Fig. 6 | Nature Communications

Fig. 6

From: A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

Fig. 6

Activation of H3K27me3 marked genes during stress. a TRAP-seq: Volcano plot showing differential gene expression in mDA neurons from lesioned and unlesioned hemispheres 14 days after unilateral 6-OHDA injections (n = 5 mice) (Methods). b As in a where H3K27me3 and/or H3K9me3-marked and regulated genes are marked with red. c Gene ontology (GO) of selected (−log10(adj p-value), Fisher’s exact test) biological processes for upregulated genes in mDA neurons of the lesioned hemisphere (n = 87). d Bars indicate the odds-ratio fold enrichment for upregulated genes after 6-OHDA treatments per chromatin state. Absolute numbers of genes per state are given in parenthesis. Red bars indicate significant enrichment according to Fisher’s exact test and are adjusted for multiple testing. e TRAP-qPCR confirming induction of Hrk relative to Tbp in mDA after 6-OHDA. Bars indicate average expression ± SD. Two-tailed Student’s t-test assuming equal variances. *p ≤ 0.05. f Genome browser excerpt showing H3K4me3 (K4, red, vertical scale 0–160 RPKM) and H3K27me3 (K27, gray, vertical scale 0–100 RPKM) enrichment at the Hrk locus in naive mDA nuclei. g ChIP-qPCR in mDA nuclei showing fold-enrichment of IgG, K4, and K27 relative to input near the Hrk TSS. Bars indicate average enrichment ± SD. K4 enrichment was significantly higher near Hrk compared to near the Hoxa2 TSS and K27 enrichment was significantly higher compared to near the Tbp TSS (Supplementary Fig. 11f,h). Two-tailed Student’s t-test assuming equal variances. ***p ≤ 0.001. hj As in eg for Penk. k TRAP-seq: Volcano plot showing differential gene expression in mDA neurons 2 h after a single methamphetamine injection compared to saline-injected controls, similar to a. l As in k where H3K27me3 and/or H3K9me3-marked and regulated genes are marked with red. m GO for selected (−log10 (adj p-value), Fisher’s exact test) biological processes for upregulated genes in mDA neurons after methamphetamine (n = 52). n Odds ratio for upregulated genes after methamphetamine per chromatin state as in d. ot Examples of upregulated K4/K27 genes after methamphetamine, similar to eg. u Silent genes with K4/K27-marked promoters are commonly involved in stress responses: GO for selected (−log10 (adj p-value), Fisher’s exact test) biological processes for K4/K27 genes with log2(RPKM + 1)<1 in naive mDA neurons

Back to article page