Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells

Human chromosomes are pervasively transcribed, but systematic understanding of coding and long noncoding RNA (lncRNA) genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens—assessing 18,905 protein-coding and 10,678 lncRNA loci—and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared with proliferation. Further, we applied CRISPRi perturbation coupled with single-cell RNA-seq (Perturb-seq) to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.