Bisulfite-Treated Chromatin-Immunoprecipitated DNA / ChIP of Bisulfite-treated chromatin-Bisulfite Sequencing / Chromatin Immunoprecipitation with Bisulfite Methylation Sequencing Assay

BisChIP-seq, ChIP-BS-seq, and ChIP-BMS all refer to essentially the same method (Plongthongkum et al., 2014). It is a direct, quantitative approach to assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors (Brinkman et al., 2012). The ChIP-capturing step is used to obtain a restricted representation of the genome occupied by the epigenetic feature of interest. The captured DNA fragments are subjected to end-repair, adapter ligation using methylated adapters, bisulfite conversion, PCR amplification, and NGS.


  • Genome-wide coverage of 5mC in dense CpG areas and repeat regions
  • MBD proteins do not interact with 5hmC


  • Does not cover genome-wide CpGs and non-CpG methylation; misses areas with less dense 5mC
  • Base-pair resolution is lower (~150 bp), as opposed to single-base resolution with other methods
  • Protein-based selection is biased toward hypermethylated regions


Illumina Library prep and Array Kit Selector


Plongthongkum N., Diep D. H. and Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014;15:647-661

Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651


Jin J., Lian T., Gu C., Yu K., Gao Y. Q. and Su X. D. The effects of cytosine methylation on general transcription factors. Sci Rep. 2016;6:29119

Varshney D., Vavrova-Anderson J., Oler A. J., Cowling V. H., Cairns B. R. and White R. J. SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun. 2015;6:6569