Abstract
We present Nanopore-DamID, a method to simultaneously detect cytosine methylation and DNA-protein interactions from single molecules, via selective sequencing of adenine-labelled DNA. Assaying LaminB1 and CTCF binding with Nanopore-DamID, we identify escape from LAD-associated repression of hypomethylated promoters amidst generalised hypermethylation of LaminB1-associated regulatory elements. We detect novel CTCF binding sites in highly repetitive regions, and allele-specific CTCF binding to imprinted genes and the active X chromosome. Nanopore-DamID highlights the importance of DNA methylation to transcription factor activity.
Competing Interest Statement
Registration, travel and accommodation at the 2022 Lorne Genome conference for S.W.C were paid for by Oxford Nanopore Technologies.
Footnotes
The manuscript is updated with the inclusion of profiling of the transcription factor CTCF and further controls.