{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T08:36:19Z","timestamp":1785832579748,"version":"3.56.0"},"reference-count":84,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["WA3365\/2-1"],"award-info":[{"award-number":["WA3365\/2-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["WA3365\/5-1"],"award-info":[{"award-number":["WA3365\/5-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["431984000"],"award-info":[{"award-number":["431984000"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["WA3365\/4-1"],"award-info":[{"award-number":["WA3365\/4-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["K99HL127275"],"award-info":[{"award-number":["K99HL127275"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390939984"],"award-info":[{"award-number":["390939984"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>\n                    Foxi1 is a master regulator of ionocytes (ISCs\/INCs) across species and organs. Two subtypes of ISCs exist, and both \u03b1- and \u03b2-ISCs regulate pH- and ion-homeostasis in epithelia. Gain and loss of FOXI1 function are associated with human diseases, including Pendred syndrome, male infertility, renal acidosis, and cancers. Foxi1 was predominantly studied in the context of ISC specification, however, reports indicate additional functions in early and ectodermal development. Here, we re-investigated the functions of Foxi1 in\n                    <jats:italic>Xenopus laevis<\/jats:italic>\n                    embryonic mucociliary epidermis developpment and found a novel function for Foxi1 in the generation of Notch-ligand expressing mucociliary multipotent progenitors (MPPs). We demonstrate that MPPs are a distinct sub-population of epidermal cells in which Foxi1 has two concentration-dependent functions: At low levels, Foxi1 maintains ectodermal competence in MPPs through transcriptional and epigenetic mechanisms, while at high levels, Foxi1 induces a multi-step process of ISC specification and differentiation in cooperation with Ubp1 and Dmrt2. We further describe how\n                    <jats:italic>foxi1<\/jats:italic>\n                    expression is affected through auto- and Notch-regulation, and how this developmental program affects mucociliary patterning. Together, we reveal novel functions for MPPs and Foxi1 in\n                    <jats:italic>Xenopus<\/jats:italic>\n                    mucociliary epidermis formation, relevant to our understanding of vertebrate development and human disease.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003583","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T18:34:15Z","timestamp":1767638055000},"page":"e3003583","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Foxi1 regulates multipotent mucociliary progenitors and ionocyte specification through transcriptional and epigenetic mechanisms"],"prefix":"10.1371","volume":"24","author":[{"given":"Sarah","family":"Bowden","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena Maria","family":"Brislinger-Engelhardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona","family":"Hansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aisha","family":"Andricek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Africa","family":"Temporal-Plo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damian","family":"Weber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"H\u00e4gele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian","family":"Lorenz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Litwin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemens","family":"Kreutz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2332-6068","authenticated-orcid":true,"given":"Peter","family":"Walentek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"issue":"1","key":"pbio.3003583.ref001","doi-asserted-by":"crossref","first-page":"3516","DOI":"10.1038\/s41598-023-30603-1","article-title":"Transcriptomic profile comparison reveals conservation of ionocytes across multiple organs","volume":"13","author":"C Pou Casellas","year":"2023","journal-title":"Sci Rep"},{"issue":"9","key":"pbio.3003583.ref002","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1242\/dev.00376","article-title":"Lack of pendrin expression leads to deafness and expansion of the endolymphatic compartment in inner ears of Foxi1 null mutant mice","volume":"130","author":"M Hulander","year":"2003","journal-title":"Development"},{"issue":"4","key":"pbio.3003583.ref003","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1242\/dev.055699","article-title":"Specification of ion transport cells in the Xenopus larval skin","volume":"138","author":"IK Quigley","year":"2011","journal-title":"Development"},{"issue":"2","key":"pbio.3003583.ref004","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.ydbio.2007.04.044","article-title":"Foxi3 transcription factors and Notch signaling control the formation of skin ionocytes from epidermal precursors of the zebrafish embryo","volume":"307","author":"M J\u00e4nicke","year":"2007","journal-title":"Dev Biol"},{"issue":"4","key":"pbio.3003583.ref005","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1242\/dev.02768","article-title":"FoxI1e activates ectoderm formation and controls cell position in the Xenopus blastula","volume":"134","author":"A Mir","year":"2007","journal-title":"Development"},{"issue":"7","key":"pbio.3003583.ref006","article-title":"Foxi2 is an animally localized maternal mRNA in Xenopus, and an activator of the zygotic ectoderm activator Foxi1e","volume":"7","author":"S-W Cha","year":"2012","journal-title":"PLoS One"},{"issue":"12","key":"pbio.3003583.ref007","doi-asserted-by":"crossref","first-page":"2733","DOI":"10.1242\/dev.01865","article-title":"Xema, a foxi-class gene expressed in the gastrula stage Xenopus ectoderm, is required for the suppression of mesendoderm","volume":"132","author":"C Suri","year":"2005","journal-title":"Development"},{"key":"pbio.3003583.ref008","doi-asserted-by":"crossref","DOI":"10.1002\/dvg.23001","article-title":"What we can learn from a tadpole about ciliopathies and airway diseases: using systems biology in Xenopus to study cilia and mucociliary epithelia","volume":"55","author":"P Walentek","year":"2017","journal-title":"Genesis"},{"key":"pbio.3003583.ref009","doi-asserted-by":"crossref","DOI":"10.1002\/dvg.23406","article-title":"Xenopus epidermal and endodermal epithelia as models for mucociliary epithelial evolution, disease, and metaplasia","volume":"59","author":"P Walentek","year":"2021","journal-title":"Genesis"},{"key":"pbio.3003583.ref010","doi-asserted-by":"crossref","DOI":"10.1513\/AnnalsATS.201802-128AW","article-title":"Airway epithelial differentiation and mucociliary clearance","volume":"15","author":"JA Whitsett","year":"2018","journal-title":"Ann Am Thorac Soc"},{"issue":"6","key":"pbio.3003583.ref011","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1159\/000514579","article-title":"Signaling control of mucociliary epithelia: stem cells, cell fates, and the plasticity of cell identity in development and disease","volume":"211","author":"P Walentek","year":"2022","journal-title":"Cells Tissues Organs"},{"key":"pbio.3003583.ref012","article-title":"Pulmonary ionocytes regulate airway surface liquid pH in primary human bronchial epithelial cells","author":"X Luan","year":"2024","journal-title":"Am J Respir Crit Care Med"},{"issue":"7718","key":"pbio.3003583.ref013","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","article-title":"A revised airway epithelial hierarchy includes CFTR-expressing ionocytes","volume":"560","author":"DT Montoro","year":"2018","journal-title":"Nature"},{"issue":"11","key":"pbio.3003583.ref014","doi-asserted-by":"crossref","first-page":"1560","DOI":"10.1172\/JCI20665","article-title":"Distal renal tubular acidosis in mice that lack the forkhead transcription factor Foxi1","volume":"113","author":"SR Blomqvist","year":"2004","journal-title":"J Clin Invest"},{"issue":"17","key":"pbio.3003583.ref015","doi-asserted-by":"crossref","first-page":"4131","DOI":"10.1038\/sj.emboj.7601272","article-title":"Epididymal expression of the forkhead transcription factor Foxi1 is required for male fertility","volume":"25","author":"SR Blomqvist","year":"2006","journal-title":"EMBO J"},{"issue":"6","key":"pbio.3003583.ref016","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1086\/518314","article-title":"Transcriptional control of SLC26A4 is involved in Pendred syndrome and nonsyndromic enlargement of vestibular aqueduct (DFNB4)","volume":"80","author":"T Yang","year":"2007","journal-title":"Am J Hum Genet"},{"issue":"6","key":"pbio.3003583.ref017","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1016\/j.celrep.2017.07.043","article-title":"Cell-type-specific gene programs of the normal human nephron define kidney cancer subtypes","volume":"20","author":"D Lindgren","year":"2017","journal-title":"Cell Rep"},{"issue":"5","key":"pbio.3003583.ref018","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1007\/s00428-023-03721-4","article-title":"Characterization of two transcriptomic subtypes of marker-null large cell carcinoma of the lung suggests different origin and potential new therapeutic perspectives","volume":"484","author":"M Simbolo","year":"2024","journal-title":"Virchows Arch"},{"issue":"1","key":"pbio.3003583.ref019","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.eururo.2020.03.003","article-title":"Next-generation RNA sequencing-based biomarker characterization of chromophobe renal cell carcinoma and related oncocytic neoplasms","volume":"78","author":"SL Skala","year":"2020","journal-title":"Eur Urol"},{"issue":"11","key":"pbio.3003583.ref020","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/s41419-022-05428-x","article-title":"Pulmonary cancers across different histotypes share hybrid tuft cell\/ionocyte-like molecular features and potentially druggable vulnerabilities","volume":"13","author":"Y Yamada","year":"2022","journal-title":"Cell Death Dis"},{"key":"pbio.3003583.ref021","doi-asserted-by":"crossref","unstructured":"Hendrickson CL, Blitz IL, Hussein A, Paraiso KD, Cho J, Klymkowsky MW, et al. Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification. bioRxiv. 2025.","DOI":"10.1101\/2025.01.09.632114"},{"key":"pbio.3003583.ref022","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/1471-213X-8-92","article-title":"An ontology for Xenopus anatomy and development","volume":"8","author":"E Segerdell","year":"2008","journal-title":"BMC Dev Biol"},{"issue":"2","key":"pbio.3003583.ref023","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S1534-5807(02)00113-2","article-title":"Intrinsic differences between the superficial and deep layers of the Xenopus ectoderm control primary neuronal differentiation","volume":"2","author":"AD Chalmers","year":"2002","journal-title":"Dev Cell"},{"issue":"21","key":"pbio.3003583.ref024","doi-asserted-by":"crossref","first-page":"4715","DOI":"10.1242\/dev.126.21.4715","article-title":"A two-step mechanism generates the spacing pattern of the ciliated cells in the skin of Xenopus embryos","volume":"126","author":"GA Deblandre","year":"1999","journal-title":"Development"},{"issue":"13","key":"pbio.3003583.ref025","doi-asserted-by":"crossref","first-page":"2507","DOI":"10.1242\/dev.02417","article-title":"Radial intercalation of ciliated cells during Xenopus skin development","volume":"133","author":"JL Stubbs","year":"2006","journal-title":"Development"},{"issue":"14","key":"pbio.3003583.ref026","article-title":"A single-cell, time-resolved profiling of Xenopus mucociliary epithelium reveals nonhierarchical model of development","volume":"9","author":"J Lee","year":"2023","journal-title":"Sci Adv"},{"issue":"4","key":"pbio.3003583.ref027","doi-asserted-by":"crossref","DOI":"10.1016\/j.devcel.2020.12.005","article-title":"Notch signaling induces either apoptosis or cell fate change in multiciliated cells during mucociliary tissue remodeling","volume":"56","author":"A Tasca","year":"2021","journal-title":"Dev Cell"},{"issue":"17","key":"pbio.3003583.ref028","doi-asserted-by":"crossref","DOI":"10.1242\/dev.201612","article-title":"Bidirectional multiciliated cell extrusion is controlled by Notch-driven basal extrusion and Piezo1-driven apical extrusion","volume":"150","author":"R Ventrella","year":"2023","journal-title":"Development"},{"issue":"1","key":"pbio.3003583.ref029","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1128\/MCB.26.1.155-168.2006","article-title":"The forkhead transcription factor FoxI1 remains bound to condensed mitotic chromosomes and stably remodels chromatin structure","volume":"26","author":"J Yan","year":"2006","journal-title":"Mol Cell Biol"},{"key":"pbio.3003583.ref030","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/978-1-4939-8784-9_18","article-title":"Manipulating and Analyzing Cell Type Composition of the Xenopus Mucociliary Epidermis","volume":"1865","author":"P Walentek","year":"2018","journal-title":"Methods Mol Biol"},{"key":"pbio.3003583.ref031","article-title":"Animal cap isolation from Xenopus laevis","volume":"2007","author":"HL Sive","year":"2007","journal-title":"CSH Protoc"},{"issue":"6","key":"pbio.3003583.ref032","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1440-169X.2005.00809.x","article-title":"Regulatory targets for transcription factor AP2 in Xenopus embryos","volume":"47","author":"T Luo","year":"2005","journal-title":"Dev Growth Differ"},{"issue":"6","key":"pbio.3003583.ref033","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.modgep.2005.11.011","article-title":"Expression of TFAP2beta and TFAP2gamma genes in Xenopus laevis","volume":"6","author":"Y Zhang","year":"2006","journal-title":"Gene Expr Patterns"},{"issue":"1","key":"pbio.3003583.ref034","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1002\/dvdy.21002","article-title":"Zac1 promotes a M\u00fcller glial cell fate and interferes with retinal ganglion cell differentiation in Xenopus retina","volume":"236","author":"L Ma","year":"2007","journal-title":"Dev Dyn"},{"key":"pbio.3003583.ref035","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/S0925-4773(01)00461-0","article-title":"Differential gene expression of Xenopus Pitx1, Pitx2b and Pitx2c during cement gland, stomodeum and pituitary development","volume":"107","author":"A Schweickert","year":"2001","journal-title":"Mech Dev"},{"issue":"10","key":"pbio.3003583.ref036","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1002\/dvdy.24145","article-title":"Characterization of the Rx1-dependent transcriptome during early retinal development","volume":"243","author":"G Giudetti","year":"2014","journal-title":"Dev Dyn"},{"issue":"2","key":"pbio.3003583.ref037","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.ydbio.2020.05.012","article-title":"The transcription factor Hypermethylated in Cancer 1 (Hic1) regulates neural crest migration via interaction with Wnt signaling","volume":"463","author":"H Ray","year":"2020","journal-title":"Dev Biol"},{"issue":"4","key":"pbio.3003583.ref038","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1242\/dev.01647","article-title":"GATA4, 5 and 6 mediate TGFbeta maintenance of endodermal gene expression in Xenopus embryos","volume":"132","author":"BA Afouda","year":"2005","journal-title":"Development"},{"issue":"1","key":"pbio.3003583.ref039","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/0092-8674(91)90573-H","article-title":"Expression of a Xenopus homolog of Brachyury (T) is an immediate-early response to mesoderm induction","volume":"67","author":"JC Smith","year":"1991","journal-title":"Cell"},{"issue":"11","key":"pbio.3003583.ref040","doi-asserted-by":"crossref","first-page":"3409","DOI":"10.1002\/j.1460-2075.1989.tb08505.x","article-title":"MyoD expression in the forming somites is an early response to mesoderm induction in Xenopus embryos","volume":"8","author":"ND Hopwood","year":"1989","journal-title":"EMBO J"},{"issue":"3","key":"pbio.3003583.ref041","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.bbagrm.2013.10.001","article-title":"OCT4: dynamic DNA binding pioneers stem cell pluripotency","volume":"1839","author":"S Jerabek","year":"2014","journal-title":"Biochim Biophys Acta"},{"issue":"9","key":"pbio.3003583.ref042","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.15252\/embr.201540467","article-title":"Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells","volume":"16","author":"TK Mistri","year":"2015","journal-title":"EMBO Rep"},{"issue":"2","key":"pbio.3003583.ref043","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.ydbio.2009.11.008","article-title":"BMP antagonists and FGF signaling contribute to different domains of the neural plate in Xenopus","volume":"337","author":"AE Wills","year":"2010","journal-title":"Dev Biol"},{"issue":"1","key":"pbio.3003583.ref044","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1006538","article-title":"Rfx2 stabilizes Foxj1 binding at chromatin loops to enable multiciliated cell gene expression","volume":"13","author":"IK Quigley","year":"2017","journal-title":"PLoS Genet"},{"issue":"13","key":"pbio.3003583.ref045","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2019.08.063","article-title":"\u0394N-Tp63 mediates Wnt\/\u03b2-catenin-induced inhibition of differentiation in basal stem cells of mucociliary epithelia","volume":"28","author":"M Haas","year":"2019","journal-title":"Cell Rep"},{"key":"pbio.3003583.ref046","article-title":"Temporal Notch signaling regulates mucociliary cell fates through Hes-mediated competitive de-repression","author":"MM Brislinger-Engelhardt","year":"2023","journal-title":"bioRxiv"},{"issue":"2","key":"pbio.3003583.ref047","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1242\/dmm.006494","article-title":"Embryonic frog epidermis: a model for the study of cell-cell interactions in the development of mucociliary disease","volume":"4","author":"E Dubaissi","year":"2011","journal-title":"Dis Model Mech"},{"key":"pbio.3003583.ref048","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.24265","article-title":"Transcription factor TFCP2L1 patterns cells in the mouse kidney collecting ducts","volume":"6","author":"M Werth","year":"2017","journal-title":"Elife"},{"issue":"5","key":"pbio.3003583.ref049","doi-asserted-by":"crossref","DOI":"10.1242\/dmm.052211","article-title":"A homozygous human WNT11 variant is associated with laterality, heart and renal defects","volume":"18","author":"H Berns","year":"2025","journal-title":"Dis Model Mech"},{"issue":"21","key":"pbio.3003583.ref050","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1016\/j.cub.2015.09.015","article-title":"Mechanical strain determines the axis of planar polarity in ciliated epithelia","volume":"25","author":"Y-H Chien","year":"2015","journal-title":"Curr Biol"},{"key":"pbio.3003583.ref051","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1042\/BJ20051094","article-title":"The forkhead transcription factor Foxi1 directly activates the AE4 promoter","volume":"393","author":"I Kurth","year":"2006","journal-title":"Biochem J"},{"issue":"1","key":"pbio.3003583.ref052","doi-asserted-by":"crossref","first-page":"6841","DOI":"10.1038\/s41467-024-50822-y","article-title":"Combinatorial regulatory states define cell fate diversity during embryogenesis","volume":"15","author":"JE Valencia","year":"2024","journal-title":"Nat Commun"},{"issue":"2","key":"pbio.3003583.ref053","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.ydbio.2015.03.013","article-title":"ATP4a is required for development and function of the Xenopus mucociliary epidermis\u2014a potential model to study proton pump inhibitor-associated pneumonia","volume":"408","author":"P Walentek","year":"2015","journal-title":"Dev Biol"},{"issue":"5","key":"pbio.3003583.ref054","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1681\/ASN.0000000000000319","article-title":"Foxp1 is required for renal intercalated cell differentiation and acid-base regulation","volume":"35","author":"S-T Wu","year":"2024","journal-title":"J Am Soc Nephrol"},{"issue":"6441","key":"pbio.3003583.ref055","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1126\/science.aav9996","article-title":"Identification of a regeneration-organizing cell in the Xenopus tail","volume":"364","author":"C Aztekin","year":"2019","journal-title":"Science"},{"key":"pbio.3003583.ref056","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ydbio.2020.08.005","article-title":"Foxi1 inactivation rescues loss of principal cell fate selection in Hes1-deficient kidneys but does not ensure maintenance of principal cell gene expression","volume":"466","author":"M Mukherjee","year":"2020","journal-title":"Dev Biol"},{"issue":"13","key":"pbio.3003583.ref057","first-page":"2352","article-title":"BMP signalling controls the construction of vertebrate mucociliary epithelia","volume":"142","author":"M Cibois","year":"2015","journal-title":"Development"},{"issue":"2","key":"pbio.3003583.ref058","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/ncb2406","article-title":"Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation","volume":"14","author":"JL Stubbs","year":"2012","journal-title":"Nat Cell Biol"},{"issue":"6392","key":"pbio.3003583.ref059","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar5780","article-title":"The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution","volume":"360","author":"JA Briggs","year":"2018","journal-title":"Science"},{"issue":"2","key":"pbio.3003583.ref060","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S1534-5807(02)00113-2","article-title":"Intrinsic differences between the superficial and deep layers of the Xenopus ectoderm control primary neuronal differentiation","volume":"2","author":"AD Chalmers","year":"2002","journal-title":"Dev Cell"},{"key":"pbio.3003583.ref061","doi-asserted-by":"crossref","first-page":"1282273","DOI":"10.3389\/fcell.2023.1282273","article-title":"Alcohol induces neural tube defects by reducing retinoic acid signaling and promoting neural plate expansion","volume":"11","author":"T Edri","year":"2023","journal-title":"Front Cell Dev Biol"},{"issue":"5","key":"pbio.3003583.ref062","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1002\/jez.b.21189","article-title":"Tfap2 transcription factors in zebrafish neural crest development and ectodermal evolution","volume":"308","author":"TL Hoffman","year":"2007","journal-title":"J Exp Zool B Mol Dev Evol"},{"issue":"20","key":"pbio.3003583.ref063","doi-asserted-by":"crossref","DOI":"10.1242\/dev.164384","article-title":"GATA transcription factors in development and disease","volume":"145","author":"M Tremblay","year":"2018","journal-title":"Development"},{"key":"pbio.3003583.ref064","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.semcdb.2016.08.005","article-title":"Molecular basis for the genome engagement by Sox proteins","volume":"63","author":"L Hou","year":"2017","journal-title":"Semin Cell Dev Biol"},{"key":"pbio.3003583.ref065","doi-asserted-by":"crossref","first-page":"204019","DOI":"10.1016\/j.cdev.2025.204019","article-title":"Mucociliary cell type compositions\u2014bridging the gap between genes and emergent tissue functions","volume":"184","author":"P Walentek","year":"2025","journal-title":"Cells Dev"},{"issue":"7718","key":"pbio.3003583.ref066","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","article-title":"A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte","volume":"560","author":"LW Plasschaert","year":"2018","journal-title":"Nature"},{"issue":"1","key":"pbio.3003583.ref067","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyad018","article-title":"Xenbase: key features and resources of the Xenopus model organism knowledgebase","volume":"224","author":"M Fisher","year":"2023","journal-title":"Genetics"},{"key":"pbio.3003583.ref068","article-title":"Xenopus laevis in vitro fertilization and natural mating methods","volume":"2007","author":"HL Sive","year":"2007","journal-title":"CSH Protoc"},{"issue":"12","key":"pbio.3003583.ref069","article-title":"Microinjection of Xenopus embryos","volume":"2010","author":"HL Sive","year":"2010","journal-title":"Cold Spring Harb Protoc"},{"issue":"12","key":"pbio.3003583.ref070","doi-asserted-by":"crossref","first-page":"1454","DOI":"10.1038\/ng.267","article-title":"The forkhead protein Foxj1 specifies node-like cilia in Xenopus and zebrafish embryos","volume":"40","author":"JL Stubbs","year":"2008","journal-title":"Nat Genet"},{"issue":"7","key":"pbio.3003583.ref071","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1242\/dev.102426","article-title":"A secretory cell type develops alongside multiciliated cells, ionocytes and goblet cells, and provides a protective, anti-infective function in the frog embryonic mucociliary epidermis","volume":"141","author":"E Dubaissi","year":"2014","journal-title":"Development"},{"issue":"7","key":"pbio.3003583.ref072","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1242\/dev.102343","article-title":"A novel serotonin-secreting cell type regulates ciliary motility in the mucociliary epidermis of Xenopus tadpoles","volume":"141","author":"P Walentek","year":"2014","journal-title":"Development"},{"issue":"1","key":"pbio.3003583.ref073","doi-asserted-by":"crossref","first-page":"9382","DOI":"10.1038\/s41598-023-35979-8","article-title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","volume":"13","author":"AA Vetrova","year":"2023","journal-title":"Sci Rep"},{"key":"pbio.3003583.ref074","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/S0091-679X(08)60307-6","article-title":"In situ hybridization: an improved whole-mount method for Xenopus embryos","volume":"36","author":"RM Harland","year":"1991","journal-title":"Methods Cell Biol"},{"issue":"5","key":"pbio.3003583.ref075","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.celrep.2012.03.005","article-title":"ATP4a is required for Wnt-dependent Foxj1 expression and leftward flow in Xenopus left-right development","volume":"1","author":"P Walentek","year":"2012","journal-title":"Cell Rep"},{"key":"pbio.3003583.ref076","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.ydbio.2023.10.004","article-title":"Small molecule-mediated reprogramming of Xenopus blastula stem cells to a neural crest state","volume":"505","author":"PB Huber","year":"2024","journal-title":"Dev Biol"},{"issue":"7","key":"pbio.3003583.ref077","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"},{"issue":"1","key":"pbio.3003583.ref078","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.ydbio.2020.02.013","article-title":"Chromatin accessibility and histone acetylation in the regulation of competence in early development","volume":"462","author":"M Esmaeili","year":"2020","journal-title":"Dev Biol"},{"issue":"12","key":"pbio.3003583.ref079","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"JD Buenrostro","year":"2013","journal-title":"Nat Methods"},{"issue":"2","key":"pbio.3003583.ref080","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"Gigascience"},{"issue":"9","key":"pbio.3003583.ref081","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1038\/nprot.2012.101","article-title":"Identifying ChIP-seq enrichment using MACS","volume":"7","author":"J Feng","year":"2012","journal-title":"Nat Protoc"},{"key":"pbio.3003583.ref082","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"F Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pbio.3003583.ref083","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"S Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"pbio.3003583.ref084","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Community Galaxy","year":"2024","journal-title":"Nucleic Acids Res"}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003583","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T18:34:31Z","timestamp":1767638071000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003583"}},"subtitle":[],"editor":[{"given":"Marianne E.","family":"Bronner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":84,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3003583","relation":{},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,5]]}}}