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

David Wu; Aunoy Poddar; Elpiniki Ninou; Elizabeth Hwang; Mitchel A Cole; S John Liu; Max A Horlbeck; Jin Chen; Joseph M Replogle; Giovanni A Carosso; Nicolas W L Eng; Jonghoon Chang; Yin Shen; Jonathan S Weissman; Daniel A Lim

doi:10.1016/j.xgen.2022.100177

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

Cell Genom. 2022 Nov 9;2(11):100177. doi: 10.1016/j.xgen.2022.100177. Epub 2022 Sep 14.

Authors

David Wu^{1

2

3

4}, Aunoy Poddar^{1

2

3

4}, Elpiniki Ninou^{1

2

5}, Elizabeth Hwang^{3

4}, Mitchel A Cole^{1

2

3

4}, S John Liu^{1

6}, Max A Horlbeck^{7

8

9}, Jin Chen^{10

11}, Joseph M Replogle^{4

12

13

14}, Giovanni A Carosso^{1

2}, Nicolas W L Eng¹⁵, Jonghoon Chang¹⁵, Yin Shen^{15

16}, Jonathan S Weissman^{7

8

13

14

17}, Daniel A Lim^{1

2

18

19}

Affiliations

¹ Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
² Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
³ Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
⁴ Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
⁵ Biomedical Research Foundation Academy of Athens, Athens, Greece.
⁶ Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.
⁷ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
⁸ Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
⁹ Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
¹⁰ Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
¹¹ Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
¹² Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
¹³ Whitehead Institute, Cambridge, MA, USA.
¹⁴ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁵ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
¹⁷ David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁸ San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.
¹⁹ Lead Contact.

Abstract

Human chromosomes are pervasively transcribed, but systematic understanding of coding and 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 to proliferation. Further, we applied 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 (danlimlab.shinyapps.io/dualgenomewide) 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; Perturb-seq; genome-wide pooled screens; human pluripotent stem cells; iPSCs; long noncoding RNA; neural induction; neurodevelopment; single-cell RNA-Seq.

Abstract

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