Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

Abstract

Enhancer RNAs (eRNA) are unstable non-coding RNAs, transcribed bidirectionally from active regulatory sequences, whose expression levels correlate with enhancer activity. We use capped-nascent-RNA sequencing to efficiently capture bidirectional transcription initiation across several human lymphoblastoid cell lines (Yoruba population) and detect ~75,000 eRNA transcription sites with high sensitivity and specificity. The use of nascent-RNA sequencing sidesteps the confounding effect of eRNA instability. We identify quantitative trait loci (QTLs) associated with the level and directionality of eRNA expression. High-resolution analyses of these two types of QTLs reveal distinct positions of enrichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation regions, both of which are associated with mRNA expression QTLs. These two regions—the central TF-binding footprint and the eRNA initiation cores—define a bipartite architecture of enhancers, inform enhancer function, and can be used as an indicator of the significance of non-coding regulatory variants.

Transcription imparts architecture, function and logic to enhancer units

“…2 ). Our results strengthen previous associations between transcription and enhancer activity 10 , 22 , 28 , 29 , provide compelling evidence that essentially all active enhancers are transcribed, and suggest a functional role for transcription from active enhancers.…”

“…Using the distal enhancer design of STARR-seq, we find that enhancer activity requires at least one core promoter in addition to TF binding in the flexible upstream region, suggesting a functional role for RNAPII recruitment at enhancers. Likewise, recent analyses of population variants affecting gene-distal GRO-cap TSSs suggest that core promoter mutations in distal enhancers can disrupt enhancer function 28 . The requirement for core promoters at enhancers is particularly intriguing given reports that core promoters confer specificity for enhancers and co-activators 24 , 33 , 34 ; this suggests enhancers could target promoters by recruiting similar core promoter machinery.…”

Genetic Dissection of the RNA Polymerase II Transcription Cycle

“…Likewise, weak motifs that correlate with pausing and Pol II termination are reported (Gressel et al, 2017; Schwalb et al, 2016; Tome et al, 2018). These DNA sequences that underlie initiation play an important role in gene regulation, and SNPs affecting these core transcriptional processes can alter the rates of mRNA production (Kristjánsdóttir et al, 2020). However, the DNA sequence specificity of the core promoter is extremely weak, degenerate, and spread across the promoter region.…”

Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases

“…We used multiple QTL datasets (eQTL, caQTL, bQTL, and hQTL) to search for regulatory variants. However, other types of QTL have also been generated recently, e.g., splicing QTL (sQTL), 52 DNA methylation QTL (meQTL), 53 protein QTL (pQTL), 54 transcription initiation QTL (tiQTL), directionality of initiation QTL (diQTL), 55 promoter interacting eQTL (pieQTL), 56 and mRNA N 6 - methyladenosine QTL (m6A QTL). 57 TiQTL and diQTL are variants associated with enhancer RNA expression levels, and pieQTL is eQTL overlapping active regulatory elements that interact with their target gene promoters.…”