Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome (original) (raw)

• Machnicka, M.A. et al. MODOMICS: a database of RNA modification pathways—2013 update. Nucleic Acids Res. 41, D262–D267 (2013).
  Article CAS PubMed Google Scholar
• Ozanick, S., Krecic, A., Andersland, J. & Anderson, J.T. The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11, 1281–1290 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Chujo, T. & Suzuki, T. Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. RNA 18, 2269–2276 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Schevitz, R.W. et al. Crystal structure of a eukaryotic initiator tRNA. Nature 278, 188–190 (1979).
  Article CAS PubMed Google Scholar
• Saikia, M., Fu, Y., Pavon-Eternod, M., He, C. & Pan, T. Genome-wide analysis of _N_1-methyl-adenosine modification in human tRNAs. RNA 16, 1317–1327 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Helm, M. et al. The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res. 26, 1636–1643 (1998).
  Article CAS PubMed PubMed Central Google Scholar
• Jühling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159–D162 (2009).
  Article PubMed Google Scholar
• Suzuki, T., Nagao, A. & Suzuki, T. Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu. Rev. Genet. 45, 299–329 (2011).
  Article CAS PubMed Google Scholar
• Sharma, S., Watzinger, P., Kötter, P. & Entian, K.D. Identification of a novel methyltransferase, Bmt2, responsible for the _N_-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res. 41, 5428–5443 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Srivastava, R. & Gopinathan, K.P. Ribosomal RNA methylation in Mycobacterium smegmatis SN2. Biochem. Int. 15, 1179–1188 (1987).
  CAS PubMed Google Scholar
• Peifer, C. et al. Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41, 1151–1163 (2013).
  Article CAS PubMed Google Scholar
• Chan, C.T. et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet. 6, e1001247 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Helm, M. & Alfonzo, J.D. Posttranscriptional RNA modifications: playing metabolic games in a cell's chemical Legoland. Chem. Biol. 21, 174–185 (2014).
  Article CAS PubMed Google Scholar
• Ballesta, J.P. & Cundliffe, E. Site-specific methylation of 16S rRNA caused by pct, a pactamycin resistance determinant from the producing organism, Streptomyces pactum. J. Bacteriol. 173, 7213–7218 (1991).
  Article CAS PubMed PubMed Central Google Scholar
• Motorin, Y., Muller, S., Behm-Ansmant, I. & Branlant, C. Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol. 425, 21–53 (2007).
  Article CAS PubMed Google Scholar
• Behm-Ansmant, I., Helm, M. & Motorin, Y. Use of specific chemical reagents for detection of modified nucleotides in RNA. J. Nucleic Acids 2011, 408053 (2011).
  Article PubMed PubMed Central Google Scholar
• Hodgkinson, A. et al. High-resolution genomic analysis of human mitochondrial RNA sequence variation. Science 344, 413–415 (2014).
  Article CAS PubMed Google Scholar
• Hauenschild, R. et al. The reverse transcription signature of _N_-1-methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Res. 43, 9950–9964 (2015).
  CAS PubMed PubMed Central Google Scholar
• Falnes, P.O., Johansen, R.F. & Seeberg, E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419, 178–182 (2002).
  Article CAS PubMed Google Scholar
• Trewick, S.C., Henshaw, T.F., Hausinger, R.P., Lindahl, T. & Sedgwick, B. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419, 174–178 (2002).
  Article CAS PubMed Google Scholar
• Duncan, T. et al. Reversal of DNA alkylation damage by two human dioxygenases. Proc. Natl. Acad. Sci. USA 99, 16660–16665 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Aas, P.A. et al. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421, 859–863 (2003).
  Article CAS PubMed Google Scholar
• Ougland, R. et al. AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation. Mol. Cell 16, 107–116 (2004).
  Article CAS PubMed Google Scholar
• Dango, S. et al. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Mol. Cell 44, 373–384 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Li, X. et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat. Chem. Biol. 11, 592–597 (2015).
  Article CAS PubMed Google Scholar
• Macon, J.B. & Wolfenden, R. 1-Methyladenosine. Dimroth rearrangement and reversible reduction. Biochemistry 7, 3453–3458 (1968).
  Article CAS PubMed Google Scholar
• Jia, G. et al. _N_6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
  Article 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).
  Article CAS PubMed Google Scholar
• Maden, B.E. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 39, 241–303 (1990).
  Article CAS PubMed Google Scholar
• Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835–837 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Cozen, A.E. et al. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879–884 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
  Article CAS PubMed Google Scholar
• Meyer, K.D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
  Article 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).
  Article 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).
  Article CAS PubMed PubMed Central Google Scholar
• Araujo, P.R. et al. Before it gets started: regulating translation at the 5′ UTR. Comp. Funct. Genomics 2012, 475731 (2012).
  Article 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).
  Article CAS PubMed PubMed Central Google Scholar
• Meyer, K.D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Dominissini, D. et al. The dynamic _N_1-methyladenosine methylome in eukaryotic messenger RNA. Nature http://dx.doi.org/10.1038/nature16998 (2016).
• Liu, N. et al. _N_6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).
  Article CAS PubMed PubMed Central 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
• Wang, X. et al. _N_6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
  Article PubMed Google Scholar
• Wang, X. et al. _N_6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Alarcón, C.R. et al. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).
  Article 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).
  Article CAS PubMed Google Scholar
• Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Reports 8, 284–296 (2014).
  Article 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).
  Article CAS PubMed PubMed Central Google Scholar
• Zhu, C. & Yi, C. Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues. Angew. Chem. Int. Edn Engl. 53, 3659–3662 (2014).
  Article CAS Google Scholar
• Kim, D., Langmead, B. & Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
  Article CAS PubMed PubMed Central Google Scholar