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Limits in the detection of m6A changes using MeRIP/m6A-seq.

Publication ,  Journal Article
McIntyre, ABR; Gokhale, NS; Cerchietti, L; Jaffrey, SR; Horner, SM; Mason, CE
Published in: Sci Rep
April 20, 2020

Many cellular mRNAs contain the modified base m6A, and recent studies have suggested that various stimuli can lead to changes in m6A. The most common method to map m6A and to predict changes in m6A 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 m6A 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 m6A 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.

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Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

April 20, 2020

Volume

10

Issue

1

Start / End Page

6590

Location

England

Related Subject Headings

  • Software
  • Sequence Analysis, RNA
  • RNA, Messenger
  • RNA
  • Methylation
  • Immunoprecipitation
  • Humans
  • Base Sequence
  • Algorithms
  • Adenosine
 

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McIntyre, A. B. R., Gokhale, N. S., Cerchietti, L., Jaffrey, S. R., Horner, S. M., & Mason, C. E. (2020). Limits in the detection of m6A changes using MeRIP/m6A-seq. Sci Rep, 10(1), 6590. https://doi.org/10.1038/s41598-020-63355-3
McIntyre, Alexa B. R., Nandan S. Gokhale, Leandro Cerchietti, Samie R. Jaffrey, Stacy M. Horner, and Christopher E. Mason. “Limits in the detection of m6A changes using MeRIP/m6A-seq.Sci Rep 10, no. 1 (April 20, 2020): 6590. https://doi.org/10.1038/s41598-020-63355-3.
McIntyre ABR, Gokhale NS, Cerchietti L, Jaffrey SR, Horner SM, Mason CE. Limits in the detection of m6A changes using MeRIP/m6A-seq. Sci Rep. 2020 Apr 20;10(1):6590.
McIntyre, Alexa B. R., et al. “Limits in the detection of m6A changes using MeRIP/m6A-seq.Sci Rep, vol. 10, no. 1, Apr. 2020, p. 6590. Pubmed, doi:10.1038/s41598-020-63355-3.
McIntyre ABR, Gokhale NS, Cerchietti L, Jaffrey SR, Horner SM, Mason CE. Limits in the detection of m6A changes using MeRIP/m6A-seq. Sci Rep. 2020 Apr 20;10(1):6590.

Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

April 20, 2020

Volume

10

Issue

1

Start / End Page

6590

Location

England

Related Subject Headings

  • Software
  • Sequence Analysis, RNA
  • RNA, Messenger
  • RNA
  • Methylation
  • Immunoprecipitation
  • Humans
  • Base Sequence
  • Algorithms
  • Adenosine