Figure 1.
CTCF Occupancy in Five Placental Mammalian Genomes Reveals a Large Core Set of Conserved Binding
(A) The total numbers of CTCF-binding events found in orthologous locations between each pair of placental species are shown as row-column intersections. The right-most numbers for each species represent all alignable CTCF-binding peaks (total peaks are in parentheses). Percentages are percentage-averages between pairwise species (Experimental Procedures).
(B) Five-way comparison of CTCF binding in five placental mammals identified a shared set of 5,178 CTCF-binding events.
(C) The upper track shows CTCF binding after CTCF knockdown (CTCF) in human MCF-7 cells (Figure S1F). The track immediately below shows CTCF binding with control RNAi (mock). The bottom five tracks show CTCF-binding data in liver of five mammalian species in syntenic regions, demonstrating that highly conserved CTCF-binding events are less sensitive to perturbation by RNAi knockdown.
(D) The fraction of binding events found only in human (human only) or shared among all placental (five-way) were characterized by their sensitivity to RNAi knockdown of CTCF protein. Very few deeply shared CTCF-binding events were affected by CTCF knockdown.
(E) Relation between motif information content and motif sequence conservation for nine TFs in human. (F) Relation between motif length and motif sequence conservation for the same TFs as in (E).