m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq.

Ye, Haokai, Li, Tenglong, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Wei, Zhen (2024) m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. Nucleic acids research. gkae280-gkae280.

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Official URL: http://dx.doi.org/10.1093/nar/gkae280

Abstract

We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.

Item Type:	Article
Uncontrolled Keywords:	Genetics, Human Genome, Biotechnology, Generic health relevance, 3 Good Health and Well Being
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	22 Apr 2024 07:44
Last Modified:	26 Apr 2024 21:47
DOI:	10.1093/nar/gkae280
Open Access URL:	https://academic.oup.com/nar/advance-article/doi/1...
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3180474