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Taken together, it appears that E2F4 has a substantial number of binding events that are entirely dispensable for proper transcription of downstream genes, despite the well-characterized role it plays in cell cycle control.
As such, the unknown footprints may correspond to non-specific binding events that are facilitated by an adjacent specific binding event.
The SRP concentration at which the smFRET experiments are performed is relevant only in that, at higher SRP concentrations, arrival times are faster such that the number of individual binding events that are observed is larger.
Once it is possible to distinguish true binding events that are functional from those that are non-functional, we will also be able to investigate the molecular factors distinguishing one from the other.
The question has been raised therefore whether a large proportion of binding events are "opportunistic" rather than "functional" (John et al, 2011; Zhu et al, 2012), where "functional" would refer to those binding events that are relevant in terms of transcriptional control processes.
Consequently, binding events that are biologically consistent but only occur within a small fraction of the cells, because these cells are in a transient transcriptional state, will give low or undetectable ChIP-seq peaks that can appear to be random events.
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The assessment of correlation between transcriptional changes of the FFRP and its target genes revealed the subset of binding events that were conditionally functional in specific environmental contexts.
In the third and last set of RW simulations, we studied binding events that were registered during a transient response in the cleft.
This overlap is higher than the number of CTCF binding events that were common to only one of the ER-positive cell lines and the ER-negative cell line (795 CTCF binding regions shared between MCF-7 and MCF10A and 1, 354 CTCF binding events shared between ZR75-1 and MCF10A), suggesting a link between CTCF and ER binding.
This result corresponds to the failure of detecting a significant difference between the average number of binding events that was registered in the RW simulations and the number given by the continuous model (see the results of the Student's t-tests in Table 2).
Given that the authors acknowledge that this protein-protein interaction has previously been reported there would be some merit in further emphasizing the new aspects of the binding event that are demonstrated in this new data.
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