The human genome contains thousands of long noncoding RNAs (lncRNAs), of which very few have been linked to a functional role. Although DNA-targeting CRISPR screens have identified functional lncRNAs, these screens suffer from limited specificity as DNA-based perturbation of lncRNA loci might also suppress nearby protein-coding genes and other regulatory elements. Writing in Cell, Liang et al. overcome this limitation. They use the RNA-targeting Cas13 nuclease to develop a transcriptome-wide CRISPR perturbation screen that targets lncRNA, and identify 778 lncRNAs with context-specific or broad essentiality.

The authors systemically identified essential lncRNAs and simultaneously assessed the essentiality of nearby protein-coding genes. They constructed a library of about 75,000 guide RNAs that target 6,199 lncRNAs and 4,390 protein-coding transcripts. Comparing the effect on cell growth upon loss of lncRNAs across five human cell lines revealed both shared and cell-type-specific essential lncRNAs. Among the 778 essential lncRNAs, 61% were cell-type specific, 33% were shared in several cell lines and 6% were shared in all cell lines tested. The universally essential transcripts contained several lncRNAs that had previously been described, including MALAT1 and MIR17HG, as well as many new lncRNAs. Interestingly, Liang et al. show that the majority of essential lncRNAs act independently of the nearest protein-coding gene. Mechanistically, they found that essential lncRNAs regulate cellular proliferation and are highly expressed in vivo during the early stages of development. Moreover, essential lncRNAs were often differentially expressed in tumors, which correlated with survival. This systemic approach to linking lncRNAs to functional roles lays the groundwork for the further assessment of noncoding transcripts, which might lead to new targets for therapeutics.