How do I measure histone modification?

Histone modification can be measured using different techniques such as mass spectrometry and genomics techniques. Examples of genomic techniques include ChIP-chip and ChIP-seq. ChIp-chip and ChIP-seq combine chromatin immunoprecipitation of modified histones and their corresponding DNA with microarray (ChIP-chip) or NSG (ChIP-seq) of molecules to identify regions of the genome which correspond to these modifications. ChIP uses antibodies to isolate a protein or modification of interest, together with any bound DNA. This is used to determine where the protein of modification of interest is found within the genome and its abundance at each location.

Due to its high throughput, flexibility, and accuracy, mass spectrometry can also be used to measure histone modification. It allows for a comprehensive analysis of histone PTMs and chromatin associate factors. Following the procedure of MS, database searching algorithms compare experimental mass spectra against a database of theoretical spectra from known histone sequences with various modifications. One can then compare the observed and theoretical data, and determine histone modification sites.