King MY, Redman KL (2002) RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Sugimoto Y, Konig J, Hussain S, Zupan B, Curk T, Frye M, Ule J (2012) Genome Biol 13:R67 Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB (2003) CLIP identifiesNova-regulated RNA networks in the brain. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y et al (2011) N 6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Front Cell Neurosci 9:420īokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman FM (1997) Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. Hussain S, Bashir ZI (2015) The epitranscriptome in modulating spatiotemporal RNA translation in neuronal post-synaptic function. Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR (2015) 5' UTR m(6)A promotes cap-independent translation. Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H et al (2015) N(6)-methyladenosine modulates messenger RNA translation efficiency. Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D et al (2014) N 6-methyladenosine-dependent regulation of messenger RNA stability. ![]() Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimot Y et al (2013a) NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Khoddami V, Cairns BR (2013) Identification of direct targets and modified bases of RNA cytosine methyltransferases. Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ et al (2012) Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Nucleic Acids Res 2:1653–1668ĭominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S et al (2012) Topology of the human and mouse m 6A RNA methylomes revealed by m 6A-seq. Here we describe the m5C-miCLIP protocol, discuss how it yields the nucleotide-resolution RNA modification maps, and comment on how these have contributed to the new field of molecular genetics research coined “epitranscriptomics.” Key wordsĭubin DT, Taylor RH (1975) The methylation state of poly A-containing messenger RNA from cultured hamster cells. Variants of miCLIP have been used to map the methyl-5-cytosine (m5C) or methyl-6-adenosine (m6A) modification at nucleotide resolution in the human transcriptome. We and others have recently modified this method to profile RNA methylation, and we refer to this customized technique as methylation-iCLIP (miCLIP). Immunoprecipitation-based transcriptomic methods such as individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) have also allowed high-resolution analysis of the RNA interactions of a protein of interest, thus revealing new regulatory mechanisms. ![]() This yielded insights into fundamental transcriptomic processes such as gene transcription, RNA processing, and mRNA splicing. Next-generation sequencing technologies have enabled the transcriptome to be profiled at a previously unprecedented speed and depth.
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