It is important to note that this deletion removes multiple transcription factor binding sites, including the FUSE binding element known to be required for proper MYC expression [16].
The basic assumption is that many putative binding sites, including the sites of TFexp and of other factors, not just the single best match, may contribute to interaction of this sequence to TFexp.
Specifically, we report the results of virtually screening ∼11,000 diverse fragment-like compounds against a total of 152 protein binding sites, including the training dataset and external dataset studied by Hajduk and coworkers [27].
Thereafter, analysis of the genomic region surrounding the miRNA 17-5p-92 cluster for putative MYCN binding sites (including the canonical E-box CACGTG and the non-canonical sequences CATGTG, CACGGG and CAAGTG) revealed the presence of five MYCN putative binding sites, four upstream and one downstream the cluster (Figure 1C).
53 Other regions of the mRNA can also contain functional miRNA binding sites, including the 5′UTR and the amino acid coding sequence.
There are similarities between neurons and platelets regarding the mechanisms of 5-HT transport and the presence of certain binding sites including the 5-HT2 receptor [ 32, 33].
For this analysis, we extracted the 110 c-Myc binding sites including the flanking sequences (100 bp flanking the 5 bp core sequence to both sides (= 205 bp)).
Based on prediction programs, the mutation at c.−270_−269 position would disrupt several transcription factor binding sites, including the zinc-finger protein SP1.
The conservation of these putative binding sites, including the conservation of the flanking A and T nucleotides (see Additional file 3), suggests GlnR represses the amtB-glnK operon in all analyzed species, and thus also in B. subtilis.
