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Foxn3 is a transcriptional repressor and numerous genes linked to cilia structure or assembly were upregulated in embryonic retinas with disrupted Foxn3. CUT&amp;RUN analysis revealed that many upregulated retinal genes were bound by the Foxn3 and Rfx3 proteins. A short hydrophobic motif (LXXLXWL) shared by Foxn3, Foxn4 and Foxj1 was required for association with Rfx3 and for full transcriptional repression by Foxn3, as well as for full transcriptional activation by Foxj1 or Foxn4. AlphaFold 3 predicted interaction between the hydrophobic motif and the Rfx3 dimerization domain. Mutations in Rfx3 at the predicted interaction site disrupted association of Rfx3 with Foxn3, Foxn4 or Foxj1. These results reveal a new layer of transcriptional regulation of genes required for cilia, with Foxn3 functioning as a repressor of cilia genes and limiting primary cilia formation in the developing retina.<\/jats:p>","DOI":"10.1242\/dev.205233","type":"journal-article","created":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T07:52:52Z","timestamp":1772437972000},"source":"Crossref","is-referenced-by-count":1,"title":["Foxn3 is part of a transcriptional network that regulates primary cilia in the developing retina"],"prefix":"10.1242","volume":"153","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-8140-0184","authenticated-orcid":false,"given":"Huanqing","family":"Zhang","sequence":"first","affiliation":[{"name":"Michigan Neuroscience Institute, University of Michigan 1 , Ann Arbor, MI 48109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3825-5131","authenticated-orcid":false,"given":"Thejas","family":"Nair","sequence":"additional","affiliation":[{"name":"Michigan Neuroscience Institute, University of Michigan 1 , Ann Arbor, MI 48109 ,","place":["USA"]},{"name":"University of Michigan 2 Department of Biological Chemistry , , Ann Arbor, MI 48109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8002-0615","authenticated-orcid":false,"given":"Fan","family":"Meng","sequence":"additional","affiliation":[{"name":"Michigan Neuroscience Institute, University of Michigan 1 , Ann Arbor, MI 48109 ,","place":["USA"]},{"name":"University of Michigan 3 Department of Psychiatry , , Ann Arbor, MI 48109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0080-0924","authenticated-orcid":false,"given":"David L.","family":"Turner","sequence":"additional","affiliation":[{"name":"Michigan Neuroscience Institute, University of Michigan 1 , Ann Arbor, MI 48109 ,","place":["USA"]},{"name":"University of Michigan 2 Department of Biological Chemistry , , Ann Arbor, MI 48109 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2026,3,10]]},"reference":[{"key":"2026031008275054300_DEV205233C1","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/s41586-020-2493-4","article-title":"Expanded encyclopaedias of DNA elements in the human and mouse genomes","volume":"583","author":"Abascal","year":"2020","journal-title":"Nature"},{"key":"2026031008275054300_DEV205233C2","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026031008275054300_DEV205233C3","doi-asserted-by":"publisher","first-page":"9354","DOI":"10.1038\/s41598-019-45839-z","article-title":"The ENCODE blacklist: identification of problematic regions of the genome","volume":"9","author":"Amemiya","year":"2019","journal-title":"Sci. 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