The active nuclease is a dimer, requiring that the DNA target site contain two zinc finger binding sites separated by a short spacer.
According to the crystal structures32,33, every monomer of GRDBD or ERDBD interacts with only hexametric half sites (6 bp) on both binding sites separated by 3 to 4 bp spacer.
Despite this, several highly specific promoter modules containing three transcription factor binding sites separated by a specific distance with a specific strand orientation were found in ERα target genes differentially regulated by cAMP.
The known Smad2/3 target genes Nodal, Lefty2 and Pitx2 contain pairs of FoxH1 binding sites separated by 30 200 bps [33], [42], [13], [43] these were termed asymmetric elements (ASEs) as they drive Nodal-dependent asymmetric gene expression.
The MMP-1 promoter contains at least two proximal AP-1 binding sites, separated by less than 100 nucleotides.
The hin enhancer contains two Fis dimer binding sites separated by 47 bp between their centers (Johnson and Simon, 1985; Bruist et al., 1987; Johnson et al., 1987).
Many simple motif extraction algorithms have been proposed primarily for extracting the transcription factor binding sites, where each motif consists of a unique binding site [ 4- 10] or two binding sites separated by a fixed number of gaps [ 11- 13].
We focussed on pairs of cohesin/CTCF binding sites (separated by 100 200 Kb) and computed the mean Hi-C contact intensity between all 2 Kb genomic bins located up to 40 Kb upstream and downstream of each binding site.
ZFNs and TALENs are both customizable DNA-binding proteins, which are fused to FokI nuclease domains and function in pairs by binding to tandem-oriented binding sites separated by short spacer sequences (Kim et al. 1996; see also Gaj et al. 2013 for review).
