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. Author manuscript; available in PMC: 2019 Dec 1.
Published in final edited form as: Curr Opin Cell Biol. 2018 Aug 20;55:139–149. doi: 10.1016/j.ceb.2018.08.001

Table 1:

Overview of ciliary-focused functional genomic screens in mammalian cells

Publication Method Cell type Phenotypic readout Hits Validation approach Core findings
Kim et al., 2010 RNAi on 7,784 therapeuticallyrelevant genes hTERT-RPE1 Cilia number and length: EGFP-Smo reporter 40 positive modulators and 13 negative modulators of ciliogenesis (12 ciliome proteins) Confirmation screen at optimal cell density; verification of effect on cilia length; functional studies
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    New cilium length modulators

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    Expanded link between actin dynamics, endocytic recycling, and ciliogenesis
Lai et al., 2011 siRNA on 40 uncharacterized ciliary proteome genes and high-content analysis S12; NIH/3T3; mIMCD3 Cilia length, number, and transport of ciliary cargo: Gli3 luciferase and GFP-HTR6 reporters 27 genes with impaired Hh signaling with or without cilia formation, elongation, or transport defects Validated 12 strongest hits from primary screen; correlated mRNA levels with Hh signaling defects 7 validated hits:
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    absent or nearly absent cilia (mC21orf2 and Ssa2)

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    cilia elongation defects (Ift46)

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    grossly normal cilia but defective Hh signaling (Arl3 Nme7, Ssna1)

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    elongated cilia (Ptpdc1)
Roosing et al., 2015 Genome-wide siRNA (18,045 genes; (Dharmacon library; 4–5 siRNAs/gene) hTERT-RPE1 Cilia number and length: EGFP-Smo reporter; co-transfected nuclear cell cycle reporter (mCherry-Geminin) 591 likely regulators of ciliogenesis Combined cell-based screen with WES (145 individuals with unexplained JBTS)
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    First genomewide siRNA screen for ciliogenesis

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    KIAA0586 (Talpid3 ortholog) mutations in individuals from 15 families with unsolved JBTS (~5% of unsolved cases)
Wheway et al., 2015 Genome-wide siRNA (19,059 genes; ThermoFisher siGENOME library) hTERT-RPE1; mIMCD3 Loss of cilium: acetylated tubulin immunostaining 68 validated genes involved in ciliogenesis in mIMCD3 cells; 37 validated genes in hTERT-RPE1 cells qPCR, Western-blot, immunostaining, cross-comparison of hits with WES data (JBTS and JATD), in vivo validation in zebrafish
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    New components of ciliogenesis pathway: UPS, PRPFs and GPCRs

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    PIBF1 mutated in JBTS and C2orf2 mutated in JATD
Pusapati et al., 2018 Genome-wide CRISPR library (Brie library) NIH/3T3-CG Quantitative assessment of Hh signaling: GLI-GFP reporter 641 genes: 40% of known Hh genes, 20% of all known cilia genes, 30% of known ciliopathy genes Clonal knockout analysis in NIH/3T3 and NPC derived from mESC for 11 top regulators
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    Confirmation of Megf8 and Mgrn1 role in Hh signaling

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    Novel negative regulator of Sonic Hh pathway: Atthog
Breslow et al., 2018 Genome wide CRISPR (10 sgRNAs/gene) NIH/3T3-CG Assessment of Hh signaling: Gli:BlastR reporter conferring blasticidin resistance 472 genes affecting Hh signaling (10% FDR) Clonal knockout analysis for 6 new genes, immunofluorescence, mass spectrometry, luciferase assay
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    Depletion of hits in NPHP associated genes

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    Confirmation that TZ protein FAM92A regulates ciliogenesis

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    TXNDC15 mutated in MKS

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    Tedc1 and Tedc2 required for centriole stability