Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity

Enhancer RNAs (eRNAs) are a pivotal class of enhancer-derived non-coding RNAs that drive gene expression. Here we identify the SNAI1 enhancer RNA (SNAI1e; SCREEM2) as a key activator of SNAI1 expression and a potent enforcer of transforming growth factor-β (TGF-β)/SMAD signaling in cancer cells. SNAI1e depletion impairs TGF-β-induced epithelial-mesenchymal transition (EMT), migration, in vivo extravasation, stemness, and chemotherapy resistance in breast cancer cells. SNAI1e functions as an eRNA to cis-regulate SNAI1 enhancer activity by binding to and strengthening the enrichment of the transcriptional co-activator bromodomain-containing protein 4 (BRD4) at the local enhancer. SNAI1e selectively promotes the expression of SNAI1, which encodes the EMT transcription factor SNAI1. Furthermore, we reveal that SNAI1 interacts with and anchors the inhibitory SMAD7 in the nucleus, and thereby prevents TGF-β type I receptor (TβRI) polyubiquitination and proteasomal degradation. Our findings establish SNAI1e as a critical driver of SNAI1 expression and TGF-β-induced cell plasticity. 4C-seq data with a VP located at eSNAI1 in MDA-MB-231 cells treated with or without TGFb.

增强子RNA（enhancer RNAs, eRNAs）是一类关键的增强子来源非编码RNA，可驱动基因表达。本研究鉴定出SNAI1增强子RNA（SNAI1e；SCREEM2），其既是SNAI1基因表达的关键激活因子，也是癌细胞中转化生长因子-β（TGF-β）/SMAD信号通路的强效强化因子。敲降SNAI1e会削弱乳腺癌细胞中TGF-β诱导的上皮间质转化（epithelial-mesenchymal transition, EMT）、细胞迁移、体内血管外渗、干细胞样特性及化疗耐药性。SNAI1e作为增强子RNA，通过结合并增强转录共激活因子溴结构域包含蛋白4（bromodomain-containing protein 4, BRD4）在局部增强子区域的富集，顺式调控SNAI1增强子的活性。SNAI1e可选择性促进编码上皮间质转化转录因子SNAI1的SNAI1基因的表达。此外，本研究发现SNAI1可与抑制性SMAD7结合并将其锚定在细胞核内，从而阻止转化生长因子-βⅠ型受体（TGF-β type I receptor, TβRI）的多泛素化修饰及蛋白酶体降解。本研究结果证实，SNAI1e是SNAI1基因表达及TGF-β诱导的细胞可塑性的关键驱动因子。本数据集涵盖经或未经TGF-β处理的MDA-MB-231细胞中，定位于eSNAI1的VP的环状染色体构象捕获测序（4C-seq）数据。