Analysis showed that the majority of CTCF binding events were shared between all three interrogated cell lines and that these common CTCF binding events were generally the strongest bound regions.
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.
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.
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).
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.
Alternatively, the two binding events are not necessarily sequential.
Shared binding events were initially identified in a pair-wise fashion using the 9-way EPO-MSA.
