Chromatin Immunoprecipitation of Histone Modifications

Chromatin Immunoprecipitation was performed with anti-H3 antibodies (Abcam, Cambridge, United Kingdom, ab1791), anti-H3K9ac antibodies (Abcam, Cambridge, United Kingdom, ab12179), anti-H3K9me2 antibodies (Abcam, Cambridge, United Kingdom, ab1220), anti-H4K5ac antibodies (Abcam, Cambridge, United Kingdom, ab51997), anti-DNA-RNA Hybrid antibodies (Kerafast, Boston, MA, United States), following the procedure used by Cong et al. (2012) (link). Rabbit serum was used as a negative control for mock immunoprecipitation. Precipitated genomic DNA was subjected to quantitative PCR with primers below that were designed to amplify approximately 200–1000 bp fragments encompassing the promoter region, the exon region and the intergenic spacer (IGS) region of the rDNA gene according to the real-time PCR procedure mentioned above. All primer sequences for ChIP were referenced from published data (Cong et al., 2012 (link)).