To better understand the functions of non-coding enhancer RNAs (eRNAs), we annotated the estrogen-regulated eRNA transcriptome in estrogen receptor α (ERα)-positive breast cancer cells using PRO-cap and RNA sequencing. We then cloned a subset of the eRNAs identified, fused them to single guide RNAs, and targeted them to their ERα enhancers of origin using CRISPR/dCas9. Some of the eRNAs tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ERα recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a ∼40 nucleotide functional eRNA regulatory motif (FERM) present in many eRNAs that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an RNA-binding protein amplified in breast cancers. The ectopic expression of a targeted eRNA controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of eRNAs in breast cancer.

为了更好地了解非编码增强子 RNA (eRNA) 的功能，我们使用 PRO-cap 和 RNA 测序注释了雌激素受体 α (ERα) 阳性乳腺癌细胞中雌激素调节的 eRNA 转录组。然后，我们克隆了所识别的 eRNA 的一个子集，将它们融合到单个指导 RNA 上，并使用 CRISPR/dCas9 将它们靶向其 ERα 增强子。一些测试的 eRNA 在雌激素处理后通过增加 ERα 募集和刺激增强子处的 p300 催化的 H3K27 乙酰化来调节同源而非异源靶基因的表达。我们在许多 eRNA 中发现了~40个核苷酸的功能性 eRNA 调节基序 (FERM)，它对于调节雌激素处理后的基因表达是必要且充分的，但不是激活的特异性。 FERM 与 BCAS2 相互作用，BCAS2 是一种在乳腺癌中扩增的 RNA 结合蛋白。控制癌基因表达的靶向 eRNA 的异位表达导致细胞增殖增加，证明了 eRNA 在乳腺癌中的调节潜力。