The sequence of the putative GAS site present in the LKB1 promoter, when reverse complemented, was found to be identical to both a PRL-responsive distal GAS site located in the human cyclin D1 promoter (TTCTTGGAA) [ 32, 33] and a canonical STAT5 binding site (PRE) within the β-casein promoter [ 30, 31], differing by only one base pair from a binding site described for STAT3 (TTCTGGGAA) [ 43].
A nuclear factor III (NF-III) binding site described as conserved among most human adenoviruses as a 5'ATGNNAATGA 3' sequence motif (ATGCAAATAA in HAdV-E4) [ 26] was not identified in the HAdV-A31 ITR, but a 5'ATGAAGTGGG 3' sequence at position bp 46-55 may function as a binding site for NF-III.
The two Na+ ions were positioned equivalently to those in LeuT and a Cl− ion was placed based on the chloride binding site described in [42].
Interestingly, the promoter regions of the ISA1307 genes predicted to encode gluconeogenic enzymes, enzymes of the TCA cycle or enzymes required for acetate or glyoxylate metabolism, all subjected to glucose repression in S. cerevisiae in a Mig1-dependent manner, harbour DNA motifs similar to the binding site described for ScMig1 (results not shown).
Alterations in the IPP binding site described above did not affect the position of RIS in the binding pocket in either mutant (Fig. 4A).
As described in detail, the models included the substrate, dopamine (DA), docked in the S1 site, two Na+ ions, positioned equivalently to those in the LeuT crystal structure, and a Cl– ion coordinated by residues Asn82, Tyr102, Ser321, and Asn353 of hDAT, based on the chloride binding site described previously.
The general location of the hydrophobic binding site described here and the interaction between the alkyl chains of the blockers and the inner helix main chain at residue G99 suggest that an alternative phrase such as "finger in the hinge" might more aptly describe the action of these blockers.
The analyses of Kaiso binding sites described above were performed using GM12878 cells, which is an EBV immortalized normal lymphoblastoid cell line.
However, when we included only 1 kb of the promoter, a region that lacks the Atf4 binding sites described above, GFP mRNA levels were not significantly changed during ER stress.
We have argued that our scoring function captures the essence of true cis-binding sites in a genome so that if the genome contains functional binding sites described by the profiles, its LOR(s) will become positive when the score value s increases beyond some threshold; and the larger a LOR(s) value is, the higher the confidence for the prediction is [ 13].
