Table 2. Methods for Studying Histone Modifications.

Method
ChIP	Involves lightly fixing tissue to cross-link DNA to associated proteins; followed by fragmenting the fixed chromatin by sonication or micrococcal nuclease digestion; and finally, immunoprecipitating the fragmented chromatin with an antibody specific for a given modification of interest (e.g. acetylated or methylated histone).
qChIP	Involves quantifying the amount of immunoprecipitated chromatin at a single genomic region using qPCR analysis.
ChIP-chip	Involves quantifying the amount of immunoprecipitated chromatin at thousands of promoter regions using a promoter-specific DNA microarray.
ChIP-seq	Involves quantifying the amount of immunoprecipitated chromatin for all genomic regions by high- throughput sequencing. ChIP-seq has the additional advantage over ChIP-chip of providing higher base-pair resolution for each genomic region.
RNA-seq	Involves isolating RNA and converting it to cDNA, followed by high-throughput sequencing. RNA-seq has several advantages over older microarray methods, including higher base-pair resolution, detection of non-coding RNAs, and the ability to identify alternative splice variants.

Detailed descriptions for the methods discussed herein are listed. Abbreviations: ChIP, chromatin immunoprecipitation; qChIP, quantitative ChIP; seq, high throughput sequencing.