Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells

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 massively parallel RNA-targeting CRISPR-Cas13 screens, we probed how loss of ~6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with either context-specific or broad essentiality. We observe a high level of consistency between distinct guide RNAs targeting the same lncRNA in the pooled screens and confirm their essentiality with individual perturbations. We find that the overwhelming majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that essential lncRNAs modulate key cellular pathways for proliferation and that their loss can impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development and, 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.