A genomewide survey of developmentally relevant genes in Ciona intestinalis

Adams MD, Celniker SE, Holt RA et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195

Blank B, Andrews CN (1997) The Maf transcription factors: regulators of differentiation. Trends Biol Sci 22:437–441

Bowles J, Schepers G, Koopman P (2000) Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227:239–255

Chinenov Y, Kerppola TK (2001) Close encounters of many kinds: Fos-Jun interactions that mediate transcription regulatory specificity. Oncogene 20:2438–2452

Cremazy F, Berta P, Girald F (2001) Genome-wide analysis of Sox genes in Drosophila melanogaster. Mech Dev 109:371–375

Dehal P, Satou Y, Campbell RK et al (2002) The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157–2167

Duan H, Skeath JB, Nguyen HT (2001) Drosophila Lame duck, a novel member of the Gli superfamily, acts as a key regulator of myogenesis by controlling fusion-competent myoblast development. Development 128:4489–4500

Fujiwara S, Corbo JC, Levine M (1998) The Snail repressor establishes a muscle/notochord boundary in the Ciona embryo. Development 125:2511–2520

Hai T, Hartman MG (2001) The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis. Gene 273:1-11

Imai K, Takada N, Satoh N, Satou Y (2000) β-Catenin mediates the specification of endoderm cells in ascidian embryos. Development 127:3009–3020

Imai KS, Satou Y, Satoh N (2002) Multiple functions of a Zic-like gene in the differentiation of notochord, central nervous system and muscle in Ciona savignyi embryos. Development 129:2723–2732

Kim YS, Lewandoski M, Perantoni A, Kurebayashi S, Nakanishi G, Jetten AM (2002) Identification of Glis1, a novel gene Gli-related, Kruppel-like zinc finger protein containing transactivation and repressor functions. J Biol Chem 227:30901–30913

Landschulz WH, Johnson PF, McKnight SL (1988) The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240:1759–1764

Laudet V, Stephelin D, Clevers H (1993) Ancestry and diversity of the HMG box superfamily. Nucleic Acids Res 21:2493–2501

Lowry JA, Atchley WR (2000) Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J Mol Evol 50:103–115

Matise MP, Joyner AL (1999) Gli genes in development and cancer. Oncogene 18:7852–7859

Mayor R, Aybar MJ (2001) Induction and development of neural crest in Xenopus laevis. Cell Tissue Res 305:203–209

Murphy FV 4th, Sweet RM, Churchill ME (1999) The structure of a chromosomal high mobility group protein – DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J 18:6610–6618

Nieto MA (2002) The snail superfamily of zinc-finger transcription factors. Nat Rev Mol Cell Biol 3:155–166

Oyake T, Itoh K, Motohashi H, Hayashi N, Hoshino H, Nishizawa M, Yamamoto M, Igarashi K (1996) Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site. Mol Cell Biol 16:6083–6095

Patient RK, McGhee JD (2002) The GATA family (vertebrates and invertebrates). Curr Opin Genet Dev 12:416–422

Pevny LH, Lovell-Badge R (1997) SOX genes find their feet. Curr Opin Genet Dev 7:338–344

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

Satou Y, Yamada L, Mochizuki Y, Takatori N, Kawashima T, Sasaki A, Hamaguchi M, Awazu S, Yagi K, Sasakura Y, Nakayama A, Ishikawa H, Inaba K, Satoh N (2002a) A cDNA resource from the basal chordate Ciona intestinalis. Genesis 33:153–154

Satou Y, Yagi K, Imai KS, Yamada L, Nishida H, Satoh N (2002b) macho-1-related genes in Ciona embryos. Dev Genes Evol 212:87–92

Satou Y, Imai KS, Levine M, Kohara Y, Rokhsar D, Satoh N (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Dev Genes Evol DOI 10.1007/s00427-003-0319-7

Schepers GE, Teasdale RD, Koopman P (2002) Twenty pairs of sox: extent, homology, and nomenclature of the mouse and human sox transcription factor gene families. Dev Cell 3:167–170

Soullier S, Jay P, Poulat F, Vanacker JM, Berta P, Laudet V (1999) Diversification pattern of the HMG and SOX family members during evolution. J Mol Evol 48:517–527

van de Wetering M, Clevers H (1992) Sequence-specific interaction of the HMG box proteins TCF-1 and SRY occurs within the minor groove of a Watson-Click double helix. EMBO J 11:3039–3044

van Noort M, Clevers H (2002) TCF transcription factors, mediators of Wnt-signaling in development and cancer. Dev Biol 244:1–8

Wada S, Saiga H (1999) Cloning and embryonic expression of Hrsna, a snail family gene of the ascidian Halocynthia roretzi: Implication in the origins of mechanisms for mesoderm specification and body axis formation in chordates. Dev Growth Differ 41:9–18

Wada S, Saiga H (2002) HrzicN, a new Zic family gene of ascidians, plays essential roles in the neural tube and notochord development. Development 129:5597–5608

Wegner M (1999) From head to toes: the multiple faces of Sox proteins. Nucleic Acids Res 27:1409–1420

Zhang F, Nakanishi G, Kurebayashi S, Yoshino K, Perantoni A, Kim YS, Jetten AM (2002) Characterization of Glis2, a novel gene encoding a Gli-related, Kruppel-like transcription factor with transactivation and repressor functions. Roles in kidney development and neurogenesis. J Biol Chem 227:10139–10149