DataSheet1_A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs.PDF

The genome is pervasively transcribed to produce a vast array of non-coding RNAs (ncRNAs). Long non-coding RNAs (lncRNAs) are transcripts of >200 nucleotides and are best known for their ability to regulate gene expression. Enhancer RNAs (eRNAs) are subclass of lncRNAs that are synthesized from enhancer regions and have also been shown to coordinate gene expression. The biological function and significance of most lncRNAs and eRNAs remain to be determined. Epithelial to mesenchymal transition (EMT) is a ubiquitous cellular process that occurs during cellular migration, homeostasis, fibrosis, and cancer-cell metastasis. EMT-transcription factors, such as SNAI1 induce a complex transcriptional program that coordinates the morphological and molecular changes associated with EMT. Such complex transcriptional programs are often subject to coordination by networks of ncRNAs and thus can be leveraged to identify novel functional ncRNA loci. Here, using a genome-wide CRISPR activation (CRISPRa) screen targeting ∼10,000 lncRNA loci we identified ncRNA loci that could either promote or attenuate EMT. We discovered a novel locus that we named SCREEM (SNAI1 cis-regulatory eRNAs expressed in monocytes). The SCREEM locus contained a cluster of eRNAs that when activated using CRISPRa induced expression of the neighboring gene SNAI1, driving concomitant EMT. However, the SCREEM eRNA transcripts themselves appeared dispensable for the induction of SNAI1 expression. Interestingly, the SCREEM eRNAs and SNAI1 were co-expressed in activated monocytes, where the SCREEM locus demarcated a monocyte-specific super-enhancer. These findings suggest a potential role for SNAI1 in monocytes. Exploration of the SCREEM-SNAI axis could reveal novel aspects of monocyte biology.

基因组在广泛转录的过程中产生大量非编码RNA（ncRNAs）。长非编码RNA（lncRNAs）的长度超过200个核苷酸，以其调控基因表达的能力而闻名。增强子RNA（eRNAs）是lncRNAs的一个亚类，它们由增强子区域合成，并已被证明可以协调基因表达。大多数lncRNAs和eRNAs的生物功能和重要性尚待确定。上皮到间质转化（EMT）是一种普遍的细胞过程，它发生在细胞迁移、稳态、纤维化和癌细胞转移过程中。EMT转录因子，如SNAI1，诱导一个复杂的转录程序，以协调与EMT相关的形态和分子变化。此类复杂的转录程序往往受到ncRNA网络的协调，因此可以用来识别新的功能ncRNA位点。在此，我们利用针对约10,000个lncRNA位点的全基因组CRISPR激活（CRISPRa）筛选，鉴定出可以促进或抑制EMT的ncRNA位点。我们发现了一个新的位点，命名为SCREEM（在单核细胞中表达的SNAI1顺式调控eRNAs）。SCREEM位点包含一组eRNAs，当使用CRISPRa激活时，可诱导邻近基因SNAI1的表达，从而驱动伴随的EMT。然而，SCREEM eRNA转录本本身对于SNAI1表达的诱导似乎是可替代的。有趣的是，SCREEM eRNAs和SNAI1在激活的单核细胞中共表达，其中SCREEM位点界定了单核细胞特异的超级增强子。这些发现表明SNAI1在单核细胞中可能具有潜在的作用。对SCREEM-SNAI轴的探索可能揭示单核细胞生物学的新的方面。