Ashery-Padan, R., and Gruss, P. (2001). Pax6 lights-up the way for eye development. Curr. Opin. Cell Biol. 13, 706–714.
Bernier, G., Panitz, F., Zhou, X., Hollemann, T., Gruss, P., and Pieler, T. (2000). Expanded retina territory by midbrain transformation upon overexpression of Six6 (Optx2) in Xenopus embryos. Mech. Dev. 93, 59–69.
Bertuzzi, S., Hindges, R., Mui, S.H., O’Leary, D.D., and Lemke, G. (1999). The homeodomain protein vax1 is required for axon guidance and major tract formation in the developing forebrain. Genes Dev. 13, 3092–3105.
Boulet, A.M., and Capecchi, M.R. (1996). Targeted disruption of hoxc-4 causes esophageal defects and vertebral transformations. Dev. Biol. 177, 232–249.
Brady, J.P., Garland, D., Duglas-Tabor, Y., Robison, W.G., Groome, A., and Wawrousek, E.F. (1997). Targeted disruption of the mouse alpha A-crystallin gene induces cataract and cytoplasmic inclusion bodies containing the small heat shock protein alpha B-crystallin. Proc. Natl. Acad. Sci. U.S.A. 94, 884–889.
Bruel, A.-L., Masurel‐Paulet, A., Rivière, J.-B., Duffourd, Y., Lehalle, D., Bensignor, C., Huet, F., Borgnon, J., Roucher, F., Kuentz, P., et al. (2017). Autosomal recessive truncating MAB21L1 mutation associated with a syndromic scrotal agenesis. Clinical Genetics 91, 333–338.
Bruneau, S., Johnson, K.R., Yamamoto, M., Kuroiwa, A., and Duboule, D. (2001). The mouse Hoxd13(spdh) mutation, a polyalanine expansion similar to human type II synpolydactyly (SPD), disrupts the function but not the expression of other Hoxd genes. Dev. Biol. 237, 345–353.
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., and Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology 36, 411–420.
Chow, R.L., and Lang, R.A. (2001). Early eye development in vertebrates. Annu. Rev. Cell Dev. Biol. 17, 255–296.
Collinson, J.M., Hill, R.E., and West, J.D. (2000). Different roles for Pax6 in the optic vesicle and facial epithelium mediate early morphogenesis of the murine eye.Development 127, 945–956.
Condie, B.G., and Capecchi, M.R. (1994). Mice with targeted disruptions in the paralogous genes hoxa-3 and hoxd-3 reveal synergistic interactions. Nature 370, 304– 307.
Davis, A.P., and Capecchi, M.R. (1994). Axial homeosis and appendicular skeleton defects in mice with a targeted disruption of hoxd-11. Development 120, 2187–2198.
Favor, J., Sandulache, R., Neuhäuser-Klaus, A., Pretsch, W., Chatterjee, B., Senft, E., Wurst, W., Blanquet, V., Grimes, P., Spörle, R., et al. (1996). The mouse Pax2(1Neu) mutation is identical to a human PAX2 mutation in a family with renal-coloboma syndrome and results in developmental defects of the brain, ear, eye, and kidney. Proc. Natl. Acad. Sci. U.S.A. 93, 13870–13875.
Fujiwara, M., Uchida, T., Osumi-Yamashita, N., and Eto, K. (1994). Uchida rat (rSey): a new mutant rat with craniofacial abnormalities resembling those of the mouse Sey mutant. Differentiation 57, 31–38.
Furukawa, T., Kozak, C.A., and Cepko, C.L. (1997). rax, a novel paired-type homeobox gene, shows expression in the anterior neural fold and developing retina. Proc. Natl. Acad. Sci. U.S.A. 94, 3088–3093.
Godwin, A.R., and Capecchi, M.R. (1998). Hoxc13 mutant mice lack external hair. Genes Dev. 12, 11–20.
Grainger, R.M. (1992). Embryonic lens induction: shedding light on vertebrate tissue determination. Trends Genet. 8, 349–355.
Greer, J.M., and Capecchi, M.R. (2002). Hoxb8 is required for normal grooming behavior in mice. Neuron 33, 23–34.
Grindley, J.C., Davidson, D.R., and Hill, R.E. (1995). The role of Pax-6 in eye and nasal development. Development 121, 1433–1442.
Grün, D., Lyubimova, A., Kester, L., Wiebrands, K., Basak, O., Sasaki, N., Clevers, H., and van Oudenaarden, A. (2015). Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251–255.
Hallonet, M., Hollemann, T., Pieler, T., and Gruss, P. (1999). Vax1, a novel homeobox- containing gene, directs development of the basal forebrain and visual system. Genes Dev. 13, 3106–3114.
Hill, R.E., Favor, J., Hogan, B.L.M., Ton, C.C.T., Saunders, G.F., Hanson, I.M., Prosser, J., Jordan, T., Hastie, N.D., and Heyningen, V. van (1991). Mouse Small eye results from mutations in a paired-like homeobox-containing gene. Nature 354, 522– 525.
Hirsch, N., and Grainger, R.M. (2000). Induction of the lens. Results Probl Cell Differ31, 51–68.
Hogan, B.L., Horsburgh, G., Cohen, J., Hetherington, C.M., Fisher, G., and Lyon, M.F. (1986). Small eyes (Sey): a homozygous lethal mutation on chromosome 2 which affects the differentiation of both lens and nasal placodes in the mouse. J Embryol Exp Morphol 97, 95–110.
Hughes, C.L., and Kaufman, T.C. (2002). Hox genes and the evolution of the arthropod body plan. Evol. Dev. 4, 459–499.
Hwang, B., Lee, J.H., and Bang, D. (2018). Single-cell RNA sequencing technologies and bioinformatics pipelines. Experimental & Molecular Medicine 50, 96.
Ilicic, T., Kim, J.K., Kolodziejczyk, A.A., Bagger, F.O., McCarthy, D.J., Marioni, J.C., and Teichmann, S.A. (2016). Classification of low quality cells from single-cell RNA- seq data. Genome Biology 17, 29.
Jaitin, D.A., Weiner, A., Yofe, I., Lara-Astiaso, D., Keren-Shaul, H., David, E., Salame, T.M., Tanay, A., van Oudenaarden, A., and Amit, I. (2016). Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell 167, 1883-1896.e15.
Jonason, J.H., and O’Keefe, R.J. (2014). Isolation and culture of neonatal mouse calvarial osteoblasts. Methods Mol. Biol. 1130, 295–305.
Kamachi, Y., Uchikawa, M., Tanouchi, A., Sekido, R., and Kondoh, H. (2001). Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. Genes Dev. 15, 1272–1286.
Kmita, M., Fraudeau, N., Hérault, Y., and Duboule, D. (2002). Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420, 145–150.
Koike, C., Nishida, A., Ueno, S., Saito, H., Sanuki, R., Sato, S., Furukawa, A., Aizawa, S., Matsuo, I., Suzuki, N., et al. (2007). Functional roles of Otx2 transcription factor in postnatal mouse retinal development. Mol. Cell. Biol. 27, 8318–8329.
Kondoh, H. (1999). Transcription factors for lens development assessed in vivo. Curr. Opin. Genet. Dev. 9, 301–308.
Kondoh, H., Uchikawa, M., and Kamachi, Y. (2004). Interplay of Pax6 and SOX2 in lens development as a paradigm of genetic switch mechanisms for cell differentiation. Int. J. Dev. Biol. 48, 819–827.
Koshiba-Takeuchi, K., Takeuchi, J.K., Matsumoto, K., Momose, T., Uno, K., Hoepker, V., Ogura, K., Takahashi, N., Nakamura, H., Yasuda, K., et al. (2000). Tbx5 and the retinotectum projection. Science 287, 134–137.
Krumlauf, R. (1992). Evolution of the vertebrate Hox homeobox genes. Bioessays 14, 245–252.
Lengler, J., Krausz, E., Tomarev, S., Prescott, A., Quinlan, R.A., and Graw, J. (2001). Antagonistic action of Six3 and Prox1 at the gamma-crystallin promoter. Nucleic Acids Res. 29, 515–526.
Lewis, W.H. (1904). Experimental studies on the development of the eye in amphibia.I. On the origin of the lens. Rana palustris. American Journal of Anatomy 3, 505–536.
Liu, I.S., Chen, J.D., Ploder, L., Vidgen, D., van der Kooy, D., Kalnins, V.I., and McInnes, R.R. (1994). Developmental expression of a novel murine homeobox gene (Chx10): evidence for roles in determination of the neuroretina and inner nuclear layer. Neuron 13, 377–393.
Liu, R., Wang, H., and Yu, X. (2018). Shared-nearest-neighbor-based clustering by fast search and find of density peaks. Information Sciences 450, 200–226.
Liu, W., Lagutin, O.V., Mende, M., Streit, A., and Oliver, G. (2006). Six3 activation of Pax6 expression is essential for mammalian lens induction and specification. EMBO J 25, 5383–5395.
Loosli, F., Winkler, S., and Wittbrodt, J. (1999). Six3 overexpression initiates the formation of ectopic retina. Genes Dev. 13, 649–654.
Macdonald, R., Barth, K.A., Xu, Q., Holder, N., Mikkola, I., and Wilson, S.W. (1995). Midline signalling is required for Pax gene regulation and patterning of the eyes.Development 121, 3267–3278.
Marquardt, T., and Gruss, P. (2002). Generating neuronal diversity in the retina: one for nearly all. Trends Neurosci. 25, 32–38.
Martinez-Morales, J.R., Signore, M., Acampora, D., Simeone, A., and Bovolenta, P. (2001). Otx genes are required for tissue specification in the developing eye.Development 128, 2019–2030.
Mathers, P.H., Grinberg, A., Mahon, K.A., and Jamrich, M. (1997). The Rx homeobox gene is essential for vertebrate eye development. Nature 387, 603–607.
Matsuo, I., Kuratani, S., Kimura, C., Takeda, N., and Aizawa, S. (1995). Mouse Otx2 functions in the formation and patterning of rostral head. Genes Dev. 9, 2646–2658.
Matt, N., Dupé, V., Garnier, J.-M., Dennefeld, C., Chambon, P., Mark, M., and Ghyselinck, N.B. (2005). Retinoic acid-dependent eye morphogenesis is orchestrated by neural crest cells. Development 132, 4789–4800.
McGinnis, W., and Krumlauf, R. (1992). Homeobox genes and axial patterning. Cell68, 283–302.
Meyer, A. (1998). Hox gene variation and evolution. Nature 391, 225, 227–228.
Nguyen, M., and Arnheiter, H. (2000). Signaling and transcriptional regulation in early mammalian eye development: a link between FGF and MITF. Development 127, 3581–3591.
Nguyen, D., Yamada, R., Yoshimitsu, N., Oguri, A., Kojima, T., and Takahashi, N. (2017). Involvement of the Mab21l1 gene in calvarial osteogenesis. Differentiation 98, 70–78.
Nishida, A., Furukawa, A., Koike, C., Tano, Y., Aizawa, S., Matsuo, I., and Furukawa,T. (2003). Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development. Nat. Neurosci. 6, 1255–1263.
Ohsaki, K., Morimitsu, T., Ishida, Y., Kominami, R., and Takahashi, N. (1999). Expression of the Vax family homeobox genes suggests multiple roles in eye development. Genes Cells 4, 267–276.
Oliver, G., Mailhos, A., Wehr, R., Copeland, N.G., Jenkins, N.A., and Gruss, P. (1995). Six3, a murine homologue of the sine oculis gene, demarcates the most anterior border of the developing neural plate and is expressed during eye development. Development 121, 4045–4055.
Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S.P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., and Lanner, F. (2016). Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. Cell 165, 1012–1026.
Pillai-Kastoori, L., Wen, W., Wilson, S.G., Strachan, E., Lo-Castro, A., Fichera, M., Musumeci, S.A., Lehmann, O.J., and Morris, A.C. (2014). Sox11 Is Required to Maintain Proper Levels of Hedgehog Signaling during Vertebrate Ocular Morphogenesis. PLoS Genet 10.
Porter, F.D., Drago, J., Xu, Y., Cheema, S.S., Wassif, C., Huang, S.P., Lee, E., Grinberg, A., Massalas, J.S., Bodine, D., et al. (1997). Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development. Development 124, 2935–2944.
Quinn, J.C., West, J.D., and Hill, R.E. (1996). Multiple functions for Pax6 in mouse eye and nasal development. Genes Dev. 10, 435–446.
Rizvi, A.H., Camara, P.G., Kandror, E.K., Roberts, T.J., Schieren, I., Maniatis, T., and Rabadan, R. (2017). Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. Nature Biotechnology 35, 551–560.
Saito, Y., Kojima, T., and Takahashi, N. (2012). Mab21l2 is essential for embryonic heart and liver development. PLoS ONE 7, e32991.
Sanger, F., Nicklen, S., and Coulson, A.R. (1977). DNA sequencing with chain- terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74, 5463–5467.
Schulte, D., Furukawa, T., Peters, M.A., Kozak, C.A., and Cepko, C.L. (1999). Misexpression of the Emx-related homeobox genes cVax and mVax2 ventralizes the retina and perturbs the retinotectal map. Neuron 24, 541–553.
Segerstolpe, Å., Palasantza, A., Eliasson, P., Andersson, E.-M., Andréasson, A.-C., Sun, X., Picelli, S., Sabirsh, A., Clausen, M., Bjursell, M.K., et al. (2016). Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.Cell Metabolism 24, 593–607.
Stadler, H.S., Higgins, K.M., and Capecchi, M.R. (2001). Loss of Eph-receptor expression correlates with loss of cell adhesion and chondrogenic capacity in Hoxa13 mutant limbs. Development 128, 4177–4188.
Suemori, H., Takahashi, N., and Noguchi, S. (1995). Hoxc-9 mutant mice show anterior transformation of the vertebrae and malformation of the sternum and ribs. Mech. Dev. 51, 265–273.
Sun, M., Ahmad, N., Zhang, R., and Graw, J. (2018). Crybb2 associates with Tmsb4X and is crucial for dendrite morphogenesis. Biochemical and Biophysical Research Communications 503, 123–130.
Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A., et al. (2009). mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382.
Treutlein, B., Brownfield, D.G., Wu, A.R., Neff, N.F., Mantalas, G.L., Espinoza, F.H., Desai, T.J., Krasnow, M.A., and Quake, S.R. (2014). Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371– 375.
Treutlein, B., Lee, Q.Y., Camp, J.G., Mall, M., Koh, W., Shariati, S.A.M., Sim, S., Neff, N.F., Skotheim, J.M., Wernig, M., et al. (2016). Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature 534, 391–395.
Tropepe, V., Coles, B.L., Chiasson, B.J., Horsford, D.J., Elia, A.J., McInnes, R.R., and van der Kooy, D. (2000). Retinal stem cells in the adult mammalian eye. Science 287, 2032–2036.
van der Maaten L, and Hinton G (2008). Visualizing Data using t-SNE. J Mach Learn Res. 2579–2605.
Xue, Z., Huang, K., Cai, C., Cai, L., Jiang, C., Feng, Y., Liu, Z., Zeng, Q., Cheng, L., Sun, Y.E., et al. (2013). Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500, 593–597.
Yamada, R., Mizutani-Koseki, Y., Hasegawa, T., Osumi, N., Koseki, H., and Takahashi, N. (2003). Cell-autonomous involvement of Mab21l1 is essential for lens placode development. Development 130, 1759–1770.
Yamada, R., Mizutani-Koseki, Y., Koseki, H., and Takahashi, N. (2004). Requirement for Mab21l2 during development of murine retina and ventral body wall. Dev. Biol.274, 295–307.
Yoshida, T., and Yasuda, K. (2002). Characterization of the chicken L-Maf, MafB and c-Maf in crystallin gene regulation and lens differentiation. Genes Cells 7, 693–706.
Yun, S., Saijoh, Y., Hirokawa, K.E., Kopinke, D., Murtaugh, L.C., Monuki, E.S., and Levine, E.M. (2009). Lhx2 links the intrinsic and extrinsic factors that control optic cup formation. Development 136, 3895–3906.
Zhang, L., Mathers, P.H., and Jamrich, M. (2000). Function of Rx, but not Pax6, is essential for the formation of retinal progenitor cells in mice. Genesis 28, 135–142.
Zhao, Y., and Potter, S.S. (2002). Functional comparison of the Hoxa 4, Hoxa 10, and Hoxa 11 homeoboxes. Dev. Biol. 244, 21–36.
論文の公開元へ
