Genome binding/occupancy profiling by high throughput sequencing
Summary
Enhancer clusters are platforms occupied at high-density by the transcription machinery to activate lineage-specific genes. However, it is not clear yet whether they are merely a collection of conventional enhancers or represent unique and new types of regulatory elements. Specifically, the question remains whether they activate additional enhancer programs in multigene loci. We addressed this issue in the mouse mammary gland, where genes are highly activated during pregnancy. We identify a 300kb multi-gene locus with twenty-one regulatory elements, including a cytokine-dependent primary enhancer cluster (PEC). Using genome editing in combination with ChIP-seq, RNA-seq and 3C-technologies, we show that the PEC initiates the activation of lineage-specific genes through contacting and activating secondary enhancers. This new framework of enhancer clusters indicates a hitherto unrecognized hierarchy of regulation by which a PEC activates genes via regulating secondary enhancers.
Overall design
ChIP-seq for STAT5A, GR, NFIB, RNA Pol II, H3K27ac and H3K4me3 in the mammary tissues of wild type, and mutant mice,at day one, day 6 and 18 of pregnancy. Mutant mice carry enhancer deletions at Csn1s2b and Csn3, but also single and combined deletions of one enhancer cluster in the casein locus (single deletions: enhancer element one, two and four; combined deletions: one and two together, and a complete deletion of the cluster)
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