A novel workflow for the qualitative analysis of DNA methylation data

Sarnataro, Antonella; Riso, Giulia De; Cocozza, Sérgio; Pezone, Antonio; Majello, Barbara; Amente, Stefano; Scala, Giovanni

doi:10.1016/j.csbj.2022.10.027

Cited by 3 publications

(1 citation statement)

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“…For RRBS data, epiallele counts were extracted from BAM files using the EpiStatProfiler R package (( 52 ), https://github.com/BioinfoUninaScala/epistats ). First, genomic regions covered by at least 50 reads were individuated through the filterByCoverage function.…”

Section: Materials and Methodsmentioning

confidence: 99%

MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data

Riso

Sarnataro

Scala

et al. 2022

NAR Genomics and Bioinformatics

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DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.

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Section: Materials and Methodsmentioning

confidence: 99%