m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome (original) (raw)

• Fu, Y. & He, C. Nucleic acid modifications with epigenetic significance. Curr. Opin. Chem. Biol. 16, 516–524 (2012).
  CAS PubMed PubMed Central Google Scholar
• Sibbritt, T., Patel, H.R. & Preiss, T. Mapping and significance of the mRNA methylome. Wiley Interdiscip. Rev. RNA 4, 397–422 (2013).
  CAS PubMed Google Scholar
• Meyer, K.D. & Jaffrey, S.R. The dynamic epitranscriptome: _N_6-methyladenosine and gene expression control. Nat. Rev. Mol. Cell Biol. 15, 313–326 (2014).
  CAS PubMed PubMed Central Google Scholar
• Klungland, A. & Dahl, J.A. Dynamic RNA modifications in disease. Curr. Opin. Genet. Dev. 26, 47–52 (2014).
  CAS PubMed Google Scholar
• Pan, T. _N_6-methyl-Adenosine modification in messenger and long non-coding RNA. Trends Biochem. Sci. 38, 204–209 (2013).
  CAS PubMed PubMed Central Google Scholar
• Schwartz, S. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409–1421 (2013).
  CAS PubMed PubMed Central Google Scholar
• Wang, Y. et al. _N_6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat. Cell Biol. 16, 191–198 (2014).
  CAS PubMed PubMed Central Google Scholar
• Wang, X. et al. m6A-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
  PubMed Google Scholar
• Meyer, K.D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).
  CAS PubMed PubMed Central Google Scholar
• Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).
  CAS PubMed PubMed Central Google Scholar
• Wang, X. et al. _N_6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).
  CAS PubMed PubMed Central Google Scholar
• Bokar, J.A., Shambaugh, M.E., Polayes, D., Matera, A.G. & Rottman, F.M. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 3, 1233–1247 (1997).
  CAS PubMed PubMed Central Google Scholar
• Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA _N_6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).
  CAS PubMed Google Scholar
• Ping, X.L. et al. Mammalian WTAP is a regulatory subunit of the RNA _N_6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014).
  CAS PubMed PubMed Central Google Scholar
• Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Rep. 8, 284–296 (2014).
  CAS PubMed PubMed Central Google Scholar
• Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
  CAS PubMed Google Scholar
• Jia, G. _N_6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
  CAS PubMed PubMed Central Google Scholar
• Batista, P.J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719 (2014).
  CAS PubMed PubMed Central Google Scholar
• Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002–1006 (2015).
  CAS PubMed Google Scholar
• Dominissini, D., Moshitch-Moshkovitz, S., Amariglio, N. & Rechavi, G. Transcriptome-wide mapping of _N_6-methyladenosine by m6A-seq. Methods Enzymol. 560, 131–147 (2015).
  CAS PubMed Google Scholar
• Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
  CAS PubMed Google Scholar
• Liu, N. et al. Probing _N_6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19, 1848–1856 (2013).
  CAS PubMed PubMed Central Google Scholar
• Horowitz, S., Horowitz, A., Nilsen, T.W., Munns, T.W. & Rottman, F.M. Mapping of _N_6-methyladenosine residues in bovine prolactin mRNA. Proc. Natl. Acad. Sci. USA 81, 5667–5671 (1984).
  CAS PubMed PubMed Central Google Scholar
• Neff, A.T., Lee, J.Y., Wilusz, J., Tian, B. & Wilusz, C.J. Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res. 22, 1457–1467 (2012).
  CAS PubMed PubMed Central Google Scholar
• Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12, 767–772 (2015).
  CAS PubMed PubMed Central Google Scholar
• Wei, C., Gershowitz, A. & Moss, B. _N_6, O2′-dimethyladenosine a novel methylated ribonucleoside next to the 5′ terminal of animal cell and virus mRNAs. Nature 257, 251–253 (1975).
  CAS PubMed Google Scholar
• Kruse, S. et al. A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA. Sci. Rep. 1, 126 (2011).
  PubMed PubMed Central Google Scholar
• Keith, J.M., Ensinger, M.J. & Moss, B. HeLa cell RNA (2′-O-methyladenosine-_N_6-)-methyltransferase specific for the capped 5′-end of messenger RNA. J. Biol. Chem. 253, 5033–5039 (1978).
  CAS PubMed Google Scholar
• Robins, M.J., Naik, S.R. & Lee, A.S. Nucleic acid related compounds. 12. The facile and high-yield stannous chloride catalyzed monomethylation of the cis-glycol system of nucleosides by diazomethane. J. Org. Chem. 39, 1891–1899 (1974).
  CAS PubMed Google Scholar
• Zhao, X. et al. FTO-dependent demethylation of _N_6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 24, 1403–1419 (2014).
  CAS PubMed PubMed Central Google Scholar
• Liu, N. et al. _N_6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).
  CAS PubMed PubMed Central Google Scholar
• Spitale, R.C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).
  CAS PubMed PubMed Central Google Scholar
• Shen, S. et al. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-seq data. Nucleic Acids Res. 40, e61 (2012).
  CAS PubMed PubMed Central Google Scholar
• Shen, S. et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-seq data. Proc. Natl. Acad. Sci. USA 111, E5593–E5601 (2014).
  CAS PubMed PubMed Central Google Scholar
• Masamha, C.P. et al. CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature 510, 412–416 (2014).
  CAS PubMed PubMed Central Google Scholar
• Ke, S. et al. A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation. Genes Dev. 29, 2037–2053 (2015).
  CAS PubMed PubMed Central Google Scholar
• Di Giammartino, D.C., Nishida, K. & Manley, J.L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853–866 (2011).
  CAS PubMed PubMed Central Google Scholar
• Berkovits, B.D. & Mayr, C. Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization. Nature 522, 363–367 (2015).
  CAS PubMed PubMed Central Google Scholar
• Misra, A., Ou, J., Zhu, L.J. & Green, M.R. Global promotion of alternative internal exon usage by mRNA 3′ end formation factors. Mol. Cell 58, 819–831 (2015).
  CAS PubMed PubMed Central Google Scholar
• Shi, Y. & Manley, J.L. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev. 29, 889–897 (2015).
  CAS PubMed PubMed Central Google Scholar
• Nelles, D.A. et al. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165, 488–496 (2016).
  CAS PubMed PubMed Central Google Scholar
• Chen, K., Zhao, B.S. & He, C. Nucleic acid modifications in regulation of gene expression. Cell Chem. Biol. 23, 74–85 (2016).
  CAS PubMed PubMed Central Google Scholar
• Lianoglou, S., Garg, V., Yang, J.L., Leslie, C.S. & Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380–2396 (2013).
  CAS PubMed PubMed Central Google Scholar
• Chan, C.T. et al. Identification of _N_6,_N_6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin. Molecules 16, 5168–5181 (2011).
  CAS PubMed PubMed Central Google Scholar
• Livak, K.J. & Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-ΔΔ_CT_) method. Methods 25, 402–408 (2001).
  CAS PubMed Google Scholar
• Sigova, A.A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. USA 110, 2876–2881 (2013).
  CAS PubMed PubMed Central Google Scholar
• Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Huang da, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009).
  PubMed Google Scholar
• Müller, S. et al. APADB: a database for alternative polyadenylation and microRNA regulation events. Database (Oxford) 2014, bau076 (2014).
  Google Scholar
• Roost, C. et al. Structure and thermodynamics of _N_6-methyladenosine in RNA: a spring-loaded base modification. J. Am. Chem. Soc. 137, 2107–2115 (2015).
  CAS PubMed PubMed Central Google Scholar
• Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).
  CAS PubMed Google Scholar
• Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006).
  CAS PubMed Google Scholar
• Dittmar, K.A. et al. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol. Cell. Biol. 32, 1468–1482 (2012).
  CAS PubMed PubMed Central Google Scholar
• Anderson, E.S. et al. The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA 18, 1041–1049 (2012).
  CAS PubMed PubMed Central Google Scholar