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Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP)

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RNA Methylation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1562))

Abstract

Next-generation sequencing technologies have enabled the transcriptome to be profiled at a previously unprecedented speed and depth. This yielded insights into fundamental transcriptomic processes such as gene transcription, RNA processing, and mRNA splicing. 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. We and others have recently modified this method to profile RNA methylation, and we refer to this customized technique as methylation-iCLIP (miCLIP). 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. 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.”

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Acknowledgments

We wish to acknowledge Dr. Julian Konig who codeveloped the original iCLIP protocol, and Dr. Yoichiro Sugimoto for helpful feedback and discussions during the development of methylation-iCLIP. Research in the SH laboratory is supported by a Seed Award in Science from the Wellcome Trust (WT108285MA), and a Responsive Mode Project Grant from the Biotechnology and Biosciences Research Council (BBSRC) UK (BB/N000749/1).

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Correspondence to Shobbir Hussain .

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George, H., Ule, J., Hussain, S. (2017). Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP). 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_7

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  • DOI: https://doi.org/10.1007/978-1-4939-6807-7_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6805-3

  • Online ISBN: 978-1-4939-6807-7

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