The six up-regulated genes ABCA1, ABCG1, SMPDL3A (sphingomyelin phosphodiesterase, acid-like 3A), NR1H3, SCD (stearoyl-CoA desaturase) and TATDN2 (TatD DNase domain containing 2) and the three down-regulated genes CNNM4 (cyclin M4), HARS (histidyl-tRNA synthetase) and PUF60 (poly-U binding splicing factor 60 KDa) have LXR binding location with a motif highly similar (P < 10-6) to a DR4-type RE.
Since RXRα is an essential partner for other nuclear receptors, we compared ChIP-seq data to RXRα binding locations with locations from previous studies for PXR [ 18], LXR [ 19], FXR [ 20], and PPARα [ 19].
We extracted 200 bp sequence segments centered at TF binding locations identified with ChIP-seq and compared them with control sequences (i.e. 500 bp sequence segments starting from nucleotide positions 400 bp away from both ends of 200 bp test sequence segments).
By contrast, the majority of the assayed Paupar binding locations associated with genes that changed in expression upon Paupar but not Pax6 knockdown showed little enrichment for PAX6 (Fig 6B).
With each record, we provide the binding site location with a reference to a published sequence (usually NCBI RefSeq [ 26]), the sequence, the gene which is affected by the binding site, the evidence for the binding if any, any relevant articles pertaining to that site, and the transcription factor which binds the site.
We combined these binding location data, with new nucleosome maps built by next generation sequencing.
ATF6, a protein of interest to us, was predicted to be regulated by three of the upregulated miRNAs - miR-145, miR-221 and miR-494 (Figure 1). Figure 1A depicts the full-length human ATF6 3′UTR with predicted binding locations for miR-145, miR-221 and miR-494, and Figure 1B shows the locations and base pair matches of their proposed binding sites, adapted from TargetScan 6.2.
Furthermore, we find that within regions of high HAc, local minima of the HAc ChIP-Seq signal are particularly strongly correlated with TF binding locations.
The fungal ribosomal 18S rRNA gene and internal transcribed spacer (ITS) region with primer binding locations are shown in Figure 1.
Using Gene Ontology assignments (Ashburner et al, 2000), we next sought to characterise the set of genes associated with Paupar binding locations (Fig 4G, Supplementary Table 6).
