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bioRxiv · 10.1101/2021.08.09.455753

Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

Cheetham, S. W.·Jafrani, Y. M. A.·Andersen, S. B.·Jansz, N.·Ewing, A. D.·Faulkner, G. J.
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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.

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Cheetham, S. W., Jafrani, Y. M. A., Andersen, S. B., Jansz, N., Ewing, A. D., Faulkner, G. J.. 2021-08-10. Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID. https://doi.org/10.1101/2021.08.09.455753

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