High-Resolution Crosslinking Chromatin Immunoprecipitation Sequencing
Crosslinking chromatin immunoprecipitation (X-ChIP) is a foundational technique in chromatin research (Breiling et al., 2001) (Negre et al., 2001). With the advent of NGS this simple technique, now called X-ChIP-seq, is able produce high-resolution results (Skene et al., 2015).
The method involves crosslinking chromatin-bound DNA in cells with 1% formaldehyde for 10 minutes at room temperature. The cells are washed and resuspended in lysis buffer. After MNase digestion, the chromatin is solubilized by brief sonication and then subjected to chromatin immunoprecipitation. The DNA is extracted, enriched for short fragments, and used to prepare a sequencing library.
- Single-base resolution
- Sonication may introduce sequence bias (Teytelman et al., 2009)
- Captures protein-DNA interactions regardless of duration (Zentner et al., 2015)
Illumina Library prep and Array Kit Selector
Zentner G. E. and Henikoff S. High-resolution digital profiling of the epigenome. Nat Rev Genet. 2014;15:814-827
Schmidt S. V., Krebs W., Ulas T., et al. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res. 2016;26:151-170
Elsasser S. J., Noh K. M., Diaz N., Allis C. D. and Banaszynski L. A. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature. 2015;522:240-244