Transcriptome-wide mapping of N6-methyladenosine by m 6A-seq based on immunocapturing and massively parallel sequencing

Nature Protocols

Volumn 8, Issue 1, 2013, Pages 176-189

  Dominissini, Dan ^a,b   Moshitch Moshkovitz, Sharon ^a   Salmon Divon, Mali ^a   Amariglio, Ninette ^a   Rechavi, Gideon ^a,b  

^a SHEBA MEDICAL CENTER   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

6 N METHYLADENOSINE; TRANSCRIPTOME;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; IMMUNOCAPTURING; MASSIVELY PARALLEL SEQUENCING; PRIORITY JOURNAL; RNA ANALYSIS; RNA ISOLATION; RNA METHYLATION; RNA STRUCTURE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS;

ADENOSINE; ANIMALS; GENE EXPRESSION PROFILING; HUMANS; IMMUNOPRECIPITATION; METHYLATION; MICE; RNA PROCESSING, POST-TRANSCRIPTIONAL;

EID: 84872032385     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2012.148     Document Type: Article

References (32)

1. Cantara, W.A. et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res. 39, D195-D201 (2011).
2. He, C. Grand challenge commentary: RNA epigenetics? Nat. Chem. Biol. 6, 863-865 (2010).
3. Chan, C.T. et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet. 6, e1001247 (2010).
4. Schaefer, M. et al. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev. 24, 1590-1595 (2010).
5. Bokar, J. Fine-tuning of RNA functions by modification and editing. in Topics in Current Genetics 12 (ed. Grosjean, H.) 141-177 (Springer, 2005).
6. Zhong, S. et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 20, 1278-1288 (2008). (Pubitemid 352844182)
7. Clancy, M.J., Shambaugh, M.E., Timpte, C.S. & Bokar, J.A. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res. 30, 4509-4518 (2002). (Pubitemid 35277261)
8. Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885-887 (2011).
9. Levanon, E.Y. et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001-1005 (2004). (Pubitemid 39014477)
10. Klose, R.J. & Bird, A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89-97 (2006). (Pubitemid 43221841)
11. Dai, Q. et al. Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine. Nucleic Acids Res. 35, 6322-6329 (2007). (Pubitemid 350018592)
12. Kellner, S., Burhenne, J. & Helm, M. Detection of RNA modifications. RNA biology 7, 237-247 (2010).
13. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201-206 (2012).
14. Meyer, K.D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635-1646 (2012).
15. Czerwoniec, A. et al. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 37, D118-121 (2009).
16. Horowitz, S., Horowitz, A., Nilsen, T.W., Munns, T.W. & Rottman, F.M. Mapping of N6-methyladenosine residues in bovine prolactin mRNA. Proc. Natl. Acad. Sci. USA 81, 5667-5671 (1984). (Pubitemid 14023826)
17. Bringmann, P. & Luhrmann, R. Antibodies specific for N6-methyladenosine react with intact snRNPs U2 and U4/U6. FEBS Lett. 213, 309-315 (1987).
18. Dante, R. & Niveleau, A. Inhibition of in vitro translation by antibodies directed against N6-methyladenosine. FEBS Lett. 130, 153-157 (1981). (Pubitemid 11012167)
19. Munns, T.W., Liszewski, M.K., Oberst, R.J. & Sims, H.F. Antibody nucleic acid complexes. Immunospecific retention of N6-methyladenosine- containing transfer ribonucleic acid. Biochemistry 17, 2573-2578 (1978). (Pubitemid 8363369)
20. Munns, T.W., Liszewski, M.K. & Sims, H.F. Characterization of antibodies specific for N6-methyladenosine and for 7-methylguanosine. Biochemistry 16, 2163-2168 (1977). (Pubitemid 8120883)
21. Munns, T.W., Oberst, R.J., Sims, H.F. & Liszewski, M.K. Antibody-nucleic acid complexes. Immunospecific recognition of 7-methylguanine- and N6-methyladenine-containing 5′-terminal oligonucleotides of mRNA. J. Biol. Chem. 254, 4327-4330 (1979).
22. Munns, T.W., Sims, H.F. & Liszewski, M.K. Immunospecific retention of oligonucleotides possessing N6-methyladenosine and 7-methylguanosine. J. Biol. Chem. 252, 3102-3104 (1977). (Pubitemid 8094247)
23. Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
24. Feng, J., Liu, T. & Zhang, Y. Using MACS to identify peaks from ChIP-seq data. Curr. Protoc. Bioinformatics 34, 2.14.1-2.14.14 (2011).
25. Machanick, P. & Bailey, T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696-1697 (2011).
26. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
27. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
28. Bailey, T.L. & Machanick, P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 18, 18 (2012).
29. Salmon-Divon, M., Dvinge, H., Tammoja, K. & Bertone, P. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 11, 415 (2010).
30. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
31. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
32. Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).