Chromatin Immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest. The ChIP assay holds an enormous potential to improve our understanding of the regulation of gene expression. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.
ChIP-sequencing (ChIP-Seq) combines chromatin immunoprecipitation (ChIP) and the massively parallel sequencing technology of NGS to identify those DNA sequences bound by transcription factors in vivo.
A common form of the ChIP-Seq experiment is the Histone Modification Analysis. Histone compaction of DNA is a well-known epigenetic regulator of gene expression. Post-translational modification of histones, such as histone deacetylation, is another common form of epigenetic control, and is known to be associated with gene silencing. Therefore, evaluation of histone coverage and histone modification status are valuable tools in understanding the genome-wide regulation of gene expression.
How it works
Chromatin is first treated with formaldehyde to fasten the chromatin-bound proteins to the DNA, followed by shearing into small fragment sizes (200bp – 1kb). This step is followed by immunoprecipitation using a specific ChIP-grade antibody. Cross-linking is reversed, and followed by proteinase K treatment or DNA purification using magnetic beads (IPure kit). The purified DNA is then submitted to ACGT (see Important Considerations and Sample Submission Guidelines) and analyzed to identify the genomic regions where the specific DNA binding protein (e.g. histone) was located. A ChIP-Seq library for analysis on Illumina® NGS platforms can be generated using any number of commercially available ChIP-Seq kits (please verify the kits are Illumina platform compatible).