Corrigendum: Mod-seq: High-throughput sequencing for chemical probing of RNA structure(RNA. May(2014)20:5(713-20) DOI: 10.1261/rna.042218.113);Mod-seq: High-throughput sequencing for chemical probing of RNA structure

RNA

Volumn 20, Issue 5, 2014, Pages 713-720

  Talkish, Jason ^a   May, Gemma ^a   Lin, Yizhu ^a   Woolford Jr , John L ^a   McManus, C Joel ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

High throughput sequencing; RNA structure; RNA binding protein

Indexed keywords

DIMETHYL SULFATE; RIBOSOMAL PROTEIN L26; RIBOSOME PROTEIN; RIBOSOME RNA; RNA; RNA DIRECTED DNA POLYMERASE; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BINDING SITE; CHEMICAL ANALYSIS; CHEMICAL PROBING; CONTROLLED STUDY; DELETION MUTANT; HIGH THROUGHPUT SEQUENCING; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION; RNA SEQUENCE; RNA STRUCTURE; YEAST;

HIGH-THROUGHPUT SEQUENCING; RNA STRUCTURE; RNA-BINDING PROTEIN;

BINDING SITES; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; RNA, RIBOSOMAL; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84898949357     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.072405.119     Document Type: Erratum

References (32)

1. Babiano R, Gamalinda M, Woolford JL Jr., de la Cruz J. 2012. Saccharomyces cerevisiae ribosomal protein L26 is not essential for ribosome assembly and function. Mol Cell Biol 32: 3228-3241.
2. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B (Methodological) 57: 289-300.
3. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. 2011. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334: 1524-1529.
4. Brar GA, Rouskin S, McGeachy AM, Ingolia NT, Weissman JS. 2012. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7: 1534-1550.
5. Brunel C, Romby P. 2000. Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol 318: 3-21. (Pubitemid 30421636)
6. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, et al. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
7. Cruz JA, Westhof E. 2009. The dynamic landscapes of RNA architecture. Cell 136: 604-609.
8. Deigan KE, LiTW, Mathews DH, Weeks KM. 2009. Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci 106: 97-102.
9. Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. 2013. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505: 696-700.
10. Horsey EW, Jakovljevic J, Miles TD, Harnpicharnchai P, Woolford JL Jr. 2004. Role of the yeast Rrp1 protein in the dynamics of pre-ribosome maturation. RNA 10: 813-827. (Pubitemid 38529745)
11. Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802.
12. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. 2010. Genome-wide measurement of RNA secondary structure in yeast. Nature 467: 103-107.
13. Langmead B, Trapnell C, Pop M, Salzberg S. 2009. Ultrafast and memory- efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
14. Lau NC, Lim LP, Weinstein EG, Bartel DP. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862. (Pubitemid 33032104)
15. Lawley PD, Brookes P. 1963. Further studies on the alkylation of nucleic acids and their constituent nucleotides. Biochem J 89: 127-138.
16. Leland PA, Raines RT. 2001. Cancer chemotherapy-ribonucleases to the rescue. Chem Biol 8: 405-413.
17. Leshin JA, Heselpoth R, Belew AT, Dinman J. 2011. High throughput structural analysis of yeast ribosomes using hSHAPE. RNA Biol 8: 478-487.
18. Liebeg A, Waldsich C. 2009. Probing RNA structure within living cells. Methods Enzymol 468: 219-238.
19. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. 2011. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci 108: 11063-11068.
20. Martin M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnetjournal 17: 10-12.
21. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM. 2005. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127: 4223-4231. (Pubitemid 40463047)
22. Moazed D, Noller HF. 1986. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47: 985-994. (Pubitemid 17005071)
23. Peattie DA, Gilbert W. 1980. Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci 77: 4679-4682.
24. Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. 2013. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505: 701-705.
25. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY. 2012. RNA SHAPE analysis in living cells. Nat Chem Biol 9: 18-20.
26. Stern S, Moazed D, Noller HF. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol 164: 481-489. (Pubitemid 19067612)
27. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. 2010. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7: 995-1001.
28. Watts JM, Dang KK, Gorelick RJ, LeonardCW, Bess JW Jr, Swanstrom R, Burch CL, Weeks KM. 2009. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460: 711-716.
29. Weeks KM. 2010. Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol 20: 295-304.
30. Wells SE, Hughes JMX, Igel AH, Ares M. 2000. Use of dimethylsulfate to probe RNA structure in vivo. Methods Enzymol 318: 479-493. (Pubitemid 30421667)
31. Westhof E, Romby P. 2010. The RNA structurome: high-throughput probing. Nat Methods 7: 965-967.
32. Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM. 2008. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6: e96.