Anno C, Satou A, Fujiwara S. Transcriptional regulation of ZicL in the Ciona intestinalis embryo. Dev Genes Evol. 2006; 216: 597-605.
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen XY, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML. Diversity and Complexity in DNA Recognition by Transcription Factors. Science. 2009; 324: 1720-1723.
Behrens J, vonKries JP, Kuhl M, Bruhn L, Wedlich D, Grosschedl R, Birchmeier W. Functional interaction of beta-catenin with the transcription factor LEF-1. Nature. 1996; 382: 638-642.
Bellipanni G, Varga MT, Maegawa S, Imai Y, Kelly C, Myers AP, Chu F, Talbot WS, Weinberg ES. Essential and opposing roles of zebrafish beta-catenins in the formation of dorsal axial structures and neurectoderm. Development. 2006; 133: 1299–1309.
Bertrand V, Hudson C, Caillol D, Popovici C, Lemaire P. Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors. Cell. 2003; 115: 615-627.
Cavallo RA, Cox RT, Moline MM, Roose J, Polevoy GA, Clevers H, Peifer M, Bejsovec A.Drosophila Tcf and Groucho interact to repress Wingless signalling activity. Nature. 1998; 395: 604-608.
Davidson EH. Emerging properties of animal gene regulatory networks. Nature. 2010; 468(7326): 911-920.
Dehal P, Satou Y, Cambell RK, Chapman J, Degnan B, Tomaso AD, Davidson B, Gregorio AD, Gelpke M, Goodstein DM, Harafuji N, Hastings KEM, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S et al. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science.2002; 298; 2157-2167.
Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S. CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol. 2009; 10: R131.
Franco-Zorrilla JM, Lopez-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. DNA binding specificities of plant transcription factors and their potential to define target genes. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111: 2367-2372.
Funayama N, Fagotto F, Mccrea P, Gumbiner BM. Embryonic Axis induction by the Armadillo repeat domain of β-catenin: evidence for intracellular signaling. J. Cell Biol. 1995; 128: 959–968.
Guger KA, Gumbiner BM. Beta-catenin has Wnt-like activity and mimics the Nieuwkoop signaling center in Xenopus dorsal-ventral patterning. Dev. Biol. 1995; 172: 115–125.
Heasman J, Crawford A, Goldstone K, Garnerhamrick P, Gumbiner B, Mccrea P, Kintner C, Noro CY, Wylie C. Overexpression of cadherins and underexpression of beta-catenin inhibit dorsal mesoderm induction in early Xenopus embryos. Cell. 1994; 79: 791–803.
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis- regulatory elements required for macrophage and B cell identities. Mol Cell. 2010; 38: 576-589.
Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999; 15: 563-577.
Hudson C, Lemaire P. Induction of anterior neural fates in the ascidian Ciona intestinalis.Mech Dev. 2001; 100: 189-203.
Hudson C, Sirour C, Yasuo H. Co-expression of Foxa.a, Foxd and Fgf9/16/20 defines a transient mesendoderm regulatory state in ascidian embryos. Elife. 2016; 5.
Ikeda T, Matsuoka T, Satou Y. A time delay gene circuit is required for palp formation in the ascidian embryo. Development. 2013; 140 :4703-4708.
Ikeda T, Satou Y. Differential temporal control of Foxa.a and Zic-r.b specifies brain versus notochord fate in the ascidian embryo. Development. 2017; 144: 38-43.
Imai K, Takada N, Satoh N, Satou Y. β-catenin mediates the specification of endoderm cells in ascidian embryos. Development. 2000; 127: 3009-3020.
Imai KS, Satoh N, Satou Y. Early embryonic expression of FGF4/6/9 gene and its role in the induction of mesenchyme and notochord in Ciona savignyi embryos. Development.2002a; 129: 1729-1738.
Imai KS, Satoh N, Satou Y. An essential role of a FoxD gene in notochord induction in Ciona embryos. Development. 2002b; 129: 3441-3453.
Imai KS, Satou Y, Satoh N. Multiple functions of a Zic-like gene in the differentiation of notochord, central nervous system and muscle in Ciona savignyi embryos. Development. 2002c; 129: 2723-2732.
Imai KS, Hino K, Yagi K, Satoh N, Satou Y. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development. 2004; 131: 4047-4058.
Imai KS, Levine M, Satoh N, Satou Y. Regulatory blueprint for a chordate embryo. Science.2006; 312: 1183-1187.
Imai KS, Hikawa H, Kobayashi K, Satou Y. Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos. Development. 2017; 144: 33-37.
Jimenez G, Paroush Z, Ish-Horowicz. Groucho acts as a corepressor for a subset of negative regulators, including Hairy and Engrailed. Genes and Dev. 1997; 11: 3072-3082.
Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, et al. DNA-Binding Specificities of Human Transcription Factors. Cell. 2013; 152: 327339.
Kelly GM, Erezyilmaz DF, Moon RT. Induction of a secondary embryonic Axis in zebrafish occurs following the overexpression of beta-catenin. Mech. Dev. 1995; 53: 261–273.
Klein SL, Neilson KM, Orban J, Yaklichkin S, Hoffbauer J, Mood K, Daar IO, Moody SA. Conserved structural domains in FoxD4L1, a neural forkhead box transcription factor, are required to repress or activate target genes. PLoS One. 2013; 8: e61845.
Kubo A, Suzuki N, Yuan X, Nakai K, Satoh N, Imai KS, et al. Genomic cis-regulatory networks in the early Ciona intestinalis embryo. Development. 2010; 137: 1613-1623.
Lamy C, Rothbacher U, Caillol D, Lemaire P. Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5. Development. 2006; 133: 2835-2844.
Logan CY, Miller JR, Ferkowicz MJ, McClay DR. Nuclear β-catenin is required to specify vegetal cell fates in the sea urchin embryo. Development. 1999; 126: 345–357.
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR. DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity. Science. 2009; 324: 407-410.
Molenaar M, vandeWetering M, Oosterwegel M, PetersonMaduro J, Godsave S, Korinek V Roose J, Destree O, Clevers H. XTcf-3 transcription factor mediates beta-catenin- induced axis formation in Xenopus embryos. Cell. 1996; 86: 391-399.
Neilson KM, Klein SL, Mhaske P, Mood K, Daar IO, Moody SA. Specific domains of FoxD4/5 activate and repress neural transcription factor genes to control the progression of immature neural ectoderm to differentiating neural plate. Dev Biol. 2012; 365: 363- 375.
Nishida H. Cell Lineage Analysis in Ascidian Embryos by Intracellular Injection of a Tracer Enzyme: III. Up to the tissue restricted stage. Dev Biol. 1987; 121: 526-541.
Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302: 205-217.
Oda-Ishii I, Bertrand V, Matsuo I, Lemaire P, Saiga H. Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development. 2005; 132(7): 1663-1674.
Oda-Ishii I, Kubo A, Kari W, Suzuki N, Rothbacher U, Satou Y. A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PLoS genetics. 2016; 12: e1006045.
Oda-Ishii I, Abe T, Satou Y. Dynamics of two key maternal factors that initiate zygotic regulatory programs in ascidian embryos. Dev Biol. 2018; 437: 50-59.
Ohta N, Satou Y. Multiple signaling pathways coordinate to induce a threshold response in a chordate embryo. PLoS genetics. 2013; 9: e1003818.
Range R. Specification and positioning of the anterior neuroectoderm in deuterostome embryos. Genesis. 2014; 52: 222–234.
Roose J, Molenaar M, Peterson J, Hurenkamp J, Brantjes H, Moerer P, van de Wetering M, Destree O, Clevers H. The Xenopus Wnt effector XTcf-3 interacts with Groucho-related transcriptional repressors. Nature. 1998; 395: 608-612.
Rothbächer U, Bertrand V, Lamy C, Lemaire P. A combinatorial code of maternal GATA, Ets and β-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm. Development. 2007; 134: 4023-4032.
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004; 32: D91-94.
Satou Y, Imai KS, Satoh N. Early embryonic expression of a LIM-homeobox gene Cs-lhx3 is downstream of β-catenin and responsible for the endoderm differentiation in Ciona savignyi embryos. Development. 2001; 128: 3559-3570.
Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N. An integrated database of the ascidian, Ciona intestinalis: Towards functional genomics. Zool Sci. 2005; 22: 837-843.
Satou Y, Mieta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KEM, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K. Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biology. 2008; 9:R152
Satou Y, Nakamura R, Yu D, Yoshida R, Hamada M, Fujie M, Hisata K, Takeda H, Satoh N. A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. Genome Biology and Evolution. 2019; 11: 3144-3157.
Schneider S, Steinbeisser H, Warga RM, Hausen P. β-catenin translocation into nuclei demarcates the dorsalizing centers in frog and fish embryos. Mech. Dev. 1996; 57: 191- 198.
Schneider TD, Stephens RM. Sequence Logos: New Way to Display Consensus Sequences.Nucleic Acids Research. 1990; 18: 6097-6100.
Shimauchi Y, Chiba S, Satoh N. Synergistic action of HNF-3 and Brachyury in the notochord differentiation of ascidian embryos. Int J Dev Biol. 2001; 45: 643-652.
Surjit M, Ganti KP, Mukherji A, Ye T, Hua G, Metzger D, Li M, Chambon P. Widespread Negative Response Elements Mediate Direct Repression by Agonist-Liganded Glucocorticoid Receptor. Cell. 2011; 145: 224-241.
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: A matter of depth. Genome Res. 2011; 21: 2213-2223.
Tresser J, Chiba S, Veeman M, El-Nachef D, Newman-Smith E, Horie T, et al. doublesex/mab3 related-1 (dmrt1) is essential for development of anterior neural plate derivatives in Ciona. Development. 2010; 137: 2197-2203.
Vincentelli R, Cimino A, Geerlof A, Kubo A, Satou Y, Cambillau C. High-throughput protein expression screening and purification in Escherichia coli. Methods. 2011; 55: 65- 72.
Wagner E, Levine M. FGF signaling establishes the anterior border of the Ciona neural tube. Development. 2012; 139: 2351-2359.
Wikramanayake AH, Huang L, Klein WH. beta-Catenin is essential for patterning the maternally specified animal-vegetal axis in the sea urchin embryo. Proc. Natl. Acad. Sci.U. S. A. 1998; 95: 9343–9348.
Yaguchi S, Yaguchi J, Angerer RC, Angerer LM. A Wnt-FoxQ 2-nodal pathway links primary and secondary axis specification in sea urchin embryos. Dev. Cell. 2008; 14: 97– 107.
Yasuo H, Satoh N. Function of vertebrate T gene. Nature. 1993; 364: 582-583.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biology. 2008; 9.