Limits in the detection of m6 A changes using MeRIP/m6 A-seq.

Journal Article (Journal Article)

Many cellular mRNAs contain the modified base m6 A, and recent studies have suggested that various stimuli can lead to changes in m6 A. The most common method to map m6 A and to predict changes in m6 A between conditions is methylated RNA immunoprecipitation sequencing (MeRIP-seq), through which methylated regions are detected as peaks in transcript coverage from immunoprecipitated RNA relative to input RNA. Here, we generated replicate controls and reanalyzed published MeRIP-seq data to estimate reproducibility across experiments. We found that m6 A peak overlap in mRNAs varies from ~30 to 60% between studies, even in the same cell type. We then assessed statistical methods to detect changes in m6 A peaks as distinct from changes in gene expression. However, from these published data sets, we detected few changes under most conditions and were unable to detect consistent changes across studies of similar stimuli. Overall, our work identifies limits to MeRIP-seq reproducibility in the detection both of peaks and of peak changes and proposes improved approaches for analysis of peak changes.

Full Text

Duke Authors

Cited Authors

  • McIntyre, ABR; Gokhale, NS; Cerchietti, L; Jaffrey, SR; Horner, SM; Mason, CE

Published Date

  • April 20, 2020

Published In

Volume / Issue

  • 10 / 1

Start / End Page

  • 6590 -

PubMed ID

  • 32313079

Pubmed Central ID

  • PMC7170965

Electronic International Standard Serial Number (EISSN)

  • 2045-2322

International Standard Serial Number (ISSN)

  • 2045-2322

Digital Object Identifier (DOI)

  • 10.1038/s41598-020-63355-3

Language

  • eng