BisChIP-Seq/ChIP-BS-Seq/ChIP-BMS
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.
Advantages:
- Genome-wide coverage of 5mC in dense CpG areas and repeat regions
- MBD proteins do not interact with 5hmC
Disadvantages:
- 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
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
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
References:
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
Related
History: BisChIP-Seq/ChIP-BS-Seq/ChIP-BMS
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
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.
Advantages:- Genome-wide coverage of 5mC in dense CpG areas and repeat regions
- MBD proteins do not interact with 5hmC
Disadvantages:- 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
Reagents:Illumina Library prep and Array Kit SelectorReviews:Plongthongkum N., Diep D. H. and Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014;15:647-661Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651References: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;6:29119Varshney 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