Lee I , Razaghi R , Gilpatrick T , Sadowski N , Sedlazeck FJ , Timp W . Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Technical Report https://doi.org/10.1101/504993, bioRxiv, 2018.
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Understanding how the genome and the epigenome work together to control gene transcription has applications in our understanding of diseases such as human cancer. In this study, we combine the ability of NOMe-seq to simultaneously evaluate CpG and chromatin accessibility, with long-read nanopore sequencing technology, a method we call nanoNOMe. We generated >60Gb whole-genome nanopore sequencing data for each of four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231) including normally poorly mapped repetitive regions. Using the long reads, we find that we can observe phased methylation and chromatin accessibility, large scale pattern changes, and genetic changes such as structural variations from a single assay.