EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

Genome Biol. 2019 Nov 21;20(1):248. doi: 10.1186/s13059-019-1853-6.

Abstract

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.

Keywords: ATAC; CTCF; ChIP; Chromatin accessibility; DNA methylation; KLF4.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation Sequencing*
  • DNA Methylation*
  • Genomics / methods*
  • Humans
  • Transcription Factors / metabolism

Substances

  • Chromatin
  • Transcription Factors