Table 3.

Overlapping dmPFC gene expression changes caused by a history of alcohol dependence (RNA-seq data from PD versus CTL), as well as knockdown of PRDM2 (n = 8–9)

Gene name	RNA-seq: PD versus CTL		PRDM2 shRNA versus scramble		H3K9me1 ChIP: PD versus CTL
	Fold change	P-value	Fold change	P-value	Fold change	P-value	Region of enrichment
Abcd3	1.27	0.03	−17.5	0.02
Bsn	−1.52	0.03	−143.50	0.04	−1.32	0.008	Intron 1/11
					−2.21	0.02	Intron 1/11
Cacna1d	−1.66	0.02	−5.56	0.01	−1.27	0.005	Intron 8/50
					−1.51	0.006	Intron 9/50
Cacna1i	−1.71	0.01	−6.75	0.03	−1.27	0.0006	Introns 25/28–27/38
Helz	−1.53	0.01	−4.82	0.04
Ncor2	−1.78	0.01	−3.74	0.02
Nop14	1.42	0.02	−8.27	0.01
Rab3c	1.41	0.02	62.73	0.01
Wnk2	−1.99	0.008	−11.55	0.004	−2.06	0.01	Intron 1/26

Abbreviations: ChIP, chromatin immunoprecipitation; CTL, control; dmPFC, dorsomedial prefrontal cortex; H3K9me1, histone 3 at the lysine 9 residue; PD, postdependent; shRNA, short hairpin RNA. Several of these genes may be direct targets of PRDM2, since EdgeR significance analysis of ChIP-seq data identified differential enrichment of H3K9me1 at the indicated genomic loci in the context of alcohol dependence (n = 4).