Limits in the detection of m 6 A changes using MeRIP/m 6 A-seq.

Autor: McIntyre ABR; Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA. abm237@cornell.edu.; Tri-Institutional Program in Computational Biology and Medicine, New York City, NY, 10065, USA. abm237@cornell.edu., Gokhale NS; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA., Cerchietti L; Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York City, NY, 10065, USA., Jaffrey SR; Department of Pharmacology, Weill Cornell Medicine, New York City, NY, 10065, USA., Horner SM; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA. stacy.horner@duke.edu.; Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA. stacy.horner@duke.edu., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA. chm2042@med.cornell.edu.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA. chm2042@med.cornell.edu.; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA. chm2042@med.cornell.edu.; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA. chm2042@med.cornell.edu.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2020 Apr 20; Vol. 10 (1), pp. 6590. Date of Electronic Publication: 2020 Apr 20.
DOI: 10.1038/s41598-020-63355-3
Abstrakt: Many cellular mRNAs contain the modified base m 6 A, and recent studies have suggested that various stimuli can lead to changes in m 6 A. The most common method to map m 6 A and to predict changes in m 6 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 m 6 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 m 6 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.
Databáze: MEDLINE
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