Simultaneous Tagmentation-Based Detection of ChIP/ATAC Signal with Bisulfite Sequencing

Methods Mol Biol. 2021:2351:337-352. doi: 10.1007/978-1-0716-1597-3_19.

Abstract

DNA methylation is thought to regulate accessibility of chromatin and binding of regulatory elements; however, it is difficult to determine if chromatin accessibility or transcription factor (TF) binding overlap with methylated or unmethylated DNA if the assays are performed separately. In order to examine accessibility or TF binding simultaneously with methylation on the same DNA molecule, we developed EpiMethylTag which combines ATAC-Seq or ChIP-Seq (M-ATAC or M-ChIP) with bisulfite conversion. Our approach provides a fast, low-input, low sequencing depth method to determine whether DNAme and accessibility/TF binding are mutually exclusive or can coexist in certain locations.

Keywords: Bisulfite sequencing; Chromatin accessibility; Chromatin immunoprecipitation; CpG methylation; Tagmentation.

MeSH terms

  • Binding Sites
  • Chromatin / genetics*
  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly*
  • Chromatin Immunoprecipitation Sequencing / methods*
  • CpG Islands
  • DNA Methylation*
  • DNA Transposable Elements
  • Epigenesis, Genetic
  • High-Throughput Nucleotide Sequencing / methods
  • Protein Binding
  • Real-Time Polymerase Chain Reaction
  • Transcription Factors / metabolism*

Substances

  • Chromatin
  • DNA Transposable Elements
  • Transcription Factors