The sequence of this binding site does not resemble any known ATP binding sites, which have much higher binding affinities.
According to the 'futility theorem' put forward by Wasserman and Sandelin (2004), a genome-wide scan with a typical PWM could incur in the order of 1000 false hits per functional binding site, which would make such an approach practically infeasible for accurate determination of binding sites.
Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [ 23], [ 18].
Among many other binding sites lost in the –673 construct were an E-box, a STAT binding site which forms a sequence model (Genomatix modelInspector) together with an ets binding site, and a Myc associated zinc finger binding site (MAZF).
Any binding site which had a p < 0.01 was annotated as a potential miRNA binding site.
When binding to DNA, LysR protein forms a homodimer and targets two specific binding sites, a regulatory binding site, which has the conserved T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAAig. 2b).
Fortunately, over 65% of all protein-coding genes in the mouse genome are amenable for promoter trapping in ES cells [ 49], and the efficiency can be raised to 85% if the binding sites (which can be made removable) for a transcription factor expressed in ES cells (Oct4) are engineered into the vector [ 50].
Second, the short-life of protein chromatin interactions continuously makes available binding sites which can then be scanned by diffusing transcription factors.
The PACAP specific binding sites which were not shared VIP were termed type I, while the binding sites shared with both PACAP and VIP were termed Type II.
To generate a list of unambiguous CTCF negative RAD21 binding sites we removed these sites, leaving 667 reassessed CTCF independent RAD21 binding sites, which we define as motif and CTCF-independent RAD21 binding sites (MCIB).
