A novel workflow for the qualitative analysis of DNA methylation data.
Bisulfite sequencing
CG methylation
DNA methylation
Epialleles
Epigenetics
Non-CG methylation
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2022
2022
Historique:
received:
20
07
2022
revised:
19
10
2022
accepted:
19
10
2022
entrez:
16
11
2022
pubmed:
17
11
2022
medline:
17
11
2022
Statut:
epublish
Résumé
DNA methylation is an epigenetic modification that plays a pivotal role in major biological mechanisms, such as gene regulation, genomic imprinting, and genome stability. Different combinations of methylated cytosines for a given DNA locus generate different epialleles and alterations of these latter have been associated with several pathological conditions. Existing computational methods and statistical tests relevant to DNA methylation analysis are mostly based on the comparison of average CpG sites methylation levels and they often neglect non-CG methylation. Here, we present EpiStatProfiler, an R package that allows the analysis of CpG and non-CpG based epialleles starting from bisulfite sequencing data through a collection of dedicated extraction functions and statistical tests. EpiStatProfiler is provided with a set of useful auxiliary features, such as customizable genomic ranges, strand-specific epialleles analysis, locus annotation and gene set enrichment analysis. We showcase the package functionalities on two public datasets by identifying putative relevant loci in mice harboring the Huntington's disease-causing Htt gene mutation and in Ctcf +/- mice compared to their wild-type counterparts. To our knowledge, EpiStatProfiler is the first package providing functionalities dedicated to the analysis of epialleles composition derived from any kind of bisulfite sequencing experiment.
Identifiants
pubmed: 36382198
doi: 10.1016/j.csbj.2022.10.027
pii: S2001-0370(22)00474-3
pmc: PMC9636440
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5925-5934Informations de copyright
© 2022 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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