BisChIP-Seq/ChIP-BS-Seq
BisChIP-Seq/ChIP-BS-Seq
BisChIP-seq, ChIP-BS-seq, and ChIP-BMS all refer to essentially the same method. It is a direct, quantitative approach to assess DNA methylation patterns associated with chromatin modifications or chromatin-associated factors.1
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.
Pros:
- Genome-wide coverage of 5mC in dense CpG areas and repeat regions
- MBD proteins do not interact with 5hmC
Cons:
- 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
- BisChIP-Seq/ChIP-BS-Seq: Plongthongkum N., Diep D. H. and Zhang K. (2014) Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet 15: 647-661
- 1. Brinkman A. B., Gu H., Bartels S. J., et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012;22:1128-1138
- 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., et al. (2016) The effects of cytosine methylation on general transcription factors. Sci Rep 6: 29119
- Varshney D., Vavrova-Anderson J., Oler A. J., Cowling V. H., Cairns B. R., et al. (2015) SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun 6: 6569