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The intragenic AP-1 binding sites correspond to an additional factor in an already complex network of regulators affecting HIV-1 replication at the transcriptional level, thereby contributing to an efficient viral control of the infection.
We, therefore, conclude that the ChIP-seq reads encompassing the identified binding sites correspond to the active mtDNA rather than to NUMTs.
Moreover, 48 of the 732 genes associated with Dsx binding sites correspond to genes identified in the dimorphism microarray experiments (Additional file 2).
Indeed, the conserved positions in the Gal4p binding sites correspond to the points of contact in the crystal structure of the protein-DNA complex (fig. 2, right panel) that are required for the recognition of the target sequence [ 30].
Since the vast majority of known binding sites correspond to only one TF each in a given organism, one may assume that the TF family size is approximately equal to the number of DNA binding domains used by that family.
To examine whether DNA regions with significantly enriched motif binding sites correspond to regulatory sequences, we focused on regions that have binding sites significantly more than average (Z score ≥ 3.09, P ≤ 10−3).
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Consensus binding sites corresponded to sequences at positions –295 (CAACaG), -799 (-CAACgG), -1454 (CAACaG), and –2251 (TAACtG).
Forty-four GlnR binding sites corresponded to the differential expression of 103 genes, 91 of which were located in 21 operons (Table 1).
One binding site corresponds to the consensus CGCGCg identified as the integration site, and a second binding site with a different sequence is located in close proximity.
The nucleotide sequence of the miR-548j binding site corresponded to the PRTRSC oligopeptide.
To address whether or not the mapped ORC1/CDC6 binding sites correspond with replication origins, we employed marker frequency analysis (MFA).
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