Using chromatin immunoprecipitation (ChIP) and primers designed to flank these YB-1 putative binding sites, we found evidence that YB-1 binds to the SOX2 promoter at two adjacent regions.
Among GR binding sites, we found that 46%% occur at enhancers having all three marks.
Despite the co-localization of AGO1 with CTCF and HP1α binding sites, we found a weak but independent binding motif for AGO1.
Moreover, when we broadly searched PlasmoDBv10.0 transcripts for human microRNA binding sites, we found thousands of significant hits and that 61 transcripts harbored at least 100 predicted binding sites for a given human microRNA (p-value < 0.05) [Additional file 32].
Although the computational sequence analysis of 2.2 kb upstream of the pre-miR-29b1 stem indicated four putative CEBP binding sites, we found that none of them was CEBPA responsive in luciferase assays (data not shown).
Using literature searches as well as public databases containing known rice binding sites, we found 559 of our motifs matching 43 known regulatory sites out of 96 distinct sequences in both databases (see Table 1, 2 and Additional files 7, 8).
By mapping the genomic binding sites, we found that both TBP and Pol II display greater than 63% occupancy at transcriptional start sites (TSS) of highly expressed genes in both undifferentiated C3H10T1/2 cells and adipocytes, consistent with their roles in mediating global and general transcription functions.
For this small set of carefully annotated binding sites, we found 31% of sites were conserved within the sensu strictu Saccharomyces species but a significantly smaller fraction, 26%, were conserved in the distantly related species (P = 0.019, Mann–Whitney U test).
Scanning the whole protein without using any prior knowledge of the binding site, we find that the best scoring conformation in rhodopsin is 1.1 Å CRMS from the crystal structure for the ligand atoms.
