Figure 2.

Differential chromatin structure and transcription factor binding between consensus and Alu RBPJ binding sites. (A) Heat map of clustered reads densities for the indicated genome-wide determination or DNA sequence feature centered around RBPJ peak summits for all 28 220 RBPJ binding sites. (B) The same analysis as in A for the 4921 RBPJ peak summits that intersected with an Alu element within 200 bp. (C) Quantification of DNA ends densities for MNAse digested input, RBPJ immunoprecipitated, and DNase hypersensitive DNA for cluster 1 (without Alu) and cluster 5 (with Alu) regions.