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.

增强子RNA（eRNA）是不稳定的非编码RNA，从活性调控序列双向转录，其表达水平与增强子活性相关。我们使用带帽的新生RNA测序来有效捕获跨越几种人类淋巴母细胞系（约鲁巴族）的双向转录起始，并以高灵敏度和特异性检测〜75,000个eRNA转录位点。新生RNA测序的使用可避免eRNA不稳定的混杂效应。我们确定与eRNA表达的水平和方向性相关的数量性状基因座（QTL）。这两类QTL的高分辨率分析揭示了在中央转录因子（TF）结合区和侧翼eRNA起始区的富集位置不同，两者均与mRNA表达QTL相关。这两个区域-中央TF结合足迹和eRNA起始核心-定义了增强子的二分体系结构，告知增强子功能，并且可以用作非编码调控变体重要性的指标。