194
Xenopus
Kimelman D., and K.J. Griffn. 1998. Mesoderm induction: A postmodern view. Cell 94:419–421.
Kofron, M., T. Demel, J. Xanthos, J. Lohr, B. Sun, H. Sive,
S. Osada, C. Wright, C. Wylie, and J. Heasman. 1999.
Mesoderm induction in Xenopus is a zygotic event regulated
by maternal VegT via TGFbeta growth factors. Development
126:5759–5770.
Kofron, M., J. Xanthos, and J. Heasman. 2004. Maternal VegT and
ß-catenin: Patterning the Xenopus blastula. In Grunz, Horst
(Ed.), The Vertebrate Organizer. Springer, Berlin, New York.
Kohonen, T. 2001. Self-Organizing Maps. Springer, Berlin,
Heidelberg.
Koide, T., T. Hayata, and K.W. Cho. 2005. Xenopus as a model system to study transcriptional regulatory networks. Proc Natl
Acad Sci USA 102:4943–4948.
Kushawah G., L. Hernandez-Huertas, D.P.J. Abugattas-Nuñez,
J.R. Martinez-Morales, M.L. DeVore, H. Hassan, I. MorenoSanchez et al. 2020. CRISPR-Cas13d induces eff cient
mRNA knockdown in animal embryos. Dev Cell 54:805–817.
Latinkić, B.V., M. Umbhauer, K.A. Neal, W. Lerchner, J.C. Smith,
and V. Cunliffe. 1997. The Xenopus brachyury promoter is
activated by FGF and low concentrations of activin and suppressed by high concentrations of activin and by paired-type
homeodomain proteins. Genes Dev 11:3265–3276.
Laurent, M.N., I.L. Blitz, C. Hashimoto, U. Rothbächer, and K.W.Y.
Cho. 1997. The Xenopus homeobox gene twin mediates Wnt
induction of goosecoid in establishment of Spemann’s organizer. Development 124:4905–4916.
Lee, H.K., H.S. Lee, and S.A. Moody. 2014. Neural transcription factors: From embryos to neural stem cells. Mol Cells
37:705–712.
Loose, M., and R.A. Patient. 2004. A genetic regulatory network for
Xenopus mesendoderm formation. Dev Biol 271:467–478.
Maharana, S.K., and G. Schlosser. 2018. A gene regulatory network underlying the formation of pre-placodal ectoderm in
Xenopus laevis. BMC Biol 16:79.
Mangan, S., A. Zaslaver, and U. Alon. 2003. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334:197–204.
Maurano, M.T., R. Humbert, E. Rynes, R.E. Thurman, E. Haugen,
H. Wang, A.P. Reynolds, R. Sandstrom, H. Qu, J. Brody, A.
Shafer, F. Neri, K. Lee, T. Kutyavin, S. Stehling-Sun, A.K.
Johnson, T.K. Canfeld, E. Giste, M. Diegel, D. Bates, R.S.
Hansen, S. Neph, P.J. Sabo, S. Heimfeld, A. Raubitschek, S.
Ziegler, C. Cotsapas, N. Sotoodehnia, I. Glass, S.R. Sunyaev,
R. Kaul, J.A. Stamatoyannopoulos. 2012. Systematic localization of common disease-associated variation in regulatory
DNA. Science 337:1190–1195.
Mir, A., M. Kofron, A.M. Zorn, M. Bajzer, M Haque, J. Heasman,
and C.C. Wylie. 2007. Foxi1e activates ectoderm formation and controls cell position in the Xenopus blastula.
Development 134:779–788.
Mochizuki, T., A.A. Karavanov, P.E. Curtiss, K.T. Ault, N.
Sugimoto, T. Watabe, K. Shiokawa, M. Jamrich, K.W. Cho,
I.B. Dawid, and M. Taira. 2000. Xlim-1 and LIM domain
binding protein 1 cooperate with various transcription factors in the regulation of the goosecoid promoter. Dev Biol
224:470–485.
Mukherjee, S., P. Chaturvedi, S.A. Rankin, M.B. Fish, M. Wlizla,
K.D. Paraiso, M. MacDonald, X. Chen, M.T. Weirauch, I.L.
Blitz, K.W. Cho, and A.M. Zorn. 2020. Sox17 and β-catenin
co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. Elife 9:e58029.
Musunuru, K., et al. 2010. From noncoding variant to phenotype via
SORT1 at the 1p13 cholesterol locus. Nature 466:714–719.
Nakayama, T., M.B. Fish, M. Fisher, J. Oomen-Hajagos, G.H.
Thomsen, R.M. Grainger. 2013. Simple and eff cient CRISPR/
Cas9-mediated targeted mutagenesis in Xenopus tropicalis.
Genesis 51:835–843.
Nam, J., and E.H. Davidson. 2012. Barcoded DNA-tag reporters
for multiplex cis-regulatory analysis. PLoS One 7:e35934.
Nishita, M., M.K. Hashimoto, S. Ogata, M.N. Laurent, N. Ueno,
H. Shibuya, and K.W.Y. Cho. 2000. Interaction between
Wnt and TGF-beta signalling pathways during formation of
Spemann’s organizer. Nature 403:781–785.
Owens, N.D.L., I.L. Blitz, M.A. Lane, I. Patrushev, J.D. Overton,
M.J. Gilchrist, K.W.Y. Cho, and M.K. Khokha. 2016.
Measuring absolute RNA copy numbers at high temporal
resolution reveals transcriptome kinetics in development.
Cell Reports 14:632–647.
Paraiso, K.D., I.L. Blitz, M. Coley, J. Cheung, N. Sudou, M. Taira,
and K.W.Y. Cho. 2019. Endodermal maternal transcription
factors establish super-enhancers during zygotic genome
activation. Cell Rep 27:2962–2977.
Paraiso, K.D., J.S. Cho, J. Yong, and K.W.Y. Cho. 2020. Early
Xenopus gene regulatory programs, chromatin states, and
the role of maternal transcription factors. Curr Top Dev Biol
139:35–60.
Peter, I.S., and E.H. Davidson. 2010. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
Dev Biol 340:188–199.
Peter, I.S., and E.H. Davidson. 2015. Genomic Control Process:
Development and Evolution. Academic Press, Amsterdam.
Pomerantz, M.M., N. Ahmadiyeh, L. Jia, P. Herman, M.P. Verzi, H.
Doddapaneni, C.A. Beckwith, J.A. Chan, A. Hills, M. Davis,
K. Yao, S.M. Kehoe, H.J. Lenz, C.A. Haiman, C. Yan, B.E.
Henderson, B. Frenkel, J. Barretina, A. Bass, J. Tabernero,
J. Baselga, M.M. Regan, J.R. Manak, R. Shivdasani, G.A.
Coetzee, M.L. Freedman, 2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in
colorectal cancer. Nat Genet 41:882–884.
Rex, M., E. Hilton, and R. Old. 2002. Multiple interactions between
maternally-activated signalling pathways control Xenopus
nodal-related genes. Int J Dev Biol 46:217–226.
Ruprecht C, S. Proost, M. Hernandez-Coronado, C. Ortiz-Ramirez,
D. Lang, S.A. Rensing, J.D. Becker, K. Vandepoele, and M.
Mutwil. 2017. Phylogenomic analysis of gene co-expression
networks reveals the evolution of functional modules. Plant
J 90:447–465.
Schroeder, M.D., M. Pearce, J. Fak, H. Fan, U. Unnerstall, E.
Emberly, N. Rajewsky, E.D. Siggia, and U. Gaul. 2004.
Transcriptional control in the segmentation gene network of
Drosophila. PLoS Biology 2:e271.
Schuler-Metz, A., S. Knöchel, E. Kaufmann, and W. Knöchel. 2000.
The homeodomain transcription factor Xvent-2 mediates
autocatalytic regulation of BMP-4 expression in Xenopus
embryos. J. Biol Chem 275:34365–34374.
Schulte-Merker, S., and J.C. Smith. 1995. Mesoderm formation
in response to brachyury requires FGF signalling. Curr Biol
5:62–67.
Seal, S., and A.H. Monsoro-Burq. 2020. Insights into the early gene
regulatory network controlling neural crest and placode fate
choices at the neural border. Front Physiol 11:608812.
Smith, J.C., B.M. Price, J.B. Green, D. Weigel, and B.G. Herrmann.
1991. Expression of a Xenopus homolog of brachyury (T) is
an immediate-early response to mesoderm induction. Cell
67:79–87.
Spemann, H. and H. Mangold. 1924. Uber Induktion von
Embryonalanlagen durch Implantation artfremder
Organisatoren. Wilhelm’s Roux’s Arch. Dev. Biol 100:599–638.
Xenopus
Kimelman D., and K.J. Griffn. 1998. Mesoderm induction: A postmodern view. Cell 94:419–421.
Kofron, M., T. Demel, J. Xanthos, J. Lohr, B. Sun, H. Sive,
S. Osada, C. Wright, C. Wylie, and J. Heasman. 1999.
Mesoderm induction in Xenopus is a zygotic event regulated
by maternal VegT via TGFbeta growth factors. Development
126:5759–5770.
Kofron, M., J. Xanthos, and J. Heasman. 2004. Maternal VegT and
ß-catenin: Patterning the Xenopus blastula. In Grunz, Horst
(Ed.), The Vertebrate Organizer. Springer, Berlin, New York.
Kohonen, T. 2001. Self-Organizing Maps. Springer, Berlin,
Heidelberg.
Koide, T., T. Hayata, and K.W. Cho. 2005. Xenopus as a model system to study transcriptional regulatory networks. Proc Natl
Acad Sci USA 102:4943–4948.
Kushawah G., L. Hernandez-Huertas, D.P.J. Abugattas-Nuñez,
J.R. Martinez-Morales, M.L. DeVore, H. Hassan, I. MorenoSanchez et al. 2020. CRISPR-Cas13d induces eff cient
mRNA knockdown in animal embryos. Dev Cell 54:805–817.
Latinkić, B.V., M. Umbhauer, K.A. Neal, W. Lerchner, J.C. Smith,
and V. Cunliffe. 1997. The Xenopus brachyury promoter is
activated by FGF and low concentrations of activin and suppressed by high concentrations of activin and by paired-type
homeodomain proteins. Genes Dev 11:3265–3276.
Laurent, M.N., I.L. Blitz, C. Hashimoto, U. Rothbächer, and K.W.Y.
Cho. 1997. The Xenopus homeobox gene twin mediates Wnt
induction of goosecoid in establishment of Spemann’s organizer. Development 124:4905–4916.
Lee, H.K., H.S. Lee, and S.A. Moody. 2014. Neural transcription factors: From embryos to neural stem cells. Mol Cells
37:705–712.
Loose, M., and R.A. Patient. 2004. A genetic regulatory network for
Xenopus mesendoderm formation. Dev Biol 271:467–478.
Maharana, S.K., and G. Schlosser. 2018. A gene regulatory network underlying the formation of pre-placodal ectoderm in
Xenopus laevis. BMC Biol 16:79.
Mangan, S., A. Zaslaver, and U. Alon. 2003. The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334:197–204.
Maurano, M.T., R. Humbert, E. Rynes, R.E. Thurman, E. Haugen,
H. Wang, A.P. Reynolds, R. Sandstrom, H. Qu, J. Brody, A.
Shafer, F. Neri, K. Lee, T. Kutyavin, S. Stehling-Sun, A.K.
Johnson, T.K. Canfeld, E. Giste, M. Diegel, D. Bates, R.S.
Hansen, S. Neph, P.J. Sabo, S. Heimfeld, A. Raubitschek, S.
Ziegler, C. Cotsapas, N. Sotoodehnia, I. Glass, S.R. Sunyaev,
R. Kaul, J.A. Stamatoyannopoulos. 2012. Systematic localization of common disease-associated variation in regulatory
DNA. Science 337:1190–1195.
Mir, A., M. Kofron, A.M. Zorn, M. Bajzer, M Haque, J. Heasman,
and C.C. Wylie. 2007. Foxi1e activates ectoderm formation and controls cell position in the Xenopus blastula.
Development 134:779–788.
Mochizuki, T., A.A. Karavanov, P.E. Curtiss, K.T. Ault, N.
Sugimoto, T. Watabe, K. Shiokawa, M. Jamrich, K.W. Cho,
I.B. Dawid, and M. Taira. 2000. Xlim-1 and LIM domain
binding protein 1 cooperate with various transcription factors in the regulation of the goosecoid promoter. Dev Biol
224:470–485.
Mukherjee, S., P. Chaturvedi, S.A. Rankin, M.B. Fish, M. Wlizla,
K.D. Paraiso, M. MacDonald, X. Chen, M.T. Weirauch, I.L.
Blitz, K.W. Cho, and A.M. Zorn. 2020. Sox17 and β-catenin
co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. Elife 9:e58029.
Musunuru, K., et al. 2010. From noncoding variant to phenotype via
SORT1 at the 1p13 cholesterol locus. Nature 466:714–719.
Nakayama, T., M.B. Fish, M. Fisher, J. Oomen-Hajagos, G.H.
Thomsen, R.M. Grainger. 2013. Simple and eff cient CRISPR/
Cas9-mediated targeted mutagenesis in Xenopus tropicalis.
Genesis 51:835–843.
Nam, J., and E.H. Davidson. 2012. Barcoded DNA-tag reporters
for multiplex cis-regulatory analysis. PLoS One 7:e35934.
Nishita, M., M.K. Hashimoto, S. Ogata, M.N. Laurent, N. Ueno,
H. Shibuya, and K.W.Y. Cho. 2000. Interaction between
Wnt and TGF-beta signalling pathways during formation of
Spemann’s organizer. Nature 403:781–785.
Owens, N.D.L., I.L. Blitz, M.A. Lane, I. Patrushev, J.D. Overton,
M.J. Gilchrist, K.W.Y. Cho, and M.K. Khokha. 2016.
Measuring absolute RNA copy numbers at high temporal
resolution reveals transcriptome kinetics in development.
Cell Reports 14:632–647.
Paraiso, K.D., I.L. Blitz, M. Coley, J. Cheung, N. Sudou, M. Taira,
and K.W.Y. Cho. 2019. Endodermal maternal transcription
factors establish super-enhancers during zygotic genome
activation. Cell Rep 27:2962–2977.
Paraiso, K.D., J.S. Cho, J. Yong, and K.W.Y. Cho. 2020. Early
Xenopus gene regulatory programs, chromatin states, and
the role of maternal transcription factors. Curr Top Dev Biol
139:35–60.
Peter, I.S., and E.H. Davidson. 2010. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
Dev Biol 340:188–199.
Peter, I.S., and E.H. Davidson. 2015. Genomic Control Process:
Development and Evolution. Academic Press, Amsterdam.
Pomerantz, M.M., N. Ahmadiyeh, L. Jia, P. Herman, M.P. Verzi, H.
Doddapaneni, C.A. Beckwith, J.A. Chan, A. Hills, M. Davis,
K. Yao, S.M. Kehoe, H.J. Lenz, C.A. Haiman, C. Yan, B.E.
Henderson, B. Frenkel, J. Barretina, A. Bass, J. Tabernero,
J. Baselga, M.M. Regan, J.R. Manak, R. Shivdasani, G.A.
Coetzee, M.L. Freedman, 2009. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in
colorectal cancer. Nat Genet 41:882–884.
Rex, M., E. Hilton, and R. Old. 2002. Multiple interactions between
maternally-activated signalling pathways control Xenopus
nodal-related genes. Int J Dev Biol 46:217–226.
Ruprecht C, S. Proost, M. Hernandez-Coronado, C. Ortiz-Ramirez,
D. Lang, S.A. Rensing, J.D. Becker, K. Vandepoele, and M.
Mutwil. 2017. Phylogenomic analysis of gene co-expression
networks reveals the evolution of functional modules. Plant
J 90:447–465.
Schroeder, M.D., M. Pearce, J. Fak, H. Fan, U. Unnerstall, E.
Emberly, N. Rajewsky, E.D. Siggia, and U. Gaul. 2004.
Transcriptional control in the segmentation gene network of
Drosophila. PLoS Biology 2:e271.
Schuler-Metz, A., S. Knöchel, E. Kaufmann, and W. Knöchel. 2000.
The homeodomain transcription factor Xvent-2 mediates
autocatalytic regulation of BMP-4 expression in Xenopus
embryos. J. Biol Chem 275:34365–34374.
Schulte-Merker, S., and J.C. Smith. 1995. Mesoderm formation
in response to brachyury requires FGF signalling. Curr Biol
5:62–67.
Seal, S., and A.H. Monsoro-Burq. 2020. Insights into the early gene
regulatory network controlling neural crest and placode fate
choices at the neural border. Front Physiol 11:608812.
Smith, J.C., B.M. Price, J.B. Green, D. Weigel, and B.G. Herrmann.
1991. Expression of a Xenopus homolog of brachyury (T) is
an immediate-early response to mesoderm induction. Cell
67:79–87.
Spemann, H. and H. Mangold. 1924. Uber Induktion von
Embryonalanlagen durch Implantation artfremder
Organisatoren. Wilhelm’s Roux’s Arch. Dev. Biol 100:599–638.