Yan B , Neilson KM , Moody SA .

NS23158 NINDS NIH HHS , R01 NS023158 NINDS NIH HHS , R01 NS023158-20 NINDS NIH HHS , R01 NS023158-20S1 NINDS NIH HHS , R01 NS023158-20S2 NINDS NIH HHS , R01 NS023158-21 NINDS NIH HHS , R01 NS023158-22 NINDS NIH HHS

	Figure 2. Whole mount in situ hybridization assays of embryos injected with FoxD4L1/D5 mRNA. A: Examples of FoxD4L1/D5 causing an increase in downstream gene expression. In neural plate stage embryos, the expression domains of FoxB1 and XSpr2 are broader on the FoxD4L1/D5-injected side (right; indicated by βGal-expressing (red) cells). Lines indicate width of neural plate on injected (right) and control (left) sides of embryos. Dorsal views with anterior to the bottom. The FoxB1 expression domain also extends more anterior (bracket) compared to anterior limit on control side (arrow). At gastrula stages, the endogenous domains of Fgf8b and Oct-1 surround the yolk plug; the anterior extent of the domain is indicated by an arrow on the control side. The cells expressing FoxD4L1/D5 (red nuclei) in the neural plate (bracket) also express increased levels of Fgf8b and Oct-1. Dorsal views with anterior to the bottom. Inset in Oct-1 embryo: higher magnification showing FoxD4L1/D5-cells with red nuclei and blue cytoplasm. At gastrula stages, VegT/Brat and BJ051739 are ectopically induced in the animal cap ectoderm. Animal pole views. B: Examples of FoxD4L1/D5 causing a decrease in downstream gene expression. In neural plate stage embryos, MGC52564, MGC52940, Neptune, Dlx6, and Blimp1 are expressed in the border zone that separates the anterior neural plate (np) from the epidermis (epi). For each gene, this region shows decreased expression at the site of FoxD4L1/D5-expressing cells (red nuclei, arrows). MGC52564, MGC52940, Dlx6, Blimp1 are anterior views with dorsal to the top; control side is on the left. Neptune is a side view with anterior to top and dorsal to right. In a gastrula embryo, the normal high level of FoxI1 expression in the animal cap ectoderm (epi) is greatly reduced in the FoxD4L1/D5-expressing clone (*), which is outlined for clarity.
	Figure 3. RT-PCR assays illustrate the temporal expression patterns of uncharacterized up-regulated (A) and down-regulated (B) genes in normal, unmanipulated embryos. RT-, minus RT step; numbers across the top indicate the developmental stages (st). H4 is an internal control.
	Figure 4. Whole mount in situ hybridization assays illustrating the expression patterns of 7 uncharacterized genes that are up-regulated by FoxD4L1/D5. Gastrula stages are side views oriented with animal cap (An) to the top and vegetal pole (Veg) to the bottom. Transcripts for all 7 genes are detected in the animal cap ectoderm. At neural plate stages, embryos are oriented in an anterior frontal view, with dorsal to the top. Transcripts for all 7 genes are detected in the neural plate (np) and in the ectoderm bordering the neural plate (arrow) that will give rise to the cranial placodes and neural crest. At neural tube stages, MGC132176 is expressed throughout the neural tube (nt), with intense staining in a band in the midbrain-hindbrain (hb) region, in adjacent neural crest (nc), and the dorsal rim of the cement gland (cg). Left embryo is a dorsal view with anterior at the bottom and right embryo is a ventral view of the head. At larval stages (st328), MGC132176 is detected throughout the brain and retina (r), in the lens (L), otocyst (oto), cement gland, branchial arch (BA), and nephric mesoderm (ne). This and all larval stages are side views with anterior to the left. Transverse sections of st38 embryo confirm the labeled tissues identified in whole mount embryos, and identify the profundal ganglion (Pg). At neural tube stages, LOC496224 is expressed throughout the neural tube, retina, and somites (so). Side view with anterior to the left. At larval stages, LOC496224 is additionally expressed in the lens, otocyst, and branchial arches. BC097640 is expressed throughout the neural tube, with strong expression in the pineal primordium (pin), cement gland, several cranial placodes (dlp, dorso-lateral placode; olf, olfactory placode; Vp, trigeminal placode), and scattered cells on the ventral midline (bracket) caudal to the cement gland. Left embryo is an anterior frontal view with dorsal to the top; right embryo is a ventral view with anterior to the top. At larval stages, BC097640 is additionally expressed in the lens, otocyst, branchial arches, head mesoderm (hm), heart (ht), ventral blood islands (bl), somites, and nephric mesoderm. At neural tube stages, BJ051730 is weakly expressed throughout the neural tube, with strong expression in the midbrain-hindbrain region and adjacent neural crest. Dorsal anterior-view from the top. At larval stages, BJ051730 is additionally expressed in the lens, otocyst, branchial arches, somites, and nephric mesoderm. At neural tube stages, BJ043686 is expressed in the neural tube and the ectoderm bordering it (bz). Side view with anterior to the left. At larval stages, BJ043686 is additionally expressed at low levels in the lens, otocyst, somites, branchial arch, head, and nephric mesoderm. At neural tube stages, CB983184 is expressed in the neural tube and the ectoderm bordering it. At larval stages, CB983184 is additionally expressed in the olfactory pit, lens, retina, otocyst, somites, branchial arch mesoderm, and heart. At neural tube stages, MGC68716 is expressed in the neural tube, the ectoderm bordering it, and pineal primordium. At larval stages, MGC68716 is additionally expressed in the otocyst, somites, branchial arch mesoderm, and heart. fb, forebrain; mb, midbrain.
	Figure 5. Whole mount in situ hybridization assays illustrating the expression patterns of 5 genes that are down-regulated by FoxD4L1/D5. Abbreviations are the same as in Figure 4. A: Down-regulated, validated genes of unknown function. Gastrula stages are side views oriented with animal pole to the top and vegetal pole to the bottom. Transcripts for all 4 genes are detected in the animal cap ectoderm. At neural plate stages, embryos are oriented in an anterior frontal view, with dorsal to the top. MGC81002 is weakly detected in the neural plate, the ectoderm bordering it, and epidermis (epi). At neural tube stages, it is detected diffusely in the neural tube, retina and epidermis. Side view. At larval stages, MGC81002 is additionally detected in the otocyst and branchial arch mesoderm. Side view and transverse sections. At neural plate stages, LOC443682 is strongly expressed in the epidermis, the ectoderm bordering the neural plate, and the anterior neural ridge (anr). At neural tube stages, LOC443682 is detected throughout the epidermis, with enhanced expression bordering the retina, hatching gland (hg), and cement gland. Left embryo is a dorso-anterior view with anterior to the bottom; top right embryo is a dorsal view of the head with anterior to the left, and bottom right embryo is a ventral view of the head with anterior to the top. At larval stages, LOC443682 is detected throughout the epidermis, most strongly on the dorsal side, and in the nephric mesoderm. Side view and transverse sections. At neural plate stages, MGC53193 is detected in the epidermis, border of the neural plate, and anterior neural ridge. At neural tube stages, MGC53193 is strongly expressed in the head epidermis and tissue surrounding the cloaca (cl). Left embryo is a frontal view with dorsal to the top and right embryo is a ventral view with posterior to the left. At larval stages, MGC53193 is weakly detected in the epidermis of whole mount embryos (side view), but transverse sections reveal additional weak expression in brain (b), lens, otocyst, and anterior pharynx (ph). At neural plate stages, MGC52940 is strongly expressed in the ectoderm bordering the neural plate and cement gland, and weakly in the epidermis. At neural tube stages, MGC52940 expression is pronounced in a dorsal midline stripe in the epidermis, surrounding the retinas, in a patch over the forebrain (between the retinas), and in the cement gland. Anterior-frontal view with dorsal to the top. At larval stages, MGC52940 is highly expressed in the olfactory placode and in cells dotted throughout the epidermis; it is weakly expressed in the cement gland and anterior pharynx. Side view and transverse sections. B: Expression pattern of Xenopus Elf-1. Elf-1 is weakly expressed in the animal cap ectoderm at gastrulation, throughout the neural plate and border zone, and then is barely detectable in the anterior neural tube (*). At larval stages it is weakly detected in the brain, lens, and branchial arch mesoderm (side views and transverse sections).
	Supporting Figure S1: Expression pattern of BG161338 (eif5b) , which was up-regulated in the microarray assay, but not validated by RT-PCR or ISH assays. A: RT-PCR analysis of unmanipulated embryos shows that BG161338 is highly expressed at all developmental stages investigated. B: ISH analysis shows that at gastrula stages, BG161338 is expressed in the animal cap ectoderm (an) and the marginal zone (bracket) that will give rise to mesoderm; side view with animal to the top. Veg, vegetal pole. At neural plate stages, it is strongly expressed in the neural plate (np) and the ectoderm bordering the neural plate (arrow); anterior view with dorsal to the top. At neural tube stages, it is strongly expressed throughout the neural tube (nt), in the migrating neural crest (nc), and in the lens (L); anterior view with dorsal to the top. At larval stages, it is additionally expressed in the otocyst (oto), branchial arch mesoderm (BA), somites (so), nephric mesoderm (ne), and ventral blood islands (bl); side view with anterior to the left.
	eif5b (eukaryotic translation initiation factor 5B) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 10, lateral view, dorsal up.
	eif5b (eukaryotic translation initiation factor 5B) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 14, anterior view, dorsal up.
	eif5b (eukaryotic translation initiation factor 5B) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 20, anterior view, dorsal up.
	eif5b (eukaryotic translation initiation factor 5B) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 32, lateral view, anterior left.

Bertwistle, GATA factors and the origins of adult and embryonic blood in Xenopus: responses to retinoic acid. 1996, Pubmed, Xenbase

Bertwistle, GATA factors and the origins of adult and embryonic blood in Xenopus: responses to retinoic acid. 1996, Pubmed , Xenbase
Blak, Expression of Fgf receptors 1, 2, and 3 in the developing mid- and hindbrain of the mouse. 2005, Pubmed
Bodoy, Identification of LAT4, a novel amino acid transporter with system L activity. 2005, Pubmed , Xenbase
Bromley, Identification and characterisation of the posteriorly-expressed Xenopus neurotrophin receptor homolog genes fullback and fullback-like. 2004, Pubmed , Xenbase
Christian, Xwnt-8, a Xenopus Wnt-1/int-1-related gene responsive to mesoderm-inducing growth factors, may play a role in ventral mesodermal patterning during embryogenesis. 1991, Pubmed , Xenbase
Chung, FGF signal regulates gastrulation cell movements and morphology through its target NRH. 2005, Pubmed , Xenbase
Dalgin, GATA-2 functions downstream of BMPs and CaM KIV in ectodermal cells during primitive hematopoiesis. 2007, Pubmed , Xenbase
Delaune, Neural induction in Xenopus requires early FGF signalling in addition to BMP inhibition. 2005, Pubmed , Xenbase
de Souza, The zinc finger gene Xblimp1 controls anterior endomesodermal cell fate in Spemann's organizer. 1999, Pubmed , Xenbase
Fainsod, On the function of BMP-4 in patterning the marginal zone of the Xenopus embryo. 1994, Pubmed , Xenbase
Ferreiro, XASH1, a Xenopus homolog of achaete-scute: a proneural gene in anterior regions of the vertebrate CNS. 1993, Pubmed , Xenbase
Fetka, Neuroectodermal specification and regionalization of the Spemann organizer in Xenopus. 2000, Pubmed , Xenbase
Fletcher, FGF8 spliceforms mediate early mesoderm and posterior neural tissue formation in Xenopus. 2006, Pubmed , Xenbase
Frazzetto, Xenopus marginal coil (Xmc), a novel FGF inducible cytosolic coiled-coil protein regulating gastrulation movements. 2002, Pubmed , Xenbase
Friesel, Spatially restricted expression of fibroblast growth factor receptor-2 during Xenopus development. 1992, Pubmed , Xenbase
Fuentealba, Integrating patterning signals: Wnt/GSK3 regulates the duration of the BMP/Smad1 signal. 2007, Pubmed , Xenbase
Gamse, Early anteroposterior division of the presumptive neurectoderm in Xenopus. 2001, Pubmed , Xenbase
Golub, Evolutionarily conserved and divergent expression of members of the FGF receptor family among vertebrate embryos, as revealed by FGFR expression patterns in Xenopus. 2000, Pubmed , Xenbase
Grow, Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration. 2006, Pubmed , Xenbase
Hawley, Disruption of BMP signals in embryonic Xenopus ectoderm leads to direct neural induction. 1995, Pubmed , Xenbase
Heeg-Truesdell, Neural induction in Xenopus requires inhibition of Wnt-beta-catenin signaling. 2006, Pubmed , Xenbase
Hesterberg, Demonstration of three distinct calcium-binding sites in villin, a modulator of actin assembly. 1983, Pubmed
Horb, A vegetally localized T-box transcription factor in Xenopus eggs specifies mesoderm and endoderm and is essential for embryonic mesoderm formation. 1997, Pubmed , Xenbase
Hufton, Genomic analysis of Xenopus organizer function. 2006, Pubmed , Xenbase
Kuroda, Default neural induction: neuralization of dissociated Xenopus cells is mediated by Ras/MAPK activation. 2005, Pubmed , Xenbase
Lee, Evidence that FGF8 signalling from the midbrain-hindbrain junction regulates growth and polarity in the developing midbrain. 1997, Pubmed
Luo, Induction of neural crest in Xenopus by transcription factor AP2alpha. 2003, Pubmed , Xenbase
Luo, Differential regulation of Dlx gene expression by a BMP morphogenetic gradient. 2001, Pubmed , Xenbase
Marchal, BMP inhibition initiates neural induction via FGF signaling and Zic genes. 2009, Pubmed , Xenbase
Matsuo-Takasaki, An essential role of Xenopus Foxi1a for ventral specification of the cephalic ectoderm during gastrulation. 2005, Pubmed , Xenbase
Molenaar, Differential expression of the HMG box transcription factors XTcf-3 and XLef-1 during early xenopus development. 1998, Pubmed , Xenbase
Moody, Cell lineage analysis in Xenopus embryos. 2000, Pubmed , Xenbase
Moody, Fates of the blastomeres of the 16-cell stage Xenopus embryo. 1987, Pubmed , Xenbase
Nishimatsu, Ventral mesoderm induction and patterning by bone morphogenetic protein heterodimers in Xenopus embryos. 1998, Pubmed , Xenbase
Nutt, Xenopus Sprouty2 inhibits FGF-mediated gastrulation movements but does not affect mesoderm induction and patterning. 2001, Pubmed , Xenbase
Ossipova, XSPR-1 and XSPR-2, novel Sp1 related zinc finger containing genes, are dynamically expressed during Xenopus embryogenesis. 2002, Pubmed , Xenbase
Panitz, The Spemann organizer-expressed zinc finger gene Xegr-1 responds to the MAP kinase/Ets-SRF signal transduction pathway. 1998, Pubmed , Xenbase
Papalopulu, Xenopus Distal-less related homeobox genes are expressed in the developing forebrain and are induced by planar signals. 1993, Pubmed , Xenbase
Pearl, Identification of genes associated with regenerative success of Xenopus laevis hindlimbs. 2008, Pubmed , Xenbase
Rogers, Neural induction and factors that stabilize a neural fate. 2009, Pubmed , Xenbase
Rossi, Rohon-Beard sensory neurons are induced by BMP4 expressing non-neural ectoderm in Xenopus laevis. 2008, Pubmed , Xenbase
Rozen, Primer3 on the WWW for general users and for biologist programmers. 2000, Pubmed
Sabatini, RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs. 1994, Pubmed
Salic, Sizzled: a secreted Xwnt8 antagonist expressed in the ventral marginal zone of Xenopus embryos. 1997, Pubmed , Xenbase
Sasai, The neurotrophin-receptor-related protein NRH1 is essential for convergent extension movements. 2004, Pubmed , Xenbase
Sato, Localized and inducible expression of Xenopus-posterior (Xpo), a novel gene active in early frog embryos, encoding a protein with a 'CCHC' finger domain. 1991, Pubmed , Xenbase
Sinner, Global analysis of the transcriptional network controlling Xenopus endoderm formation. 2006, Pubmed , Xenbase
Sirotkin, Identification, characterization, and precise mapping of a human gene encoding a novel membrane-spanning protein from the 22q11 region deleted in velo-cardio-facial syndrome. 1997, Pubmed
Sive, Progressive determination during formation of the anteroposterior axis in Xenopus laevis. 1989, Pubmed , Xenbase
Sölter, Characterization of a subfamily of related winged helix genes, XFD-12/12'/12" (XFLIP), during Xenopus embryogenesis. 1999, Pubmed , Xenbase
Stern, Neural induction: old problem, new findings, yet more questions. 2005, Pubmed , Xenbase
Sullivan, foxD5a, a Xenopus winged helix gene, maintains an immature neural ectoderm via transcriptional repression that is dependent on the C-terminal domain. 2001, Pubmed , Xenbase
Sun, derrière: a TGF-beta family member required for posterior development in Xenopus. 1999, Pubmed , Xenbase
Takeda, Neptune is involved in posterior axis and tail formation in Xenopus embryogenesis. 2005, Pubmed , Xenbase
Takeuchi, The prickle-related gene in vertebrates is essential for gastrulation cell movements. 2003, Pubmed , Xenbase
Toyama, The LIM class homeobox gene lim5: implied role in CNS patterning in Xenopus and zebrafish. 1995, Pubmed , Xenbase
Umbhauer, Signaling specificities of fibroblast growth factor receptors in early Xenopus embryo. 2000, Pubmed , Xenbase
Umemori, Weaving the neuronal net with target-derived fibroblast growth factors. 2009, Pubmed
Veenstra, Dynamic and differential Oct-1 expression during early Xenopus embryogenesis: persistence of Oct-1 protein following down-regulation of the RNA. 1995, Pubmed , Xenbase
Wallingford, Cloning and expression of Xenopus Prickle, an orthologue of a Drosophila planar cell polarity gene. 2002, Pubmed , Xenbase
Wanner, Molecular cloning and expression of Ena/Vasp-like (Evl) during Xenopus development. 2005, Pubmed , Xenbase
White, Direct and indirect regulation of derrière, a Xenopus mesoderm-inducing factor, by VegT. 2002, Pubmed , Xenbase
Winning, Developmental regulation of transcription factor AP-2 during Xenopus laevis embryogenesis. 1991, Pubmed , Xenbase
Yan, foxD5 plays a critical upstream role in regulating neural ectodermal fate and the onset of neural differentiation. 2009, Pubmed , Xenbase
Zhang, The role of maternal VegT in establishing the primary germ layers in Xenopus embryos. 1998, Pubmed , Xenbase
Zhang, Xenopus VegT RNA is localized to the vegetal cortex during oogenesis and encodes a novel T-box transcription factor involved in mesodermal patterning. 1996, Pubmed , Xenbase
Zhao, An SP1-like transcription factor Spr2 acts downstream of Fgf signaling to mediate mesoderm induction. 2003, Pubmed , Xenbase
Zhao, Lrig3 regulates neural crest formation in Xenopus by modulating Fgf and Wnt signaling pathways. 2008, Pubmed , Xenbase
Zon, Expression of GATA-binding proteins during embryonic development in Xenopus laevis. 1991, Pubmed , Xenbase