MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

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Abstract

DNA methylation studies have been reformed with the advent of single-base resolution arrays and bisulfite sequencing methods, enabling deeper investigation of methylation-mediated mechanisms. In addition to these advancements, numerous bioinformatics tools address important computational challenges, covering DNA methylation calling up to multi-modal interpretative analyses. However, contrary to the analytical frameworks that detect driver mutational signatures, the identification of putatively actionable epigenetic events remains an unmet need. The present work describes a novel computational framework, called MeinteR, that prioritizes critical DNA methylation events based on the following hypothesis: critical aberrations of DNA methylation more likely occur on a genomic substrate that is enriched in cis-acting regulatory elements with distinct structural characteristics, rather than in genomic “deserts”. In this context, the framework incorporates functional cis-elements, e.g. transcription factor binding sites, tentative splice sites, as well as conformational features, such as G-quadruplexes and palindromes, to identify critical epigenetic aberrations with potential implications on transcriptional regulation. The evaluation on multiple, public cancer datasets revealed significant associations between the highest-ranking loci with gene expression and known driver genes, enabling for the first time the computational identification of high impact epigenetic changes based on high-throughput DNA methylation data.

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Malousi, A., Kouidou, S., Tsagiopoulou, M., Papakonstantinou, N., Bouras, E., Georgiou, E., … Stamatopoulos, K. (2019). MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-55453-8

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