In addition, we directly searched for matches to TGATNNAT[g/t][g/a] and TGATTTAT/TGATTTATTT/ATGATTTATGG in both the top 1000 embryo Ubx binding peaks and the 1875 haltere binding peaks but found none of these motifs significantly enriched in either dataset.
We have compared the TAF9B ChIP-seq binding sites to the HOXC9 ChIP-seq binding sites, in the same manner as we compared to OLIG2 ChIP-seq peaks, and found that only a limited number of TAF9B peaks (∼6% of TAF9B peaks) showed co-localization with HOXC9 ChIP-seq peaks (examples in Figure 5-figure supplement 1A and data not shown).
Since the Ubx and Abd-A binding profiles strongly mirror the chromatin accessibility profile, we first examined the DNase1 peaks and found they do not show enrichment for Hox PWMs (Fig. 4a).
When we examined the average H3K4me2 signal across a 3-kb window centered on the summit of all GR binding peaks, we found that global ChIP-Seq profiles before and after GR binding closely resemble those reported for AR (Fig. 2c) [ 18].
When the MACS identified 7693 Tip60 binding peaks were annotated to promoter-TSS, 5′- or 3′-untranslated regions (UTRs), exons, introns and intergenic regions, about 42 % of all high-confidence Tip60 binding peaks were found at promoter-TSS regions (Fig. 4a).
In a region of 2 kb up- and downstream of transcription start sites, AIRE-binding peaks were found in 30% of AIRE-upregulated genes present on the array.
Despite BRD4 peak signal intensity being similar in SEs and typical enhancers (TEs) in hESCs, more BRD4-binding peaks were found in SEs than in TEs.
Some of these tools [ 33, 39] use the locations of binding peaks to help find the CREs of a ChIP-ed TF.
Binding peaks with FDR < 0.01 were defined as the ARF6 binding peak and used in further analyses.
Thereby, luteolin-7-O-β-D-glucoside, with its two binding sites, produced higher Fe2+-binding peaks and a darker solution color than epicatechin with one binding site.
