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Understanding which genes and signalling pathways regulate their development is crucial for understanding developmental disorders as well as diseases in adulthood. We exploited unique advantages of the zebrafish model to develop a rapid and scalable CRISPR\/Cas-based mutagenesis strategy aiming at the identification of genes involved in morphogenesis and function of the thyroid. Core elements of the mutagenesis assay comprise bi-allelic gene invalidation in somatic mutants, a non-invasive monitoring of thyroid development in live transgenic fish, complementary analyses of thyroid function in fixed specimens and quantitative analyses of mutagenesis efficiency by Illumina sequencing of individual fish. We successfully validated our mutagenesis-phenotyping strategy in experiments targeting genes with known functions in early thyroid morphogenesis (<jats:italic>pax2a<\/jats:italic>, <jats:italic>nkx2.4b<\/jats:italic>) and thyroid functional differentiation (<jats:italic>duox<\/jats:italic>, <jats:italic>duoxa<\/jats:italic>, <jats:italic>tshr<\/jats:italic>). We also demonstrate that <jats:italic>duox<\/jats:italic> and <jats:italic>duoxa<\/jats:italic> crispants phenocopy thyroid phenotypes previously observed in human patients with bi-allelic <jats:italic>DUOX2<\/jats:italic> and <jats:italic>DUOXA2<\/jats:italic> mutations. The proposed combination of efficient mutagenesis protocols, rapid non-invasive phenotyping and sensitive genotyping holds great potential to systematically characterize the function of larger candidate gene panels during thyroid development and is applicable to other organs and tissues.<\/jats:p>","DOI":"10.1038\/s41598-018-24036-4","type":"journal-article","created":{"date-parts":[[2018,3,29]],"date-time":"2018-03-29T22:30:51Z","timestamp":1522362651000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":59,"title":["A Rapid CRISPR\/Cas-based Mutagenesis Assay in Zebrafish for Identification of Genes Involved in Thyroid Morphogenesis and Function"],"prefix":"10.1038","volume":"8","author":[{"given":"A.","family":"Trubiroha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Gillotay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"N.","family":"Giusti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Gacquer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Libert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Lefort","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B.","family":"Haerlingen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"X.","family":"De Deken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"Opitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Costagliola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,4,4]]},"reference":[{"key":"24036_CR1","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/S0168-9525(99)01957-5","volume":"16","author":"A Grapin-Botton","year":"2000","unstructured":"Grapin-Botton, A. & Melton, D. 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