Mod-seq: A high-throughput method for probing RNA secondary structure

Methods in Enzymology

Volumn 558, Issue 1, 2015, Pages 125-152

  Lin, Yizhu ^a   May, Gemma E ^a   McManus, C Joel ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; COMPLEMENTARY DNA; PHOSPHATASE; PHOSPHOTRANSFERASE; RNA; LONG UNTRANSLATED RNA; MOLECULAR LIBRARY; MOLECULAR PROBE; OLIGONUCLEOTIDE; RNA PROBE;

ARTICLE; CHEMICAL MODIFICATION; DATA ANALYSIS; FRAGMENTATION REACTION; GENE AMPLIFICATION; HIGH THROUGHPUT SEQUENCING; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRECIPITATION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PURIFICATION; REVERSE TRANSCRIPTION; RNA PROBE; SUBTRACTIVE HYBRIDIZATION; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; HIGH THROUGHPUT SCREENING; METABOLISM; MOLECULAR LIBRARY; MOLECULAR PROBE; RNA FOLDING; RNA PROCESSING;

DNA, COMPLEMENTARY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HIGH-THROUGHPUT SCREENING ASSAYS; MOLECULAR PROBES; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; RNA FOLDING; RNA PROBES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, LONG NONCODING; SMALL MOLECULE LIBRARIES; SOFTWARE;

EID: 84934987335     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2015.01.012     Document Type: Chapter

References (18)

1. Brunel, C., & Romby, P. (2000). Probing RNA structure and RNA-ligand complexes with chemical probes. Methods in Enzymology, 318, 3-21.
2. Cech, T. R., & Steitz, J. A. (2014). The noncoding RNA revolution-Trashing old rules to forge new ones. Cell, 157 (1), 77-94.
3. Cordero, P., Kladwang, W., VanLang, C. C., & Das, R. (2012). Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry, 51 (36), 7037-7039.
4. Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., and Bevilacqua, P. C., & Assmann, S. M. (2014). In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505, 696-700.
5. Hajdin, C. E., Bellaousov, S., Huggins, W., Leonard, C. W., and Mathews, D. H., & Weeks, K. M. (2013). Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proceedings of the National Academy of Sciences of the United States of America, 110 (14), 5498-5503.
6. Hennelly, S. P., & Sanbonmatsu, K. Y. (2012). Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure? BioArchitecture, 2 (6), 189-199.
7. Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10 (3), R25.
8. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England), 25 (16), 2078-2079.
9. Lucks, J. B., and Mortimer, S. A., Trapnell, C., Luo, S., Aviran, S., and Schroth, G. P., et al. (2011). Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America, 108 (27), 11063-11068.
10. Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal, 17 (1), 10-12.
11. Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England), 26 (6), 841-842.
12. Reuter, J. S., & Mathews, D. H. (2010). RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11 (1), 129.
13. Rouskin, S., Zubradt, M., Washietl, S., Kellis, M., & Weissman, J. S. (2014). Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505, 701-705.
14. Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E., & Weeks, K. M. (2014). rnA motif discovery by shAPe and mutational profiling (shAPe-maP). Nature Methods, 11, 959-965.
15. Talkish, J., May, G., Lin, Y., Woolford, J. L., & McManus, C. J. (2014). Mod-seq: High-throughput sequencing for chemical probing of RNA structure. RNA, 20, 713-720.
16. Vestheim, H., & Jarman, S. N. (2008). Blocking primers to enhance PCR amplification of rare sequences in mixed samples-A case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology, 5 (1), 12.
17. Weeks, K. M. (2010). Advances in RNA structure analysis by chemical probing. Current Opinion in Structural Biology, 20 (3), 295-304.
18. Wells, S. E., and Hughes, J. M., Igel, A. H., & Ares, M. (2000). Use of dimethyl sulfate to probe RNA structure in vivo. Methods in Enzymology, 318, 479-493.