Abstract
N 1-Methyladenosine (m1A) is a prevalent posttranscriptional RNA modification and commonly found in tRNA and rRNA. Very recent works have also demonstrated the prevalence of m1A in mammalian mRNA. Hence, high-throughput methods that allow transcriptome-wide mapping of m1A will be important for further functional investigations. Here, we describe a technique called “m1A-ID-Seq”, which is based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse transcription, to map m1A in the transcriptome. Utilizing this technique, highly confident m1A peaks can be obtained on a transcriptome-wide level.
* These authors contributed equally to this work.
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Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H (2013) MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res 41(Database issue):D262–D267
Liu N, Pan T (2015) RNA epigenetics. Trans Res 165(1):28–35
Roundtree IA, He C (2016) RNA epigenetics--chemical messages for posttranscriptional gene regulation. Curr Opin Chem Biol 30:46–51
Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, Zheng G, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D, Dore LC, Amariglio N, Rechavi G, He C (2016) The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 530(7591):441–446
Li X, Xiong X, Wang K, Wang L, Shu X, Ma S, Yi C (2016) Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat Chem Biol 12(5):311–316
Schevitz RW, Podjarny AD, Krishnamachari N, Hughes JJ, Sigler PB, Sussman JL (1979) Crystal structure of a eukaryotic initiator tRNA. Nature 278(5700):188–190
Peifer C, Sharma S, Watzinger P, Lamberth S, Kotter P, Entian KD (2013) Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res 41(2):1151–1163
Motorin Y, Muller S, Behm-Ansmant I, Branlant C (2007) Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol 425:21–53
Behm-Ansmant I, Helm M, Motorin Y (2011) Use of specific chemical reagents for detection of modified nucleotides in RNA. J Nucleic Acids 2011:408053
Hodgkinson A, Idaghdour Y, Gbeha E, Grenier JC, Hip-Ki E, Bruat V, Goulet JP, de Malliard T, Awadalla P (2014) High-resolution genomic analysis of human mitochondrial RNA sequence variation. Science 344(6182):413–415
Hauenschild R, Tserovski L, Schmid K, Thuring K, Winz ML, Sharma S, Entian KD, Wacheul L, Lafontaine DL, Anderson J, Alfonzo J, Hildebrandt A, Jaschke A, Motorin Y, Helm M (2015) The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Res 43(20):9950–9964
Falnes PO, Johansen RF, Seeberg E (2002) AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419(6903):178–182
Trewick SC, Henshaw TF, Hausinger RP, Lindahl T, Sedgwick B (2002) Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419(6903):174–178
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Li, X., Peng, J., Yi, C. (2017). Transcriptome-Wide Mapping of N 1-Methyladenosine Methylome. In: Lusser, A. (eds) RNA Methylation. Methods in Molecular Biology, vol 1562. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6807-7_16
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DOI: https://doi.org/10.1007/978-1-4939-6807-7_16
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