Liang Wen-Wei, Müller Simon, Hart Sydney K, Wessels Hans-Hermann, Méndez-Mancilla Alejandro, Sookdeo Akash, Choi Olivia, Caragine Christina M, Corman Alba, Lu Lu, Kolumba Olena, Williams Breanna, Sanjana Neville E
New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10013, USA.
New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10013, USA.
Cell. 2024 Dec 26;187(26):7637-7654.e29. doi: 10.1016/j.cell.2024.10.021. Epub 2024 Nov 11.
Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how the loss of ∼6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that the loss of essential lncRNAs impairs cell-cycle progression and drives apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ∼9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.
哺乳动物基因组中存在各种各样的RNA，包括蛋白质编码转录本和非编码转录本。然而，大多数长链非编码RNA（lncRNA）的功能作用仍不清楚。我们使用靶向RNA的CRISPR-Cas13筛选技术，探究了约6200种lncRNA的缺失如何影响五种人类细胞系的细胞适应性，并鉴定出778种具有特定背景或广泛必需性的lncRNA。我们通过个体扰动证实了它们的必需性，并发现大多数必需lncRNA的作用独立于其最邻近的蛋白质编码基因。通过单细胞转录组分析，我们发现必需lncRNA的缺失会损害细胞周期进程并引发细胞凋亡。许多必需lncRNA在发育过程中呈现出跨组织的动态表达。我们利用约9000个原发性肿瘤，确定了那些在肿瘤中的表达与生存相关的lncRNA，从而产生了新的生物标志物和潜在的治疗靶点。这种对功能性lncRNA的全转录组研究推进了我们对非编码转录本的理解，并展示了利用Cas13进行转录组规模非编码筛选的潜力。
