Genome-wide analysis of Gtf3c1, RNAP3 occupancy and H3K4me1, H3K27ac chromatin modifications in primary mouse cortical neurons

SINEs are a highly abundant class of retrotransposons that were initially considered a non-functional “junk” DNA due to their non coding, repetitive nature. SINEs frequently possess an internal RNAPIII promoter, which recruits the RNAPIII transcriptional machinery, including the general nuclear complex TFIIIC. We recently discovered that in response to neuronal depolarisation, SINEs may represent a novel class of neuronal enhancers and reasoned that RNAPIII and TFIIIC binding may provide a means of identifying enhancer SINEs genome-wide. To this end, we first performed ChIPseq analysis on resting and depolarised mouse cortical neurons, using an antibody that targets the DNA binding subunit of TFIIIC (Gtf3c1), RNA Polymerase III and the enhancer markers H3K4me1 and H3K27ac . Overall design: ChIPseq analysis of Gtf3c1, RNAP3, H3K4me1 and H3K27ac in primary mouse cortical neurons either untreated or depolarized with 50 mM KCl for 45 min. Total chromatin input was used as a control. For each experimental condition, 3 biological replicates were used.