Angerer, L. M., & Angerer, R. C. (2004). Disruption of gene function using antisense
morpholinos. Methods in Cell Biology, 74, 699–711.
Becker, W. M., Kleinsmith, L. J., Hardin, J. & Bertoni, G. P. (2003) The world of the cell.
San Francisco: Benjamin/Cummings Publishing Company.
Barsi, J. C., Tu, Q., Calestani, C., & Davidson, E. H. (2015). Genome‐wide assessment
of differential effector gene use in embryogenesis. Development, 142, 3892–3901.
Beeble, A., & Calestani, C. (2012). Expression pattern of polyketide synthase‐2 during
sea urchin development. Gene Expression Patterns, 12, 7–10.
Britten, R. J., Cetta, A., & Davidson, E. H. (1978). The single‐copy DNA sequence
polymorphism of the sea urchin Strongylocentrotus purpuratus. Cell, 15, 1175–1186.
Calestani, C., Rast, J. P., & Davidson, E. H. (2003). Isolation of pigment cell specific
genes in the sea urchin embryo by differential macroarray screening. Development, 130,
4587–4596.
Cameron, R. A., Fraser, S. E., Britten, R. J., & Davidson, E. H. (1991). Macromere cell
fates during sea urchin development. Development, 113, 1085–1091.
Cameron, R. A., Hough‐Evans, B. R., Britten, R. J., & Davidson, E. H. (1987). Lineage
and fate of each blastomere of the eight‐cell sea urchin embryo. Genes and Development,
1, 75–85.
Castoe, T. A., Stephens, T., Noonan, B. P., & Calestani, C. (2007). A novel group of type
I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene,
37
392, 47–58.
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013).
Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819–823.
Croce, J. C., & McClay, D. R. (2010). Dynamics of Delta/Notch signaling on
endomesoderm segregation in the sea urchin embryo. Development, 137, 83-91.
Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., … Bolouri,
H. (2002). A provisional regulatory gene network for specification of endomesoderm in
the sea urchin embryo. Developmental Biology, 246, 162–190.
Doudna, J. A., & Charpentier, E. (2014). Genome editing. The new frontier of genome
engineering with CRISPR‐Cas9. Science, 346, 1258096.
Duboc, V., Röttinger, E., Besnardeau, L., & Lepage, T. (2004). Nodal and BMP2/4
signaling organizes the oral-aboral axis of the sea urchin embryo. Developmental cell, 6,
397-410.
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D.
(2013). High‐frequency off‐target mutagenesis induced by CRISPR‐Cas nucleases in
human cells. Nature Biotechnology, 31, 822–826.
Fujiwara, A., & Yasumasu, I. (1997). Does the respiratory rate in sea urchin embryos
increase during early development without proliferation of mitochondria? Development,
growth & differentiation, 39, 179-189.
Gaj, T., Gersbach, C. A. & Barbas, C. F. (2013) ZFN, TALEN, and CRISPR/Cas-based
methods for genome engineering. Trends in biotechnology, 31, 397-405.
38
Griffiths, M. (1965). A study of the synthesis of naphthaquinone pigments by the larvae
of two species of sea urchins and their reciprocal hybrids. Developmental Biology, 11,
433–447.
Hojo, M., Omi, A., Hamanaka, G., Shindo, K., Shimada, A., Kondo, M., … Takeda, H.
(2015). Unexpected link between polyketide synthase and calcium carbonate
biomineralization. Zoological Letters, 1, 3.
Hopwood, D. A. (1997). Genetic contributions to understanding polyketide synthases.
Chemical Reviews, 97, 2465–2498.
Hopwood, D. A., & Sherman, D. H. (1990). Molecular genetics of polyketides and its
comparison to fatty acid biosynthesis. Annual Review of Genetics, 24, 37–62.
Horvath, P. & Barrangou, R. (2010) CRISPR/Cas, the immune system of bacteria and
archaea. Science, 327, 167-170.
Hosoi, S., Sakuma, T., Sakamoto, N., & Yamamoto, T. (2014). Targeted mutagenesis in
sea urchin embryos using TALENs. Development, Growth and Differentiation, 56, 92–
97.
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., …
Zhang, F. (2013). DNA targeting specificity of RNA‐guided Cas9 nucleases. Nature
Biotechnology, 31, 827–832.
Jiang, W., Bikard, D., Cox, D., Zhang, F., & Marraffini, L. A. (2013). RNA‐guided
editing of bacterial genomes using CRISPR‐Cas systems. Nature Biotechnology, 31,
233–239.
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012).
39
A programmable dual‐RNA‐guided DNA endonuclease in adaptive bacterial immunity.
Science, 337, 816–821.
Kim, S., Kim, D., Cho, S. W., Kim, J., & Kim, J. S. (2014). Highly efficient RNA‐guided
genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome
Research, 24, 1012–1019.
Kinjo, S., Kiyomoto, M., Yamamoto, T., Ikeo, K., & Yaguchi, S. (2018). HpBase: A
genome database of a sea urchin, Hemicentrotus pulcherrimus. Development, Growth
and Differentiation, 60, 174–182.
Kotani, H., Taimatsu, K., Ohga, R., Ota, S., & Kawahara, A. (2015). Efficient multiple
genome modifications induced by the crRNAs, tracrRNA and Cas9 protein complex in
zebrafish. PLoS One, 10, e0128319.
Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013).
CRISPR interference (CRISPRi) for sequence‐specific control of gene expression.
Nature Protocols, 8, 2180.
Lee, J. S., Kwak, S. J., Kim, J., Kim, A. K., Noh, H. M., Kim, J. S., & Yu, K. (2014).
RNA‐guided genome editing in Drosophila with the purified Cas9 protein. G3: Genes,
Genomes, Genetics, 4, 1291–1295.
Lee, P. Y., & Davidson, E. H. (2004). Expression of Spgatae, the Strongylocentrotus
purpuratus ortholog of vertebrate GATA4/5/6 factors. Gene Expression Patterns, 5, 161165.
Lee, P. Y., Nam, J., & Davidson, E. H. (2007). Exclusive developmental functions of
gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo.
Developmental biology, 307, 434-445.
40
Lin, C. Y., & Su, Y. H. (2016). Genome editing in sea urchin embryos by using a
CRISPR/Cas9 system. Developmental Biology, 409, 420–428.
Materna, S. C., Nam, J., & Davidson, E. H. (2010). High accuracy, high-resolution
prevalence measurement for the majority of locally expressed regulatory genes in early
sea urchin development. Gene Expression Patterns, 10, 177-184.
Materna, S. C., Ransick, A., Li, E., & Davidson, E. H. (2013). Diversification of oral and
aboral mesodermal regulatory states in pregastrular sea urchin embryos. Developmental
biology, 375, 92-104.
Mellott, D. O., Thisdelle, J., & Burke, R. D. (2017). Notch signaling patterns neurogenic
ectoderm and regulates the asymmetric division of neural progenitors in sea urchin
embryos. Development, 144, 3602–3611.
Minokawa, T., Rast, J. P., Arenas-Mena, C., Franco, C. B., & Davidson, E. H. (2004).
Expression patterns of four different regulatory genes that function during sea urchin
development. Gene Expression Patterns, 4, 449-456.
Naito, Y., Hino, K., Bono, H., & Ui-Tei, K. (2014). CRISPRdirect: software for
designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics, 31,
1120-1123.
Nakayama, T., Blitz, I. L., Fish, M. B., Odeleye, A. O., Manohar, S., Cho, K. W., &
Grainger, R. M. (2014). Cas9‐based genome editing in Xenopus tropicalis. In J. A.
Doudna & E. J. Sontheimer (Eds.), Methods in enzymology (Vol. 546, pp. 355–375).
Cambridge, MA: Academic Press.
Ochiai, H., Fujita, K., Suzuki, K. I., Nishikawa, M., Shibata, T., Sakamoto, N., &
Yamamoto, T. (2010). Targeted mutagenesis in the sea urchin embryo using zinc‐finger
41
nucleases. Genes to Cells, 15, 875–885.
Okabayashi, K., & Nakano, E. (1983). The cytochrome system of sea urchin eggs and
embryos. Archives of biochemistry and biophysics, 225, 271-278.
Oliveri, P., & Davidson, E. H. (2004). Gene regulatory network controlling embryonic
specification in the sea urchin. Current Opinion in Genetics and Development, 14, 351–
360.
Oliveri, P., Tu, Q., & Davidson, E. H. (2008). Global regulatory logic for specification
of an embryonic cell lineage. Proceedings of the National Academy of Sciences of the
United States of America, 105, 5955–5962.
Oulhen, N., Swartz, S. Z., Laird, J., Mascaro, A., & Wessel, G. M. (2017). Transient
translational quiescence in primordial germ cells. Development, 144, 1201–1210.
Oulhen, N., & Wessel, G. M. (2016). Albinism as a visual, in vivo guide for
CRISPR/Cas9 functionality in the sea urchin embryo. Molecular Reproduction and
Development, 83, 1046–1047.
Peterson, R. E., & McClay, D. R. (2005). A Fringe-modified Notch signal affects
specification of mesoderm and endoderm in the sea urchin embryo. Developmental
biology, 282, 126-137.
Ransick, A., & Davidson, E. H. (2006). cis-regulatory processing of Notch signaling
input to the sea urchin glial cells missing gene during mesoderm specification.
Developmental biology, 297, 587-602.
Ransick, A., & Davidson, E. H. (2012). Cis-regulatory logic driving glial cells missing:
self-sustaining circuitry in later embryogenesis. Developmental biology, 364, 259-267.
42
Rast, J. P. (2000). Transgenic manipulation of the sea urchin embryo. Methods in
Molecular Biology, 136, 365–373.
Sakane, Y., Iida, M., Hasebe, T., Fujii, S., Buchholz, D. R., Ishizuya‐Oka, A., … Ken‐
ichi, T. S. (2018). Functional analysis of thyroid hormone receptor beta in Xenopus
tropicalis founders using CRISPR‐Cas. Biology Open, 7, bio030338.
Sakane, Y., Suzuki, T. S., & Yamamoto, T. (2017). A simple protocol for loss‐of‐function
analysis in Xenopus tropicalis founders using the CRISPR‐cas system. In I. Hatada (Ed.),
Genome editing in animals (pp. 189–203). New York, NY: Humana Press.
Sea Urchin Genome Sequencing Consortium (2006). The genome of the sea urchin
Strongylocentrotus purpuratus. Science, 314, 941–952.
Shevidi, S., Uchida, A., Schudrowitz, N., Wessel, G. M., & Yajima, M. (2017). Single
nucleotide editing without DNA cleavage using CRISPR/Cas9‐deaminase in the sea
urchin embryo. Developmental Dynamics, 246, 1036–1046.
Shigeta, M., Sakane, Y., Iida, M., Suzuki, M., Kashiwagi, K., Kashiwagi, A., … Suzuki,
K. I. T. (2016). Rapid and efficient analysis of gene function using CRISPR‐Cas9 in
Xenopus tropicalis founders. Genes to Cells, 21, 755–771.
Smith, M. M., Cruz Smith, L., Cameron, R. A., & Urry, L. A. (2008). The larval stages
of the sea urchin, Strongylocentrotus purpuratus. Journal of Morphology, 269, 713–733.
Staunton, J., & Weissman, K. J. (2001). Polyketide biosynthesis: A millennium review.
Natural Product Reports, 18, 380–416.
Sung, Y. H., Kim, J. M., Kim, H. T., Lee, J., Jeon, J., Jin, Y., … Lee, H. W. (2014). Highly
efficient gene knockout in mice and zebrafish with RNA‐guided endonucleases. Genome
43
Research, 24, 125–131.
Yamaguchi, M., Kinoshita, T., & Ohba, Y. (1994). Fractionation of Micromeres,
Mesomeres, and Macromeres of 16‐cell Stage Sea Urchin Embryos by Elutriation.
Development, Growth & Differentiation, 36, 381-387.
Yamamoto, T., Kawamoto, R., Fujii, T., Sakamoto, N., & Shibata, T. (2007). DNA
variations within the sea urchin Otx gene enhancer. FEBS Letters, 581, 5234–5240
Zhu, X., Xu, Y., Yu, S., Lu, L., Ding, M., Cheng, J., … Meng, S. (2014). An efficient
genotyping method for genome‐modified animals and human cells generated with
CRISPR/Cas9 system. Scientific Reports, 4, 6420.
44
...