The advent of high-throughput sequencing techniques, together withbisulfite treatment of the DNA, allows for genome methylation profiling at asingle cytosine resolution. Some modern tools, as MethylExtract [1], are alsoable to detect variation (SNVs) using the same bisulfite sequencing library,which is crucial for many downstream analyses, for example when decipheringthe imp...

MOTIVATION The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either...

We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NG...

INTRODUCTION Epigenetic alterations, including DNA methylation, play an important role in the regulation of gene expression. Several methods exist for evaluating DNA methylation, but bisulfite sequencing remains the gold standard by which base-pair resolution of CpG methylation is achieved. The challenge of the method is that the desired outcome (conversion of unmethylated cytosines) positively...

Nanopore direct RNA sequencing assisted by pseudouridine- and m 5 C-specific bisulfite treatment is a technology that allows for epitranscriptomic modifications with the possibility of quantitative assessment.

RnBeads is an R package for the comprehensive analysis of genome-wide DNA methylation data with single basepair resolution. Supported assays include the Infinium 450k microarray, whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), other forms of enrichment bisulfite sequencing, and any other large-scale method that can provide DNA methylation data at si...