Computational prediction and CRISPR-Cas12a knockout and rescue assays identify many functionally conserved lncRNAs from zebrafish to human

Abstract Advances in RNA-seq studies have enabled transcriptome-scale annotation of long noncoding RNAs (lncRNAs) across vertebrates, with many of them having been implicated as regulators in diverse cellular processes1–3. However, our understanding of lncRNA function has long been hindered by the lack of methods to assess lncRNA evolution across species4–6. Here, we develop a computational pipeline, lncHOME (lncRNA Homology Explorer), to identify a special class of lncRNAs with conserved genomic locations and patterns of RNA binding protein (RBP) binding sites (coPARSE-lncRNAs). Strikingly, lncHOME identifies several hundred human coPARSE-lncRNAs that can be evolutionarily traced to zebrafish. We further develop a CRISPR-Cas12a (Cpf1) knockout screen system and find that the knockout of many of these human coPARSE-lncRNAs leads to cell proliferation defects, which could be rescued by the predicted lncRNA homologs from zebrafish. Finally, for two coPARSE-lncRNAs, we verified that their homologs from human, mouse, and zebrafish tend to bind a similar set of RBPs with cell proliferation functions. Thus, our study illustrates a general approach for studying lncRNA functional conservation and implicates numerous lncRNAs in regulating cellular physiology.