Figure 6.

Chromatin Boundaries Separated by Repeat-Associated CTCF Binding in Rodents

(A) A B2-associated CTCF-binding event separates the ApoA cluster from downstream genes on mouse chromosome 9 (top blue track). Active transcription is reflected both by H2AK5ac occupancy in mouse liver (bottom green track) and in direct sequencing of mouse liver mRNA by gene name shading (red is silent; green is active) (Mortazavi et al., 2008).

(B) Heat map representation of H2AK5ac chromatin domains flanked by CTCF binding that is shared between all five species (five-way), mouse unique and repeat-associated (mouse RABs), repeat-associated and shared between mouse and rat (mouse and rat shared RABs), and not within the previous categories (all other).

(C) Violin plots represent gene expression differences (Manhattan distances) between H2AK5ac and CTCF defined chromatin domains for different gene pair categories.

See also Figure S6.