GSE127140
Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [RNA-seq]
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: Total RNA-seq was done for mammary tissues at pregnancy day 6 and 18 for wild-type and mutant mice carrying enhancer deletions within the Casein locus. One mouse lines carries a deletion of the enhancer cluster identified next to the primordial Odam within (Csn_S1-4). The other two mouse lines carry deletions of single enhancer elements: delCsn3-PE - deletion of the proximal enhancer of Csn3 and delCsn1s2b-E - a deletion of the enhancer of Csn1s2b.