Generating sequencing-based DNA methylation maps from low DNA input samples

摘要: Reduced representation bisulfite sequencing (RRBS) is a technique used for assessing genome-wide DNA methylation patterns in eukaryotes. RRBS was introduced to focus on CpG-rich regions that are likely to be of most interest for epigenetic regulation, such as gene promoters and enhancer sequence elements (Meissner et al., Nature 454:766–770, 2008). This “reduced representation” lowers the cost of sequencing and also gives increased depth of coverage, facilitating the resolution of more subtle changes in methylation levels. Here, we describe a modified RRBS sequencing (RRBS-seq) library preparation. Our protocol is optimized for generating single base–resolution libraries when low input DNA is a concern (10–100 ng). Our protocol includes steps to optimize library preparation, such as using deparaffinization solution (when formalin-fixed material is used), and a replacement of gel size-selection with …