In addition to the authentic GhCPS2 sequence, a mutant, GhCPS2 I733T was identified and since the mutant point I733T is only one amino acid from the biocarbonate ion binding site, we decided to include it in our analysis.
Since TTR is a tetramer with two equivalent T4-binding sites, we decided to study the binding of T4 to TTL, using radiolabeled thyroxin and TTR as the sample control (Fig. 3).
The same analysis revealed other putative binding sites but we decided to focus on those potentially related to the oxidative stress response, particularly NF-κB because it is a redox-sensitive factor that has been shown to be activated by CPT [19].
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).
The x-ray crystal structure contains several water molecules located either within or close to the binding site, hence we decided to carry out two separate docking runs; one in which water molecules within 5Å of the APO866 binding site were included in the calculations, and another without water molecules.
Because the analysis here is focused on likely subtle details of binding site arrangements, we decided to work on the TF pairs with the strongest evidence of cooperative interactions.
To decide a relevant threshold for accepting a predicted binding site, we repeated the analysis in randomly selected regions with the respective PWM.
As Ser lies adjacent to the NUAK1 phosphorylation site (Ser) that controls 14-3-3 14-3-3 14-3-3 we decided to explore whether NUAK1 could indeed influence PLK1 T-loop phosphorylation.
As few Hif-1α binding sites have been identified in zebrafish and ChIP-sequencing has emerged as an appropriate technology for genome-wide DNA binding site analysis in zebrafish, we decided to sequence the ChIP material isolated from both wild-type and vhl mutants using one biological replicate of 2400 embryos for each.
While a number of methods have been suggested to use PBM data for predicting TF binding sites (in most cases using PWMs), we decided to extend k-mer based methods using a biophysically-motivated model.
Since E2F1 binding sites often overlap with the p53 ones, we decided to test whether p53 also binds this region upon DNA damage (−4 kb).
