Identification of active regulatory regions from DNA methylation data

Nucleic Acids Res. 2013 Sep;41(16):e155. doi: 10.1093/nar/gkt599. Epub 2013 Jul 4.


We have recently shown that transcription factor binding leads to defined reduction in DNA methylation, allowing for the identification of active regulatory regions from high-resolution methylomes. Here, we present MethylSeekR, a computational tool to accurately identify such footprints from bisulfite-sequencing data. Applying our method to a large number of published human methylomes, we demonstrate its broad applicability and generalize our previous findings from a neuronal differentiation system to many cell types and tissues. MethylSeekR is available as an R package at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CpG Islands
  • DNA Methylation*
  • Genetic Variation
  • Humans
  • Mice
  • Regulatory Elements, Transcriptional*
  • Sequence Analysis, DNA*
  • Software*