Cilium

Phenotype

Ciliogenesis

Biology

Gene

Hedgehog

Ciliopathy

Signal transduction

Computational biology

Hedgehog signaling pathway

Cell biology

CRISPR

Ciliopathies

Genetics

Nature Genetics

Primary cilia organize Hedgehog signaling and shape embryonic development, and their dysregulation is the unifying cause of ciliopathies. We conducted a functional genomic screen for Hedgehog signaling by engineering antibiotic-based selection of Hedgehog-responsive cells and applying genome-wide CRISPR-mediated gene disruption. The screen can robustly identify factors required for ciliary signaling with few false positives or false negatives. Characterization of hit genes uncovered novel components of several ciliary structures, including a protein complex that contains δ-tubulin and ε-tubulin and is required for centriole maintenance. The screen also provides an unbiased tool for classifying ciliopathies and showed that many congenital heart disorders are caused by loss of ciliary signaling. Collectively, our study enables a systematic analysis of ciliary function and of ciliopathies, and also defines a versatile platform for dissecting signaling pathways through CRISPR-based screening. A CRISPR-based functional screen for Hedgehog-pathway factors identifies genes required for ciliary signaling and can be used to classify genetic disorders as ciliopathies.

A CRISPR-based screen for Hedgehog signaling provides insights into ciliary function and ciliopathies