RT Journal Article
SR Electronic
T1 Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 504993
DO 10.1101/504993
A1 Lee, Isac
A1 Razaghi, Roham
A1 Gilpatrick, Timothy
A1 Molnar, Michael
A1 Sadowski, Norah
A1 Simpson, Jared T.
A1 Sedlazeck, Fritz J.
A1 Timp, Winston
YR 2019
UL http://biorxiv.org/content/early/2019/02/02/504993.abstract
AB 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 methylation 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 repetitive regions inaccessible by short read sequencing. 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.