eRNA co-expression network uncovers TF dependency and convergent cooperativity.

Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of "bivalent" TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs.

Revealing eRNA interactions: TF dependency and convergent cooperativity.

Enhancer RNAs (eRNAs) are non-coding RNAs produced from transcriptional enhancers that are highly correlated with their activities. Using capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across individuals, we identified inter-individual variation of expression in over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers interact with each other and with promoters. Mid-to-long range interactions showed distance-dependent decay, which was modified by TF occupancy. In particular, we found a class of 'bivalent' TFs, including Cohesin, which both facilitates and insulates the interaction between enhancers and/or promoters depending on the topology. In short ranges, we observed strand specific interactions between nearby eRNAs in both convergent or divergent orientations. Our finding supports a cooperative convergent eRNA model, which is compatible with eRNA remodeling neighboring enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions depending on the distance, orientation, and the binding landscapes of TFs.