Genetically determined differences in Jund expression alter the JunD cistrome and identifies primary JunD targets. (A) Distribution of JunD-peaks relative to transcriptional start sites (TSS) of Ensembl genes. Promoter region defined as 20 kilobases (kb) upstream of the TSS, upstream region between 10kb and 50kb upstream from TSS. (B) Occurrence of peaks within 100 kilobases of the TSS. (C) Twelve base pair AP-1 motif identified by de novo motif analysis present in 63% peaks. De novo motif analysis using HOMER identified two de novo motifs in basal WKY BMDMs (D) and four motifs in LPS stimulated WKY BMDMs (E). The de novo motif identified is displayed on the bottom of each the pair of motifs, the matched consensus motif for a transcription factor on the top. (F) Il1b and Prkca confirmed as primary JunD targets by qPCR validation. The aligned reads comprising peak passing the posterior probability threshold of 0.9 for each JunD-bound gene in the WKY strain in the LPS stimulated state for l1b and the basal state for Prkca are shown in genome browser views along with the peak in the WKY.LCrgn2 strain. Samples from WKY and WKY.LCrgn2 strains were amplified using three biological replicates with three technical replicates per sample. Results expressed as mean fold change over IgG. *P<0.05; **P<0.01; using a one-tailed unpaired t-test to detect statistically significant differences between the strain and condition pairs. Error bars represent standard error of the mean.
Hull et al. BMC Genomics 2013 14:92 doi:10.1186/1471-2164-14-92