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Additionally, ZR75-1-specific CTCF binding events were more likely to overlap with ZR75-1-specific ER binding events (5.6%) compared to the other cell-line specific CTCF binding events (0.1% for MCF-7 specific and 0.2% for MCF10A-specific CTCF binding events).
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For IDO, the order of binding events is more complex, but the ternary complex must still be formed before the reaction can proceed.
These binding events are more likely to be associated with cell-line specific ER binding events and are also more likely to be adjacent to genes that are expressed in that particular cell line.
As cell-line specific CTCF binding events are more likely to overlap with cell-line specific ER binding events, CTCF may direct ER binding at these regions thereby acting as a 'licensing factor' for ER.
Interestingly, depletion of KDM2B resulted in an even more dramatic effect on RING1B occupancy at these novel low magnitude sites, suggesting that these RING1B binding events are more dependent on KDM2B.
Compared to in vitro, the TF-DNA binding events are definitively more complicated in vivo since TF binding to DNA in eukaryotes is context dependant (e.g. dependant on other TFs which bind nearby DNA sites, local DNA structure), and influenced by factors like chromatin remodeling and concentration of the TF.
ER/FOXA1/CTCF binding events were also significantly biased towards estrogen-regulated genes, compared to ER/FOXA1 binding events that do not have an overlapping CTCF binding event.
One consideration about comparing singletons to CRMs is that singleton TF binding events are likely to become CRMs as more factors are tested and more peaks are called (see Figure 1 source data 1E for a comparison of the stability singleton and CRM categories).
TF binding events shared in multiple species are more likely to be found within CRMs (72% of shared human TF binding events are in CRMs vs 27% that are classified as singletons; hypergeometric test, p = 8.48 × 10−238).
The naming structure for binding events is shown below: a BINDS b forming c a BINDS b forming c If more output molecules are present than inputs, the event is a dissociation event.
Many protein binding events are random and inconsequential.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com