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. 2012 Jan 20;148(1-2):335–348. doi: 10.1016/j.cell.2011.11.058

Figure S1.

Figure S1

CTCF Binding Is Primarily Directed by Genetic Sequence and Is Highly Conserved; Western Blot Confirmation of CTCF RNAi and Tissue Specificity of Conserved CTCF Binding, Related to Figure 1

(A) In the first column (Hs-chr21), ten kilobase windows around human CTCF-binding events were ordered, based whether a syntenic CTCF-binding event is present or not in mouse liver. In the second and third columns, CTCF binding in the Tc1 mouse has been shown for the human chromosome 21 (Tc1-Hs-chr21) and for the orthologous mouse sequences (Tc1-Mm-chr16, 17, 10). Most CTCF binding found on human chromosome 21 in human liver is recapitulated in the mouse liver.

(B) Genome tracks displaying the CTCF binding found near the liver-expressed gene CLDN14 in human (red, Hs-chr21) and Tc1 mouse (blue, Tc1-Hs-chr21; green, Tc1-Mm-chr16).

(C) Genomic occupancy of HNF4A, CEBPA (orange tracks), and CTCF (blue tracks) is shown around the liver gene APOA2 in human, mouse, and dog. Grey lines connect orthologous regions between species.

(D) Binding events for CEBPA, HNF4A, and CTCF have been sorted, based on whether they occur in one, two, or three of the placental species from (C).

(E) The fraction of binding events found only in human (human only) or shared among all placental mammals (five-way) were characterized by their tissue specificity. Few deeply shared CTCF-binding events are tissue specific in humans.

(F) Western blot of nuclear extracts after CTCF RNAi, mock RNAi, and non-transfected (NT) human MCF-7 cells.

(G) Read profiles of CTCF binding after CTCF (red lines) or mock RNAi (black lines) in MCF-7 cells. CTCF binding was separated into two groups: (1) human-specific binding events in liver that are also found in MCF-7 cells (human only binding events) and (2) five-way shared binding events in liver that overlap with CTCF binding in MCF-7 cells (five-way shared binding events).

(H) The total numbers of CTCF-binding events (CTCF-bound regions) for the following data sets are shown: MCF-7 after mock RNAi (MCF-7), MCF-7 after CTCF RNAi (MCF-7 KD), human liver (Liver). The bottom two rows show the CTCF binding overlaps between MCF-7 versus Liver and MCF-7 KD versus Liver binding. Total CTCF-binding overlaps are indicated on the left and further split into three categories: five-way shared, human-specific, and all other CTCF binding.