2005, 25: 4752-4766.
51. Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, Takizawa PA, DeRisi JL. Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae. Proc Natl Acad Sci USA, 2005, 102: 18005-18010.
52. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. Meme suite: Tools for motif discovery and searching. Nucleic Acids Res, 2009, 37: W202-208.
53. Rodriguez-Gabriel MA, Burns G, McDonald WH, Martin V, Yates JR 3rd, Bahler J, Russell P. RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress. EMBO J, 2003, 22: 6256-6266.
54. Satoh R, Tanaka A, Kita A, Morita T, Matsumura Y, Umeda N, Takada M, Hayashi S, Tani T, Shinmyozu K, Sugiura R. Role of the RNA-binding protein Nrd1 in stress granule formation and its implication in the stress response in fission yeast. PLoS ONE, 2012, 7: e29683.
55. Jung HJ, Kim MK, Kang H. An ABA-regulated putative RNA-binding protein affects seed germination of Arabidopsis under ABA or abiotic stress conditions. J Plant Physiol, 2013, 170: 179-184.
56. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature, 2012, 482: 339-346.