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A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers.
A second important finding of our study is that the destruction of the RUNX1/ETO network establishes a transcription network dominated by the combinatorial binding of PU.1, RUNX1, and, in particular, C/EBPα.
The spatial and temporal pattern of activity of an enhancer is controlled by the type of epigenetic modifications attached to it, and by the combinatorial binding of transcription factors to specific binding sites in the enhancer's sequence [ 1].
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The combinatorial binding of two H3 tails by CHD4 may explain why CHD4 may not account for the H3 tail peptide binding in vitro in our experiments, yet contributes to chromatin association of NURD complex in cells.
We further show that the combinatorial binding of Insm1/Neurod1/Foxa2 seems to some degree be conserved and functionally important in humans.
The combinatorial binding of cell-type-specifying transcription factors (TFs) and epigenetic modifications drives this enhancer activity.
We next analyzed our ChIP-seq data sets to identify the core transcriptional network that characterizes the cellular identity of t(8 21) cells by determining overrepresented combinatorial binding patterns for the transcription factors RUNX1/ETO, C/EBPα, HEB, LMO2, PU.1, and RUNX1 (Tijssen et al., 2011).
They can be seen as a circuit relaying input signals into an output, which is gene activity, by combinatorial binding of TF.
We were unable to detect any other strongly over-represented binding motifs in the Otx2-bound regions that lacked Oct4 binding, suggesting that this is the most common combinatorial binding mode used by Otx2.
Importantly, meiotic recombination hotspots are clearly nonrandom: their locations involve DNA sequence motifs and, according to Wahls and Davidson [ 135], are determined by the combinatorial effect of the binding of multiple transcription factors at multiple transcription factor binding sites.
5) The Discussion should address what is missed by focusing on only combinatorial binding, only conserved binding, and both.
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