Figure 5
Tripartite approach implicates high confidence targets of PRDM2 in alcohol dependence. (a) Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis identified genomic regions subjected to histone 3 at the lysine 9 residue (H3K9me1) epigenetic regulation in control versus postdependent dorsomedial prefrontal cortex (dmPFC). (b) Overlay of ChIP-seq and RNA-sequencing (RNA-seq) analysis from control versus postdependent dmPFC identified 119 common genes. These analyses were further overlaid with NanoString gene expression analysis from rat mPFC subjected to PRDM2 short hairpin RNA (shRNA) compared with a scramble control (hypergeometric distribution test P=0.001). (c–f) ChIP-seq data from the four common genes implicated in all three approaches. Top tracks show the UCSC gene relative to the scale shown at the right. The location of the region of differential H3K9me1 enrichment is denoted by the red box below the gene track. The bottom tracks show the Spatial clustering for identification of ChIP-enriched region (SICER)-filtered read enrichment of H3K9me1 ChIP data for the control rats (gray) and postdependent rats (light red) overlaid.
