美国纽约大学Neville E. Sanjana团队发现，转录组尺度的RNA靶向CRISPR筛选揭示人类细胞中重要的lncRNA。相关论文于2024年11月11日在线发表在《细胞》杂志上。
研究人员使用RNA靶向CRISPR-Cas13筛选技术，探讨了约6200个长链非编码RNA（lncRNA）的丧失如何影响五种人类细胞系的细胞适应性，并识别出778个具有特定背景或广泛必要性的lncRNA。通过个体扰动实验，研究人员确认了这些lncRNA的必要性，并发现大多数必要的lncRNA独立于其邻近的蛋白编码基因发挥作用。
通过单细胞转录组分析，研究人员发现，丧失必要的lncRNA会损害细胞周期进程并驱动凋亡。许多必要的lncRNA在发育过程中展示了跨组织的动态表达。利用约9000个原发性肿瘤样本，研究人员识别出这些lncRNA的表达在肿瘤中的变化与生存率相关，揭示了新的生物标志物和潜在的治疗靶点。
这项广泛的功能性lncRNA转录组调查推进了人们对非编码转录本的理解，并展示了Cas13转录组尺度非编码筛选的潜力。
据悉，哺乳动物基因组中存在着多样的RNA种类，包括蛋白编码和非编码转录本。然而，大多数lncRNA的功能作用仍然不明。
附：英文原文
Title: Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells
Author: Wen-Wei Liang, Simon Müller, Sydney K. Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Akash Sookdeo, Olivia Choi, Christina M. Caragine, Alba Corman, Lu Lu, Olena Kolumba, Breanna Williams, Neville E. Sanjana
Issue&Volume: 2024-11-11
Abstract: 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.
DOI: 10.1016/j.cell.2024.10.021
Source: https://www.cell.com/cell/abstract/S0092-8674(24)01203-0