The organisation of the C-terminal region as a tandem repeat of zinc-binding modules is a shared feature of the catalytic subunit of Pol α, Pol δ and Pol ɛ.
Since the finding that estradiol binding is not shared by all ERs but restricted to vertebrate ERs contradicts this hypothesis, and to get better insight into this apparent contradiction, the sequence of the ancestral steroid receptor was reestimated.
N-terminal vesicle binding is shared with GMAP-210, a Golgin localized to the cis-Golgi (Sato et al., 2015); for other Golgins, it is presumed due to binding sites for various coat proteins.
The presence of CRX binding sites is a feature shared with other opsin regulatory regions: the mammalian LWS opsin LCR [ 40- 42], the mammalian rod expression region [ 94], zebrafish RH2 opsin LCR [ 95] and zebrafish SWS2 cis-acting regulatory elements [ 96].
Globally, CTCF binding is shared five times as often among human, dog, and mouse, as are CEBPA and HNF4A; conversely, CTCF has proportionally less lineage-specific binding.
Some molecular functions (e.g., histone lysine acetyltransferase activity) of known CM domains are relatively unique to CM, but many others (e.g., protein kinase activity and DNA binding) are shared by a broad variety of different biological processes.
We then asked whether TF binding intensity also correlated with the probability that TF binding was shared in closely related mammals.
In spite of the relative similarity between human and equine TERC, several key positions relevant for TERC/TERT binding are shared between the mouse and the equid TERC sequences.
Within the 2TF and 3TF clusters, we identified pairs of TFs whose binding was shared between two mouse species and then plotted the change in binding intensity of each TF against the other (as shown for C57BL/6J and SPRET/EiJ in Figure 4; see also Figure S4D and the section "TF Binding Intensities within Clusters Coevolve" in the Extended Experimental Procedures).
Consistent with their predominant classification in DNA dependent regulation of transcription, DNA binding was the primary shared molecular function among these 64 genes.
