{ "abstract": "Tunicates are the sister group to vertebrates within the chordate phylum, yet unlike other chordate groups, they evolved a biphasic lifecycle alternating between motile larvae and sessile adults. The papillae of most tunicate larvae are the key sensory-adhesive organ regulating their settlement and metamorphosis. The papillae are nearly always arranged as a group of three morphologically identical organs that arise from an anterior neural plate border region nested between ventral epidermis and more dorsal/posterior neural tube progenitors. Due to their embryonic origin and molecular signatures, this anterior border has been evolutionarily linked to vertebrate placode regions. It was previously shown that the specification, patterning, and morphogenesis of the embryonic papilla region all depend on BMP signaling, though downstream mechanisms remain poorly understood. Here we show that the NKX2-3/5/6 ortholog NK4 is a key transcription factor that acts downstream of BMP signaling to pattern the papillae in the Ciona embryo. We present evidence that NK4 is activated by BMP signaling and encodes a transcriptional repressor that is required to restrict the expression of the papilla regulatory gene Foxg to three cell clusters that give rise to the three papillae. Loss of NK4 function results in the formation of a single large papilla. In contrast, overexpression of NK4 represses Foxg, eliminating the papillae. We also show that the expression of NK4 is restricted dorsally by the BMP antagonist Chordin, while the ventrally-expressed transcription factor Msx can alleviate the repressive effect of NK4, potentially allowing for the characteristic tripartite patterning of the papillae. Author summary: Many marine animals, like most of our close non-vertebrate chordate relatives the tunicates, begin life as swimming larvae that must find the right surface on which to attach before undergoing metamorphosis into the sedentary adult phase. This decision relies on sensory-adhesive organs called the papillae, which frequently appear in a set of three matching parts arranged in a triangle. How an embryo builds exactly three identical papilla organs, rather than one continuous, disorganized patch of tissue, has remained unclear. Using the model tunicate Ciona, we show that a protein called NK4, homologous to human factors NKX2-3, NKX2-5, and NKX2-6, plays a central role in this process. NK4 is switched on by a signaling protein called BMP, which spreads across the region that will form the papillae. Once active, NK4 refines the activation pattern of another key factor, Foxg, so that only three small clusters of cells that go on to become the three papillae. When we removed NK4 using CRISPR gene editing, the three papillae fused into a single large one instead. Our results help explain how a uniform field of cells can reliably split into three separate organs.", "abstract_shown": true, "affiliations": [ "School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America.", "Biology Department, Colby College, Waterville, Maine, United States of America." ], "article_type": "Research Article", "arxiv": null, "author_total": 6, "authors": [ { "affs": [ 0 ], "name": "Christopher J Johnson" }, { "affs": [ 1 ], "name": "Joshua Kavaler", "orcid": "0000-0002-4603-5781" }, { "affs": [ 0 ], "name": "Timethea Slade", "orcid": "0009-0000-2450-0593" }, { "affs": [ 0 ], "name": "Kayla Wilson" }, { "affs": [ 1 ], "name": "Christina D Cota", "orcid": "0000-0003-1307-903X" }, { "affs": [ 0 ], "name": "Alberto Stolfi", "orcid": "0000-0001-7179-9700" } ], "bibtex": "https://research.draconitic.com/paper/19cr4jytrrc4c.bib", "cited_by": 0, "doi": "10.1371/journal.pgen.1012334", "fulltext_url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012334", "id": "19cr4jytrrc4c", "issns": [ "1553-7404", "1553-7390" ], "landing_url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012334", "language": "eng", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1312|Developmental Biology and Gene Regulation" ], [ "plos", "/Biology and life sciences/Bioengineering/Genome engineering/Synthetic genome editing/CRISPR" ], [ "plos", "/Biology and life sciences/Cell biology/Signal transduction/Cell signaling/BMP signaling" ], [ "plos", "/Biology and life sciences/Developmental biology/Life cycles/Larvae" ], [ "plos", "/Biology and life sciences/Developmental biology/Metamorphosis" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Molecular biology assays and analysis techniques/Gene expression and vector techniques/Hyperexpression techniques" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Transfection" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Vertebrates" ], [ "plos", "/Biology and life sciences/Synthetic biology/Synthetic genomics/Synthetic genome editing/CRISPR" ], [ "plos", "/Biology and life sciences/Taxonomy/Animal taxonomy/Chordata/Tunicata" ], [ "plos", "/Biology and life sciences/Zoology/Animal taxonomy/Chordata/Tunicata" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Vertebrates" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Animal taxonomy/Chordata/Tunicata" ], [ "plos", "/Engineering and technology/Bioengineering/Genome engineering/Synthetic genome editing/CRISPR" ], [ "plos", "/Engineering and technology/Synthetic biology/Synthetic genomics/Synthetic genome editing/CRISPR" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Molecular biology assays and analysis techniques/Gene expression and vector techniques/Hyperexpression techniques" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Transfection" ] ], "openalex": "W7221535587", "pdf_url": "https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1012334&type=printable", "pmcid": "PMC13671656", "pmid": "42862850", "published": "2026-10-12", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/19cr4jytrrc4c.ris", "sources": [ { "first_seen": "2026-10-30T12:17:30Z", "native_id": "10.1371/journal.pgen.1012334", "source": "plos", "url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1012334" }, { "first_seen": "2026-10-30T12:19:00Z", "native_id": "MED:42862850", "source": "europepmc", "url": "https://europepmc.org/article/MED/42862850" } ], "subjects": [ { "field": "biochemistry", "origin": "plos:molecular biology", "subfield": "molecular-biology" }, { "field": "biology", "origin": "plos:developmental biology", "subfield": "developmental-biology" }, { "field": "biology", "origin": "plos:bioengineering", "subfield": "systems-synthetic" } ], "title": "An NKX2-3/5/6 homolog is required downstream of BMP signaling to pattern the sensory-adhesive organ of a tunicate larva", "title_text": "An NKX2-3/5/6 homolog is required downstream of BMP signaling to pattern the sensory-adhesive organ of a tunicate larva", "type": "peer-reviewed", "updated_at": "2026-10-30T12:19:00Z", "url": "https://research.draconitic.com/paper/19cr4jytrrc4c", "venue": "PLOS Genetics", "versions": [] }