GSE104206
Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer
Enhancers are transcription factor platforms that also bind RNA polymerase II and  generate enhancer RNAs (eRNA). Although eRNAs have been suggested as predictors  of enhancer activities and possibly key components facilitating transcription, there is little  genetic evidence to support this. We address the biology of eRNAs in vivo and investigate  eRNA patterns, expression levels and possible functions within a mammary-specific  super-enhancer that is composed of three units with distinct transcriptional capacities. We  show that eRNA levels do not correspond with the activities of their respective enhancer  units. However, changes in eRNA expression upon deletion of individual enhancer units  reflect the change in overall super-enhancer activity. These data provide genetic evidence  that eRNA levels are not a reliable readout of individual enhancers, but they predict superenhancer  activity in the absence of constituent elements. Overall design: ChIP-seq for H3K27ac, H3K4me3 and PolII in mammary tissues from mutant mice at lactation day 1 (L1).