Single-molecule simultaneous profiling of DNA methylation and DNA–protein interactions with Nanopore-DamID
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Protein-DNA interactions and DNA methylation control mammalian gene expression. Here we present Nanopore-DamID 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 strict CpG methylation maintenance at transcriptional start sites amidst generalised hypomethylation of LaminB1-associated heterochromatin. Promoter methylation is required for escape of a small subset of genes from Lamin-associated repression. We detect novel CTCF binding sites in highly repetitive regions and allele-specific binding to imprinted genes and the active X chromosome, highlighting the importance of DNA methylation to transcription factor activity.