Our work extends our understanding of the repertoire of functions for the CTCF protein by demonstrating occupancy, binding, and regulation of rDNA by CTCF, and consequence of loss-of-function mutation on rDNA behavior.
We investigated the expression of the CXCL12, GREB1, PGR and PKIB genes which we previously identified as robust estrogen-regulated genes in transcriptome-wide studies [ 32] and which all demonstrate occupancy of cohesin components and ER/cohesin-based chromosomal looping [ 4, 10, 32].
Having demonstrated the occupancy of ΔNp63 to Hs II of the K5 gene, we next investigated whether this segment could function as an enhancer element.
Consistent with this hypothesis, depletion of Oct4 in ESCs caused downregulation of Cbx7, and ChIP studies demonstrated direct occupancy by Oct4, Sox2, and Nanog.
Indeed, our Runx2 ChIP-seq analysis in C4-2B/Rx2dox cells [ 52] demonstrated strong occupancy of the SPDEF transcription start site by Runx2 (Additional file 3: Supplemental Figure 1C).
Bioinformatic analysis of ChIP-seq data demonstrated promoter occupancy of PPARβ/δ for some of these genes, and also identified the presence of other transcription factor binding sites in close proximity to PPARβ/δ bound to chromatin.
In previous studies, we have demonstrated that occupancy of adenosine A2A receptors by an appropriate agonist, such as CGS-21680, promotes more rapid wound closure in both normal mice and diabetic rats and the enhancement in dermal wound healing is accompanied by an increase in matrix (collagen) in the wounds [ 2- 4].
While the original populations always demonstrate low occupancy per chromosomal site, the colonising populations (Australian and Spanish) have some sites with high occupancy.
ChIP assays to demonstrate Ebp1 occupancy on AR promoters are underway in the laboratory.
