title: Methodological aspects of whole-genome bisulfite sequencing analysis.
abstract: The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation beyond CpG sites and CpG islands. These technologies have opened new avenues to understand the interplay between epigenetic events, chromatin plasticity and gene regulation. However, the processing, managing and mining of this huge volume of data require specialized computational tools and statistical methods that are yet to be standardized. Here, we describe a complete bisulfite sequencing analysis workflow, including recently developed programs, highlighting each of the crucial analysis steps required, i.e. sequencing quality control, reads alignment, methylation scoring, methylation heterogeneity assessment, genomic features annotation, data visualization and determination of differentially methylated cytosines. Moreover, we discuss the limitations of these technologies and considerations to perform suitable analyses.
authors.forename: Swarnaseetha
authors.initials: S
authors.lastname: Adusumalli
authors.forename: Mohd Feroz
authors.initials: MF
authors.lastname: Mohd Omar
authors.forename: Richie
authors.initials: R
authors.lastname: Soong
authors.forename: Touati
authors.initials: T
authors.lastname: Benoukraf
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018899:CpG Islands / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000737:chemistry
chemical_list: D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite
keywords: DNA methylation; bisulfite sequencing; epigenetics; high-throughput sequencing