In order to determine NEUROD2 binding preference along the genome and therefore gain insight into its mechanism of action, we examined peak positions relative to annotated transcriptional units.
Interestingly, without exhibiting any specific binding preference, the 3′ overhang was unwound the most efficiently.
We next considered NS9283, which has a binding preference for the α4−α4 interface.
This binding preference of the MLL PHD3 domain was also very recently reported by others (36).
We devoted our effort into exploring the binding preference of transcription factors on the bi-directional promoters and statistically identified a set of over-represented transcription factor binding sites(TFBS) in bi-directional promoters, the research scheme is shown in figure 1.
With the assumption that the binding preference of a TF is the same to all its binding sites, we estimated the binding preference of each TF with the following heuristic.
To gain insight into the distinct NLS binding preference of CTNNBL1, we solved the crystal structure of CTNNBL1, and based on the structure, probed the putative NLS binding region by mutagenesis.
Interestingly, just a single point mutation (G198N) in Aurora A changes its binding preference for TPX2 into a preference for INCENP and rescues the loss of Aurora B in chromosome alignment and mitotic checkpoint function (Fu et al. 2009; Hans et al. 2009).
Based on binding preference and sequence homology, the Eph receptors have been divided into two subclasses, EphA (A1 A8) and EphB (B1 B6) (Gale et al, 1996).
Ephs are a large family of tyrosine kinase receptors and are subclassed into EphAs and EphBs, depending on their extracellular sequence homology and binding preference for their ligands, the membrane-bound ephrins (Pasquale, 2004).
