Studying histone modifications with ChIP

ChIP uses antibodies to isolate a protein or modification of interest, along with the DNA to which it is bound. The DNA is then sequenced and mapped to the genome to identify the protein or modification’s location and abundance.

Utilizing antibodies against specific histones and histone modifications in ChIP experiments can reveal the specific locations of

• Higher order chromatin structures, eg H3K9me3 marks heterochromatin and satellite repeats
• Active or silenced genes and genetic programs, eg AH3K9ac marks gene activation
• Genetic elements like promoters and enhancers, eg H3K27me3 marks promoters in gene-rich regions, H3K4me1 marks active enhancers

If the function of a histone modification is known, ChIP can identify specific genes and regions with this histone modification signature and the corresponding function across the genome. These genes and regions can then be further examined for their role in the biological process of interest. Using ChIP against H3K4me1, for example, will reveal the locations and sequences of active enhancers throughout the genome, pointing to genes and genetic programs of interest.

Alternatively, if the function of the histone modification is not known, ChIP can identify sequences, genes, and locations with this signature, which can then be used to infer the function of the modification. This technique was pivotal in decoding much of the histone code and is still valuable in ascertaining the function of newly discovered modifications like ubiquitylation and other novel markings.

Histone modification ChIP. Antibodies bind directly to modified histone tails. Immunoprecipitation and DNA purification allow for the isolation and identification of the genomic regions that the modifications occupy.