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Volumn 107, Issue , 2016, Pages 110-121

High-throughput sequencing for 1-methyladenosine (m1A) mapping in RNA

Author keywords

High throughput sequencing; Misincorporation signature; Reverse transcription; RNA modification

Indexed keywords

1 METHYLADENOSINE; COMPLEMENTARY DNA; NUCLEOTIDE; RNA; 1-METHYLADENOSINE; ADENOSINE;

EID: 84959094961     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.02.012     Document Type: Article
Times cited : (44)

References (35)
  • 2
    • 79953138756 scopus 로고    scopus 로고
    • Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit
    • [2] Husain, N., Obranic, S., Koscinski, L., Seetharaman, J., Babic, F., Bujnicki, J.M., et al. Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit. Nucleic Acids Res. 39 (2011), 1903–1918, 10.1093/nar/gkq1033.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1903-1918
    • Husain, N.1    Obranic, S.2    Koscinski, L.3    Seetharaman, J.4    Babic, F.5    Bujnicki, J.M.6
  • 3
    • 36749013556 scopus 로고    scopus 로고
    • Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides
    • [3] Wachino, J., Shibayama, K., Kurokawa, H., Kimura, K., Yamane, K., Suzuki, S., et al. Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob. Agents Chemother. 51 (2007), 4401–4409, 10.1128/AAC.00926-07.
    • (2007) Antimicrob. Agents Chemother. , vol.51 , pp. 4401-4409
    • Wachino, J.1    Shibayama, K.2    Kurokawa, H.3    Kimura, K.4    Yamane, K.5    Suzuki, S.6
  • 4
    • 78049423570 scopus 로고    scopus 로고
    • Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase
    • [4] Guelorget, A., Roovers, M., Guérineau, V., Barbey, C., Li, X., Golinelli-Pimpaneau, B., Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 38 (2010), 6206–6218, 10.1093/nar/gkq381.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6206-6218
    • Guelorget, A.1    Roovers, M.2    Guérineau, V.3    Barbey, C.4    Li, X.5    Golinelli-Pimpaneau, B.6
  • 5
    • 1342307286 scopus 로고    scopus 로고
    • A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
    • [5] Roovers, M., Wouters, J., Bujnicki, J.M., Tricot, C., Stalon, V., Grosjean, H., et al. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 32 (2004), 465–476, 10.1093/nar/gkh191.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 465-476
    • Roovers, M.1    Wouters, J.2    Bujnicki, J.M.3    Tricot, C.4    Stalon, V.5    Grosjean, H.6
  • 6
    • 32644447756 scopus 로고    scopus 로고
    • Post-transcriptional nucleotide modification and alternative folding of RNA
    • [6] Helm, M., Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 34 (2006), 721–733, 10.1093/nar/gkj471.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 721-733
    • Helm, M.1
  • 7
    • 84875410311 scopus 로고    scopus 로고
    • Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA
    • [7] Peifer, C., Sharma, S., Watzinger, P., Lamberth, S., Kötter, P., Entian, K.-D., Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41 (2013), 1151–1163, 10.1093/nar/gks1102.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 1151-1163
    • Peifer, C.1    Sharma, S.2    Watzinger, P.3    Lamberth, S.4    Kötter, P.5    Entian, K.-D.6
  • 8
    • 84878583858 scopus 로고    scopus 로고
    • Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae
    • [8] 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 (2013), 5428–5443, 10.1093/nar/gkt195.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 5428-5443
    • Sharma, S.1    Watzinger, P.2    Kötter, P.3    Entian, K.-D.4
  • 9
    • 0022422352 scopus 로고
    • Conformation of yeast 18S rRNA. Direct chemical probing of the 5′ domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible
    • [9] Lempereur, L., Nicoloso, M., Riehl, N., Ehresmann, C., Ehresmann, B., Bachellerie, J.P., Conformation of yeast 18S rRNA. Direct chemical probing of the 5′ domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible. Nucleic Acids Res. 13 (1985), 8339–8357.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 8339-8357
    • Lempereur, L.1    Nicoloso, M.2    Riehl, N.3    Ehresmann, C.4    Ehresmann, B.5    Bachellerie, J.P.6
  • 10
    • 38449119903 scopus 로고    scopus 로고
    • DMS footprinting of structured RNAs and RNA-protein complexes
    • [10] Tijerina, P., Mohr, S., Russell, R., DMS footprinting of structured RNAs and RNA-protein complexes. Nat. Protoc. 2 (2007), 2608–2623, 10.1038/nprot.2007.380.
    • (2007) Nat. Protoc. , vol.2 , pp. 2608-2623
    • Tijerina, P.1    Mohr, S.2    Russell, R.3
  • 11
    • 34548726200 scopus 로고    scopus 로고
    • Identification of modified residues in RNAs by reverse transcription-based methods
    • [11] Motorin, Y., Muller, S., Behm-Ansmant, I., Branlant, C., Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol. 425 (2007), 21–53, 10.1016/S0076-6879(07)25002-5.
    • (2007) Methods Enzymol. , vol.425 , pp. 21-53
    • Motorin, Y.1    Muller, S.2    Behm-Ansmant, I.3    Branlant, C.4
  • 13
    • 84921512407 scopus 로고    scopus 로고
    • High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing
    • [13] Chen, K., Lu, Z., Wang, X., Fu, Y., Luo, G.-Z., Liu, N., et al. High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew. Chem. Int. Ed. Engl. 54 (2015), 1587–1590, 10.1002/anie.201410647.
    • (2015) Angew. Chem. Int. Ed. Engl. , vol.54 , pp. 1587-1590
    • Chen, K.1    Lu, Z.2    Wang, X.3    Fu, Y.4    Luo, G.-Z.5    Liu, N.6
  • 15
    • 84872032385 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing
    • [15] Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N., Rechavi, G., Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat. Protoc. 8 (2013), 176–189, 10.1038/nprot.2012.148.
    • (2013) Nat. Protoc. , vol.8 , pp. 176-189
    • Dominissini, D.1    Moshitch-Moshkovitz, S.2    Salmon-Divon, M.3    Amariglio, N.4    Rechavi, G.5
  • 16
    • 84879642219 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs
    • [16] Edelheit, S., Schwartz, S., Mumbach, M.R., Wurtzel, O., Sorek, R., Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet., 9, 2013, e1003602, 10.1371/journal.pgen.1003602.
    • (2013) PLoS Genet. , vol.9 , pp. e1003602
    • Edelheit, S.1    Schwartz, S.2    Mumbach, M.R.3    Wurtzel, O.4    Sorek, R.5
  • 17
    • 84888791449 scopus 로고    scopus 로고
    • Characterizing 5-methylcytosine in the mammalian epitranscriptome
    • [17] Hussain, S., Aleksic, J., Blanco, S., Dietmann, S., Frye, M., Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol., 14, 2013, 215, 10.1186/gb4143.
    • (2013) Genome Biol. , vol.14 , pp. 215
    • Hussain, S.1    Aleksic, J.2    Blanco, S.3    Dietmann, S.4    Frye, M.5
  • 18
    • 84938417580 scopus 로고    scopus 로고
    • Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
    • [18] Linder, B., Grozhik, A.V., Olarerin-George, A.O., Meydan, C., Mason, C.E., Jaffrey, S.R., Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12 (2015), 767–772, 10.1038/nmeth.3453.
    • (2015) Nat. Methods , vol.12 , pp. 767-772
    • Linder, B.1    Grozhik, A.V.2    Olarerin-George, A.O.3    Meydan, C.4    Mason, C.E.5    Jaffrey, S.R.6
  • 19
    • 84860751168 scopus 로고    scopus 로고
    • Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
    • [19] Squires, J.E., Patel, H.R., Nousch, M., Sibbritt, T., Humphreys, D.T., Parker, B.J., et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40 (2012), 5023–5033, 10.1093/nar/gks144.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5023-5033
    • Squires, J.E.1    Patel, H.R.2    Nousch, M.3    Sibbritt, T.4    Humphreys, D.T.5    Parker, B.J.6
  • 20
    • 84922180958 scopus 로고    scopus 로고
    • Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
    • [20] Carlile, T.M., Rojas-Duran, M.F., Zinshteyn, B., Shin, H., Bartoli, K.M., Gilbert, W.V., Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515 (2014), 143–146, 10.1038/nature13802.
    • (2014) Nature , vol.515 , pp. 143-146
    • Carlile, T.M.1    Rojas-Duran, M.F.2    Zinshteyn, B.3    Shin, H.4    Bartoli, K.M.5    Gilbert, W.V.6
  • 21
    • 84908626586 scopus 로고    scopus 로고
    • Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae
    • [21] Lovejoy, A.F., Riordan, D.P., Brown, P.O., Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS ONE, 9, 2014, e110799, 10.1371/journal.pone.0110799.
    • (2014) PLoS ONE , vol.9 , pp. e110799
    • Lovejoy, A.F.1    Riordan, D.P.2    Brown, P.O.3
  • 22
    • 84907527348 scopus 로고    scopus 로고
    • Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA
    • [22] Schwartz, S., Bernstein, D.A., Mumbach, M.R., Jovanovic, M., Herbst, R.H., León-Ricardo, B.X., et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159 (2014), 148–162, 10.1016/j.cell.2014.08.028.
    • (2014) Cell , vol.159 , pp. 148-162
    • Schwartz, S.1    Bernstein, D.A.2    Mumbach, M.R.3    Jovanovic, M.4    Herbst, R.H.5    León-Ricardo, B.X.6
  • 24
    • 84959386536 scopus 로고    scopus 로고
    • The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
    • (advance online publication)
    • [24] Dominissini, D., Nachtergaele, S., Moshitch-Moshkovitz, S., Peer, E., Kol, N., Ben-Haim, M.S., et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature, 2016, 10.1038/nature16998 (advance online publication).
    • (2016) Nature
    • Dominissini, D.1    Nachtergaele, S.2    Moshitch-Moshkovitz, S.3    Peer, E.4    Kol, N.5    Ben-Haim, M.S.6
  • 25
    • 84957828213 scopus 로고    scopus 로고
    • Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome
    • (advance online publication)
    • [25] Li, X., Xiong, X., Wang, K., Wang, L., Shu, X., Ma, S., et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol., 2016, 10.1038/nchembio.2040 (advance online publication).
    • (2016) Nat. Chem. Biol.
    • Li, X.1    Xiong, X.2    Wang, K.3    Wang, L.4    Shu, X.5    Ma, S.6
  • 26
    • 84951734126 scopus 로고    scopus 로고
    • The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent
    • [26] Hauenschild, R., Tserovski, L., Schmid, K., Thüring, K., Winz, M.-L., Sharma, S., et al. The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Res. 43 (2015), 9950–9964, 10.1093/nar/gkv895.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 9950-9964
    • Hauenschild, R.1    Tserovski, L.2    Schmid, K.3    Thüring, K.4    Winz, M.-L.5    Sharma, S.6
  • 27
    • 79959314190 scopus 로고    scopus 로고
    • Preparation of yeast RNA
    • Frederick M. Ausubel Al. (Chapter 13, Unit13.12)
    • [27] Collart, M.A., Oliviero, S., Preparation of yeast RNA. Ausubel Al., Frederick M., (eds.) Curr. Protoc. Mol. Biol., 2001, 10.1002/0471142727.mb1312s23 (Chapter 13, Unit13.12).
    • (2001) Curr. Protoc. Mol. Biol.
    • Collart, M.A.1    Oliviero, S.2
  • 28
    • 84925490079 scopus 로고    scopus 로고
    • NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs
    • [28] Cahová, H., Winz, M.-L., Höfer, K., Nübel, G., Jäschke, A., NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature 519 (2015), 374–377, 10.1038/nature14020.
    • (2015) Nature , vol.519 , pp. 374-377
    • Cahová, H.1    Winz, M.-L.2    Höfer, K.3    Nübel, G.4    Jäschke, A.5
  • 29
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • [29] Liaw, A., Wiener, M., Classification and regression by randomForest. R. News. 2 (2002), 18–22.
    • (2002) R. News. , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 31
    • 0023453329 scopus 로고
    • Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
    • [31] Rousseeuw, P.J., Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20 (1987), 53–65, 10.1016/0377-0427(87)90125-7.
    • (1987) J. Comput. Appl. Math. , vol.20 , pp. 53-65
    • Rousseeuw, P.J.1
  • 32
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • [32] Breiman, L., Random Forests. Mach. Learn. 45 (2001), 5–32.
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 33
    • 84995340088 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • [33] Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57 (1995), 289–300.
    • (1995) J. R. Stat. Soc. Ser. B Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 35
    • 84937514684 scopus 로고    scopus 로고
    • Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome
    • [35] Li, X., Zhu, P., Ma, S., Song, J., Bai, J., Sun, F., et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat. Chem. Biol. 11 (2015), 592–597, 10.1038/nchembio.1836.
    • (2015) Nat. Chem. Biol. , vol.11 , pp. 592-597
    • Li, X.1    Zhu, P.2    Ma, S.3    Song, J.4    Bai, J.5    Sun, F.6


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