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Mapping and Quantification of tRNA 2′-O-Methylation by RiboMethSeq

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Epitranscriptomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1870))

Abstract

Current development of epitranscriptomics field requires efficient experimental protocols for precise mapping and quantification of various modified nucleotides in RNA. Despite important advances in the field during the last 10 years, this task is still extremely laborious and time-consuming, even when high-throughput analytical approaches are employed. Moreover, only a very limited subset of RNA modifications can be detected and only rarely be quantified by these powerful techniques. In the past, we developed and successfully applied alkaline fragmentation-based RiboMethSeq approach for mapping and precise quantification of multiple 2′-O-methylation residues in ribosomal RNA. Here we describe a RiboMethSeq protocol adapted for the analysis of bacterial and eukaryotic tRNA species, which also contain 2′-O-methylations at functionally important RNA regions.

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Acknowledgement

This work was supported by joint ANR-DFG grant HTRNAMod (ANR-13-ISV8-0001/HE 3397/8-1) to MH and YM, and AO Lorraine University-Lorraine Region “Aberrant RNA methylation in cancer” funding to YM.

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Authors and Affiliations

  1. IMoPA UMR7365 CNRS-UL, BioPole Lorraine University, Nancy, France

    Adeline Galvanin, Lilia Ayadi & Yuri Motorin

  2. Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany

    Mark Helm

  3. Next-Generation Sequencing Core Facility, FR3209 BMCT, CNRS-UL, BioPole Lorraine University, Nancy, France

    Yuri Motorin

  4. Next-Generation Sequencing Core Facility, UMS2008 IBSlor, CNRS-UL-INSERM, BioPole Lorraine University, Nancy, France

    Virginie Marchand

Authors
  1. Adeline Galvanin
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  2. Lilia Ayadi
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  3. Mark Helm
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  4. Yuri Motorin
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  5. Virginie Marchand
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Corresponding author

Correspondence to Virginie Marchand .

Editor information

Editors and Affiliations

  1. Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

    Narendra Wajapeyee

  2. Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA

    Romi Gupta

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Galvanin, A., Ayadi, L., Helm, M., Motorin, Y., Marchand, V. (2019). Mapping and Quantification of tRNA 2′-O-Methylation by RiboMethSeq. In: Wajapeyee, N., Gupta, R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8808-2_21

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  • DOI: https://doi.org/10.1007/978-1-4939-8808-2_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8807-5

  • Online ISBN: 978-1-4939-8808-2

  • eBook Packages: Springer Protocols

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