A likely recombination breakpoint occurred in the nucleotide region between IHF_1 and DnaA_2 (see arrow, Fig. 3A) indicating a potential shuffling among binding sites at this region.
As cell-line specific CTCF binding events are more likely to overlap with cell-line specific ER binding events, CTCF may direct ER binding at these regions thereby acting as a 'licensing factor' for ER.
Further analysis highlighted that the loss of these putative SP1-binding sites is also associated with detectable falls in the observed levels of SP1 binding at these regions (fig. 3 A).
Reduction of H3K9me3 levels through down-regulation of methyltransferases Suv39H1&2 enhances Oct4 and Sox2 binding at these regions and increases reprogramming efficiency (Onder et al, 2012; Soufi et al, 2012).
In order to discard any possibility of a direct PR binding to DNA at this region, we also used the weak matches option (−w) of MAST and FIMO tools.
Moreover, while spt16-m mutation led to a mildly reduction of Sir2 4p binding at heterochromatin region, this mutation in combination with cac1Δ rtt106Δ led to a dramatic reduction of Sir2 4p binding comparing with either single or double mutant cells (Fig. 2A).
There was a small effect (<2-fold) on chromatin compaction at 18q22.2 after SMC3 knockdown, although paradoxically there are no annotated SMC3/cohesin binding sites at this genomic region (Fig. 2B), but there was no chromatin decompaction detected at the gene-dense regions with the highest density of SMC3 ChIP peaks and which are the regions also most affected by NIPBL knockdown (Fig. 2D and E).
CYP26B1 (cytochrome P450, family 26, subfamily b, polypeptide 1) which was up-regulated in samples treated with 1,25(OH)2D3 0.5nM, was previously identified as a vitamin D induced gene in immortalized non-transformed prostate epithelial and oral squamous carcinoma cell lines, and in silico analysis has tentatively identified a VDR binding site at this genomic region [ 43, 44].
DOI: http://dx.doi.org/10.7554/eLife.06821.020 Furthermore, we do not observe binding at either region in hMSCs (Author response image 2).
