In conclusion, in addition to the promoter elements and TF binding sites, we were able to identify structural elements such as attenuators and terminators in the untranslated leader region of several genes.
Due to the definite specification of Ago binding sites, we were able to classify miRNA recognition elements contained in the mRNA 3′UTR as either functional or non-functional.
By matching the conservation profiles of putative transcription factors with the enrichment profiles of binding sites we were able to predict candidate transcription factors for a previously partially characterized ribosomal regulon.
Sites 1 and 6 are depicted in Figure 1B and C. Since junction region amino acids were predicted to be part of the potential ligand binding sites we were interested in further understanding the structure in the vicinity of the junction region.
By measuring the binding of SERS tags to microspheres with different densities of binding sites, we are able to estimate the relative single tag brightness and binding footprint of several different SERS tag compositions.
By identifying individual genes whose expression is predicted accurately by the binding sites, we are able to link transcription factors FOS, TAF1 and YY1 to a sparsely studied gene LRIG2.
By targeting an extended region of the conventional 'DFG-out' pocket of p38α, while minimizing interactions with the specificity pocket and eliminating interactions with the adenine binding site, we are able to design and synthesize a number of pyrazole-urea based DFG-out p38α inhibitors with good potencies, and excellent selectivity.
When the alternative transcripts of three genes, ATP11A, MCF2L, and RAB11-FIP3, were accounted for, 21 of the 22 (95%) of the STAT1 binding sites we identified were within 10 kbp of the nearest 1st exon of a gene (Table 1).
The binding sites we used were, TATA-box, CAAT-box, GC-box, E2F binding site, ATF/CREB binding site, Octamer1-box, AC-box, H4TF2 binding site, RT1-box, and TG-box.
Importantly, miR-134 is the most conserved of the five putative binding sites we tested, and is present in both predicted isoforms of the Pum2 3′UTR.
This region of the ribosome is known to play a role in the initiation of translation, and thus, the binding site we observe is consistent with evidence suggesting that thermorubin inhibits the initiation stage of protein synthesis.
