@article{f5bd3b4944a0460e9f5c33e0fe9b62f9,
title = "Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells",
abstract = "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.",
keywords = "CRISPR, CRISPRi, genome-wide pooled screens, human pluripotent stem cells, iPSCs, long noncoding RNA, neural induction, neurodevelopment, Perturb-seq, single-cell RNA-seq",
author = "David Wu and Aunoy Poddar and Elpiniki Ninou and Elizabeth Hwang and Cole, {Mitchel A.} and Liu, {S. John} and Horlbeck, {Max A.} and Jin Chen and Replogle, {Joseph M.} and Carosso, {Giovanni A.} and Eng, {Nicolas W.L.} and Jonghoon Chang and Yin Shen and Weissman, {Jonathan S.} and Lim, {Daniel A.}",
note = "Funding Information: We thank members of the Lim lab, as well as Min Cheol Kim, Rebecca Jaszczak, Bonnie Wong, Ethan Winkler, Deniz Goekbuget, Ryan Boileau, Tyler Fair, Bryan Pavlovic, Alex Pollen, and Faranak Fattahi, for helpful discussions. We thank the UCSF Parnassus Flow Cytometry Core (RRID: SCR_018206), supported in part by grant National Institutes of Health (NIH) P30 DK063720 and by the NIH S10 Instrumentation Grant S10 1S10OD021822-01. We thank Eric Chow at the UCSF Center for Advanced Technologies, funded by the Program for Breakthrough Biomedical Research Technologies, Methodologies, and Cores grant. This work was supported by NIH awards 5F31NS106868 and T32 2T32GM007618-39 to D.W. and 5R01NS091544-02, 1R01NS124881, 1R21NS101395-01, Veterans Affairs 5I01 BX000252–07, and Eli and Edythe Broad Stem Cell Innovation Pilot Award to D.A.L. D.W. and D.A.L. conceptualized the study, designed experiments, and wrote the manuscript. D.W. designed, performed, and analyzed experiments and prepared figures. S.J.L. M.A.H. J.C. J.M.R. Y.S. and J.S.W. designed experiments. A.P. M.A.C. J.M.R. N.W.L.E. and G.A.C. analyzed experiments. E.H. and E.N. performed experiments. All authors reviewed and edited the manuscript. The authors declare the following competing financial interests: The Regents of the University of California with J.S.W. and M.A.H. as inventors have filed patent applications related to CRISPRi/a screening and Perturb-seq (11,254,933). J.S.W. declares outside interest in 5AM Ventures, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics, and Third Rock Ventures. M.A.H. consults for Akouos. J.M.R. consults for Maze Therapeutics. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in science. The author list of this paper includes contributors from the location where the research was conducted who participated in the data collection, design, analysis, and/or interpretation of the work. Funding Information: We thank members of the Lim lab, as well as Min Cheol Kim, Rebecca Jaszczak, Bonnie Wong, Ethan Winkler, Deniz Goekbuget, Ryan Boileau, Tyler Fair, Bryan Pavlovic, Alex Pollen, and Faranak Fattahi, for helpful discussions. We thank the UCSF Parnassus Flow Cytometry Core (RRID: SCR_018206 ), supported in part by grant National Institutes of Health (NIH) P30 DK063720 and by the NIH S10 Instrumentation Grant S10 1S10OD021822-01 . We thank Eric Chow at the UCSF Center for Advanced Technologies, funded by the Program for Breakthrough Biomedical Research Technologies, Methodologies, and Cores grant. This work was supported by NIH awards 5F31NS106868 and T32 2T32GM007618-39 to D.W. and 5R01NS091544-02 , 1R01NS124881 , 1R21NS101395-01 , Veterans Affairs 5I01 BX000252–07 , and Eli and Edythe Broad Stem Cell Innovation Pilot Award to D.A.L. Publisher Copyright: {\textcopyright} 2022",
year = "2022",
month = nov,
day = "9",
doi = "10.1016/j.xgen.2022.100177",
language = "English (US)",
volume = "2",
journal = "Cell Genomics",
issn = "2666-979X",
publisher = "Cell Press",
number = "11",
}