Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-Seq Protocol

Methods in Molecular Biology

Volumn 1086, Issue , 2014, Pages 95-117

  Seetin, Matthew G ^a   Kladwang, Wipapat ^a   Bida, John P ^a   Das, Rhiju ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Chemical mapping; Footprinting; High throughput sequencing; Multiplexing; RNA structure

Indexed keywords

REAGENT; RNA;

ALGORITHM; ANALYTIC METHOD; ARTICLE; CHEMICAL MODIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; MACHINE; MEASUREMENT ERROR; MOLECULAR PROBE; MULTIPLEXED ACCESSIBILITY PROBING READ OUT THROUGH SEQUENCING 1; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; RNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84934435385     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-667-2_6     Document Type: Article

References (38)

1. Ban N, Nissen P, Hansen J et al (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289:905-920
2. Guerrier-Takada C, Gardiner K, Marsh T et al (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-857
3. Cech TR, Zaug AJ, Grabowski PJ (1981) In vitro splicing of the ribosomal RNA precursor of Tetrahymena : involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27:487-496
4. Fire A, Xu S, Montgomery MK et al (1998) Potent and specifi c genetic interference by double-stranded RNA in Caenorhabditis elegans . Nature 391:806-811
5. Greider CW, Blackburn EH (1985) Identifi cation of a specifi c telomere terminal transferase activity in Tetrahymena extracts. Cell 43:405-413
6. Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301-310
7. Pace NR, Thomas BC, Woese CR (1999) Probing RNA structure, function, and history by comparative analysis. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 113-141
8. Sripakdeevong P, Kladwang W, Das R (2011) An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci USA 108:20573-20578
9. Wang Z, Parisien M, Scheets K et al (2011) The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral capindependent translation element. Structure 19:868-880
10. Flores SC, Altman RB (2010) Turning limited experimental information into 3D models of RNA. RNA 16:1769-1778
11. Kladwang W, Cordero P, Das R (2011) A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA 17:522-534
12. Cordero P, Kladwang W, VanLang CC et al (2012) Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry 51:7037-7039
13. Bida JP, Das R (2012) Squaring theory with practice in RNA design. Curr Opin Struct Biol 22:457-466
14. Mortimer SA, Johnson JS, Weeks KM (2009) Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine. Biochemistry 48:2109-2114
15. Regulski EE, Breaker RR (2008) In-line probing analysis of riboswitches. Methods Mol Biol 419:53-67
16. Miura K, Tsuda S, Ueda T et al (1983) Chemical modifi cation of guanine residues of mouse 5 S ribosomal RNA with kethoxal. (Nucleosides and nucleotides 46). Biochim Biophys Acta 739:281-285
17. Inoue T, Cech TR (1985) Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. Proc Natl Acad Sci USA 82:648-652
18. Ehresmann C, Baudin F, Mougel M et al (1987) Probing the structure of RNAs in solution. Nucleic Acids Res 15:9109-9128
19. Fritz JJ, Lewin A, Hauswirth W et al (2002) Development of hammerhead ribozymes to modulate endogenous gene expression for functional studies. Methods 28:276-285
20. Rocca-Serra P, Bellaousov S, Birmingham A et al (2011) Sharing and archiving nucleic acid structure mapping data. RNA 17:1204-1212
21. Merino EJ, Wilkinson KA, Coughlan JL et al (2005) RNA structure analysis at single nucleotide resolution by selective 2?-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127:4223-4231
22. Mortimer SA, Weeks KM (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc 129:4144-4145
23. Kertesz M, Wan Y, Mazor E et al (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467:103-107
24. Underwood JG, Uzilov AV, Katzman S et al (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7:995-1001
25. Zheng Q, Ryvkin P, Li F et al (2010) Genomewide double-stranded RNA sequencing reveals the functional signifi cance of base-paired RNAs in Arabidopsis . PLoS Genet 6
26. Lucks JB, Mortimer SA, Trapnell C et al (2011) Multiplexed RNA structure characterization with selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci USA 108: 11063-11068
27. Aviran S, Trapnell C, Lucks JB et al (2011) Modeling and automation of sequencingbased characterization of RNA structure. Proc Natl Acad Sci USA 108:11069-11074
28. Ziehler WA, Engelke DR (2001) Probing RNA structure with chemical reagents and enzymes. Curr Protoc Nucleic Acid Chem Chapter 6, Unit 6 1
29. Blondal T, Thorisdottir A, Unnsteinsdottir U et al (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res 33:135-142
30. Li TW, Weeks KM (2006) Structureindependent and quantitative ligation of singlestranded DNA. Anal Biochem 349: 242-246
31. Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-effi cient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
32. Langmead B, Salzberg SL (2012) Fast gappedread alignment with Bowtie 2. Nat Methods 9:357-359
33. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760
34. Torchia C, Takagi Y, Ho CK (2008) Archaeal RNA ligase is a homodimeric protein that catalyzes intramolecular ligation of single-stranded RNA and DNA. Nucleic Acids Res 36: 6218-6227
35. Zhelkovsky AM, McReynolds LA (2012) Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase-engineering a thermostable ATP independent enzyme. BMC Mol Biol 13:24
36. Yoon S, Kim J, Hum J et al (2011) HiTRACE: high-throughput robust analysis for capillary electrophoresis. Bioinformatics 27:1798-1805
37. Kladwang W, VanLang CC, Cordero P et al (2011) Understanding the errors of SHAPEdirected RNA structure modeling. Bio-chemistry 50:8049-8056
38. Zadeh JN, Steenberg CD, Bois JS et al (2011) NUPACK: analysis and design of nucleic acid systems. J Comput Chem 32:170-173