Epigenomic data analysis
Epigenomics studies heritable changes in gene function that do not involve changes to the underlying DNA sequence. These changes can include modifications to DNA, such as methylation, and modifications to the proteins with which DNA interacts, such as histones.
Several different types of epigenomic data exist, including DNA methylation, histone modifications, and chromatin accessibility data. Each type of data requires specific analytical methods.
DNA methylation data analysis typically involves identifying differentially methylated regions (DMRs) between experimental groups or samples. This can be done using methods such as Bisulfite sequencing (BS-seq) or Reduced representation bisulfite sequencing (RRBS).
Histone modification data analysis typically involves identifying differentially modified regions (DMRs) between experimental groups or samples. This can be done using methods such as ChIP-seq (chromatin immunoprecipitation sequencing) or an assay for transposase-accessible chromatin using sequencing (ATAC-seq).
Once the data is generated, bioinformatics tools and pipelines are used to process it, such as alignment, quality control, peak calling, annotation, and visualisation. The final results are often interpreted in the context of functional genomics, such as gene regulation, genetic variants, and disease association.
Bisulfite sequencing (BS-seq) is used to study DNA or RNA methylations with a single-base resolution. DNA methylation is a process by which methyl groups are added to the cytosine bases in the genome, typically in the context of CpG dinucleotides. BS-seq allows the identification of methylated and unmethylated cytosines in a genome by converting unmethylated cytosines to uracils through bisulfite treatment, while methylated cytosines remain unchanged.
BS-seq can be used to study the methylation patterns of the whole genome and targeted regions, such as gene promoters or repetitive elements. The method is widely used in cancer research, developmental biology, and epigenetic research.
Bisulfite sequencing
Methylation pattern of mitochondrial 12S rRNA (Van Haute et al. 2019)
Methylation pattern of mitochondrial tRNA in the presence or absence of NSUN2 (Van Haute et al. 2019)
5-formylcytosine (5fC) is a modified form of the nucleotide cytosine, which is present in DNA and RNA. It is formed through the oxidation of 5-methylcytosine (5mC) .
5fC is an epigenetic mark that has been shown to play a role in various biological processes such as gene regulation, DNA repair, and genome stability. The presence of 5fC has been reported in both normal and cancerous tissues, and it has been associated with the regulation of gene expression and the suppression of transposable elements.
Bisulfite sequencing is not able to detect 5fC as it converts 5fC and unmethylated cytosines both to uracils, so bisulfite sequencing can only detect 5mC and 5hmC. However, this can be useful in combination with other NGS-based methods such as RedBS-Seq and fCAB-seq. (Van Haute et al. 2020)
