Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci.

RB's interaction with chromatin is key to understanding its molecular functions. Using a novel ChIP-sequencing protocol, we identify the precise chromatin loci bound by various forms of human RB. RB targets three fundamentally different types of loci (promoters, enhancers, CTCF-sites), that are largely distinguishable by the mutually exclusive presence of E2F1, c-JUN and CTCF. E2F/DP facilitates RB association with promoters, whereas AP-1 recruits RB to enhancers. RB's association with promoters and enhancers fluctuates: G1-arrest enriched RB at promoters, while S-phase progression redistributed RB towards enhancers. RB binding to RB/CTCF sites was unaltered by cell cycle progression. RB-bound promoters include the classic E2F targets and are similar between cell types. However, RB-bound enhancers are associated with different gene categories, including, notably, MAPK signaling, and they vary between cell types. We propose that RB has a well-preserved role controlling E2F in G1, and cell type-specific effects at enhancers when cells enter S-phase. Overall design: Analysis of the genomic distribution of human RB. 1. ChIP-seq data for RB wild-type, RB?CDK and the 14 mono-phosphorylated forms of RB in human RPE1 epithelial cells. 2. ChIP-seq data for E2F1, H3K4me3, H3K4me1 and H3K27ac in RPE1 cells expressing RB wild-type or RB?CDK. 3. ChIP-seq data for c-JUN and CTCF in RPE1 cells expressing shControl or shRB1. 4. ChIP-seq data for FLAG-RB in RPE1 cells expressing dominant-negative FOS (A-FOS) or dominant-negative DP1 (DNDP1) or GFP. 5. ChIP-seq data for E2F1 in RPE1 cells expressing DNDP1 or GFP. 6. ChIP-seq data for FLAG-RB in G1 accumulated RPE1 cells by contact inhibition for 6 days and S-phase accumulated RPE1 cells after release from contact inhibition for 24 hours. 7. ChIP-seq data for c-JUN and H3K4me1 in RB wild-type and RB knock-out RPE1 cells. 8. ChIP-seq data for wild-type RB and RB?CDK in human BJ fibroblasts. 9. ChIP-seq data for RB in RPE1 wild-type and RPE1 RB1 knock-out cells. 10. ChIP-seq data for wild-type RB and RB?CDK in MCF10A human breast epithelial cells. 11. ChIP-seq data for wild-type RB and RB?CDK in T47D human breast cancer cell line.