This shows that only 50 to 60% of ER binding events are shared between two ER-positive cells lines, and generally the overlapping ER binding events are the stronger ER binding events.
In particular, we observed that the frequency of a word's usage positively correlates with both the likelihood of a binding event being shared among all five species and the strength of the ChIP enrichment.
CTCF-binding events demarcate active and inactive chromatin at a similar frequency, regardless of whether the CTCF-binding events are shared between the eutherian mammals, rodent B2 associated, or mouse-specific B2 associated.
We collected mRNA sequencing data in livers of all studied species, identified the subset of tandem genes divided by at least one CTCF-binding event in each species, and further subdivided this set by whether the CTCF-binding event was shared, repeat associated, or neither.
First, a small proportion of human TF binding events were found to be shared between human and chicken (<2% for CEBPA), whereas apparently more distant Drosophila species show almost no changes in TF binding (He et al., 2011b).
Shared binding events were initially identified in a pair-wise fashion using the 9-way EPO-MSA.
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.
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).
About 2,000 binding events found within B2 elements are shared by mouse and rat, whereas approximately 5,300 B2-associated binding events are found uniquely within mouse and over 1,200 solely in rat.
