{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T04:00:51Z","timestamp":1785211251063,"version":"3.55.0"},"posted":{"date-parts":[[2026,7,3]]},"group-title":"Developmental Biology","reference-count":109,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:00:00Z","timestamp":1783036800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"NIH","award":["F30HD121208"],"award-info":[{"award-number":["F30HD121208"]}]},{"name":"NIH","award":["F32HD113384"],"award-info":[{"award-number":["F32HD113384"]}]},{"name":"NIH","award":["R01NS109425"],"award-info":[{"award-number":["R01NS109425"]}]},{"name":"NIH","award":["R37NS131117"],"award-info":[{"award-number":["R37NS131117"]}]},{"name":"NIH","award":["K99NS121595"],"award-info":[{"award-number":["K99NS121595"]}]},{"name":"NIH","award":["R01HG012761"],"award-info":[{"award-number":["R01HG012761"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Cranial motor neurons (\n                  <jats:bold>cMNs)<\/jats:bold>\n                  , form discrete nuclei that control diverse behaviors such as eye movement, feeding, facial expression, and regulation of visceral organ function. However, the developmental programs that drive cMN target choices and functional specialization have not been comprehensively studied in any vertebrate. Here, we present an integrated single-cell RNA-sequencing atlas of zebrafish cMN development and perform extensive validation by HCR\n                  <jats:italic>in situ<\/jats:italic>\n                  hybridization. We find that each cranial motor nucleus expresses a distinct transcriptional signature, and in many cases, we identify transcriptional correlates to functional subtypes within individual nuclei. We find that identity often precedes axon targeting, indicating that cranial motor neuron fate is genetically specified early in development. These distinct identities are shaped by the intersection of shared function, rhombomere origin, and developmental time. A cross-species comparison between zebrafish and mouse reveals that these genetic programs are conserved.\n                <\/jats:p>","DOI":"10.64898\/2026.07.02.731459","type":"posted-content","created":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T13:20:11Z","timestamp":1783084811000},"source":"Crossref","is-referenced-by-count":0,"title":["Distinct transcriptional programs define cranial motor neuron subtypes during vertebrate development"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0267-9355","authenticated-orcid":false,"given":"Austin Q.","family":"Seroka","sequence":"first","affiliation":[{"name":"Fred Hutchinson Cancer Center, Division of Basic Sciences, Seattle WA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2640-0462","authenticated-orcid":false,"given":"Riku","family":"Yasutomi","sequence":"additional","affiliation":[{"name":"Fred Hutchinson Cancer Center, Division of Basic Sciences, Seattle WA"},{"name":"Department of Genome Sciences, University of Washington, Seattle WA"},{"name":"Seattle Hub for Synthetic Biology, Seattle WA"},{"name":"Medical Scientist Training Program, University of Washington, Seattle WA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Italia","family":"DiChristina","sequence":"additional","affiliation":[{"name":"Fred Hutchinson Cancer Center, Division of Basic Sciences, Seattle WA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8107-6012","authenticated-orcid":false,"given":"Adam J.","family":"Isabella","sequence":"additional","affiliation":[{"name":"Fred Hutchinson Cancer Center, Division of Basic Sciences, Seattle WA"},{"name":"Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis MN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8105-4347","authenticated-orcid":false,"given":"Cole","family":"Trapnell","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle WA"},{"name":"Seattle Hub for Synthetic Biology, Seattle WA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1099-0728","authenticated-orcid":false,"given":"Cecilia B.","family":"Moens","sequence":"additional","affiliation":[{"name":"Fred Hutchinson Cancer Center, Division of Basic Sciences, Seattle WA"},{"name":"Raisbeck Endowed Chair for Basic Science"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072720250801000_2026.07.02.731459v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrn2254"},{"key":"2026072720250801000_2026.07.02.731459v2.2","doi-asserted-by":"publisher","DOI":"10.1002\/dvdy.10444"},{"key":"2026072720250801000_2026.07.02.731459v2.3","doi-asserted-by":"crossref","unstructured":"Fritzsch, B . Evolution and development of extraocular motor neurons, nerves and muscles in vertebrates. Annals of Anatomy - Anatomischer Anzeiger 253, 152225 (2024).","DOI":"10.1016\/j.aanat.2024.152225"},{"key":"2026072720250801000_2026.07.02.731459v2.4","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1146\/annurev-vision-093019-114307","article-title":"Axonal Growth Abnormalities Underlying Ocular Cranial Nerve Disorders","volume":"7","year":"2021","journal-title":"Annu. Rev. Vis. 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