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The sequence and context of DNA elements bound by transcription factors give insight into the action of those factors.
The canonical E-box sequences CACGTG and CATGTG [23] as well as non-canonical E-boxes, such as CATGCG, CACGCG, CACGAG, and CAACGTG have been identified as cis-acting elements bound by Myc [43].
The cis-regulatory elements bound by the KstR protein, a known regulator of lipid/cholesterol metabolism, are among the strongest, most highly conserved noncoding signals across the Mycobacteria.
Despite the relatively high sequence conservation of the AP2/ERF domain, the number of DNA elements bound by different AP2/ERF transcription factors is extremely wide [[ 3, 9] and [ 10]].
In order to estimate the age of the various HNF4α-Alu elements, we determined the presence of the Alu elements bound by HNF4α in the HepG2 ChIP assay in four sequenced primate genomes - marmoset, rhesus, orangutan and chimpanzee.
Such models have been applied to systems ranging from a single cis-regulatory element to diverse collections of highly divergent elements bound by a wide range of proteins [ 3, 6].
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In eukaryotes, nucleosome disruption is a basic feature of active OCRs, which contain cis-elements bound by transcription factors (TFs 5.
Furthermore, the Nip30-Rspry1 common regulatory region contains a conserved E-box enhancer, which is an element bound by myogenic regulatory factors that function in the regulation of muscle-specific gene expression.
Currently, examination of co-existing cis-elements bound by the different TFs of the same cluster is helpful if the method is applied to data from bacteria and yeast.
In addition, cluster_9_CCACC in the upstream of CesA8 is a variant of the AC element bound by MYB TFs [ 46].
The consensus sequence of the most strongly enriched motif for the monocyte to iDC transition is TGACTGA, the AP-1 response element bound by bZIP transcription factors JUN, FOS, BATF, BATF3, as well as IRF4, and IRF8 [ 23].
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