Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
Keywords: ChIP-seq; ChIP-seq, immunoprecipitated chromatin sequencing; DMR, differentially methylated region; DNA methylation; High-throughput sequencing; MBD-seq; MBD-seq, methyl binding domain protein sequencing; MeDIP-seq; methylated DNA immunoprecipitation sequencing; Psammomys obesus; RNA-seq, RNA sequencing; de novo assembly; epigenomic integration.