Devo-Dictionary

55-355

Dictionary of Developmental Genes 

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Developmental Genetics 55-455

Proposed Topics:

0.  Saved for M. Crawford - First Lecture
Gene: DM kinase
Syndrome: Myotonic muscular dystrophy
Systems affected: muscle

•  Ashley CT, Jr., Warren ST. 1995. Trinucleotide repeat expansion and human disease. Annu Rev Genet 29:703-728.
•  Tsilfidis, C.; MacKenzie, A. E.; Mettler, G.; Barcelo, J.; Korneluk, R. G. (1992). Correlation between CTG trinucleotide repeat length and frequency of severe congenital myotonic dystrophy. Nature Genet. 1: 192-195.
•  Mankodi, A.; Logigian, E.; Callahan, L.; McClain, C.; White, R.; Henderson, D.; Krym, M.; Thornton, C. A. (2000). Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat. Science 289: 1769-1772

0.1 Saved for M Crawford - 2nd Lecture
Gene:  Arx * (linked by polyalanine tracts story)
Syndrome: X-linked lissencephaly with abnormal genitalia (XLAG)
Systems affected: neural (hydra- and lissencephaly), genitals, autism,
spasms

•    Kato M, Das S, Petras K, Kitamura K, Morohashi K, Abuelo DN, Barr M, Bonneau D, Brady AF, Carpenter NJ, Cipero KL, Frisone F, Fukuda T, Guerrini R, Iida E, Itoh M, Lewanda AF, Nanba Y, Oka A, Proud VK, Saugier-Veber P, Schelley SL, Selicorni A, Shaner R, Silengo M, Stewart  F, Sugiyama N, Toyama J, Toutain A, Vargas AL, Yanazawa M, Zackai EH,  Dobyns WB. (2004). Mutations of ARX are associated with striking  pleiotropy and consistent genotype-phenotype correlation. Hum Mutat.23(2):147-59.
•    Kato M, Das S, Petras K, Sawaishi Y, Dobyns WB. (2003) Polyalanine  expansion of ARX associated with cryptogenic West syndrome. Neurology.  61(2):267-76.
• Uyanik G, Aigner L, Martin P, Gross C, Neumann D, Marschner-Schafer H, Hehr U, Winkler J. (2003) ARX mutations in X-linked lissencephaly with abnormal genitalia. Neurology. 61(2):232-5.

1.  Gene: KRIT1
Syndrome: Cavernous Angioma, Familial
Hemangioma
Affected systems: vasculature of cerebrum, spine, skin, retina

•   Mably, J.D., Chuang, L.P., Serluca, F.C., Mohideen, M.A., Chen, J.N. and Fishman, M.C. (2006) santa and valentine pattern concentric growth of cardiac myocardium in the zebrafish. Development 133, 3139-46.
•  Laberge-le Couteulx, S.; Jung, H. H.; Labauge, P.; Houtteville, J.-P.; Lescoat, C.; Cecillon, M.; Marechal, E.; Joutel, A.; Bach, J.-F.; Tournier-Lasserve, E. (1999). Truncating mutations in CCM1, encoding KRIT1, cause hereditary cavernous angiomas. Nature Genet. 23: 189-193.

•  Miller, V. M., Xia, H., Marrs, G. L., Gouvion, C. M., Lee, G., Davidson, B. L. and Paulson, H. L. (2003). Allele-specific silencing of dominant disease genes. Proc Natl Acad Sci U S A 100, 7195-200.
•  Cemal, C. K., Carroll, C. J., Lawrence, L., Lowrie, M. B., Ruddle, P., Al-Mahdawi, S., King, R. H., Pook, M. A., Huxley, C. and Chamberlain, S. (2002). YAC transgenic mice carrying pathological alleles of the MJD1 locus exhibit a mild and slowly progressive cerebellar deficit. Hum Mol Genet 11, 1075-94.
•  Kawaguchi, Y., Okamoto, T., Taniwaki, M., Aizawa, M., Inoue, M., Katayama, S., Kawakami, H., Nakamura, S., Nishimura, M., Akiguchi, I. et al. (1994). CAG expansions in a novel gene for Machado-Joseph disease at chromosome 14q32.1. Nat Genet 8, 221-8.

3. Gene:  Nodal
Role:  Dorsal Axis
Affected Tissues:  Global Patterning

•   Driever, W. (2005). Developmental biology: a message to the back side. Nature 438, 926-7.
•   Gore, A. V., Maegawa, S., Cheong, A., Gilligan, P. C., Weinberg, E. S. and Sampath, K. (2005). The zebrafish dorsal axis is apparent at the four-cell stage. Nature 438, 1030-5
• Zernicka-Goetz, M. (2002). Patterning of the embryo: the first spatial decisions in the life of a mouse. Development 129, 815-29.

4.    Gene: H+/K+ pump
Role: Laterality
Affected Tissues: Global patterning
 

• Levin, M., Thorlin, T., Robinson, K. R., Nogi, T. and Mercola, M. (2002). Asymmetries in H+/K+-ATPase and cell membrane potentials comprise a very early step in left-right patterning. Cell 111, 77-89.
• Rutenberg, J., Cheng, S. M. and Levin, M. (2002). Early embryonic expression of ion channels and pumps in chick and Xenopus development. Dev Dyn 225, 469-84.
• Stern, C. D. and Wolpert, L. (2002). Left-right asymmetry: all hands to the pump. Curr Biol 12, R802-3.

5. Gene:  Tgif
Syndrome:  Holoprosencephaly
Affected Tissues:  Central nervous system, mid-line patterning
 

• Gripp, K. W., Wotton, D., Edwards, M. C., Roessler, E., Ades, L., Meinecke, P., Richieri-Costa, A., Zackai, E. H., Massague, J., Muenke, M. et al. (2000). Mutations in TGIF cause holoprosencephaly and link NODAL signalling to human neural axis determination. Nat Genet 25, 205-8.
• Dubourg, C., Lazaro, L., Pasquier, L., Bendavid, C., Blayau, M., Le Duff, F., Durou, M. R., Odent, S. and David, V. (2004). Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: Mutation review and genotype-phenotype correlations. Hum Mutat 24, 43-51.
• Shen, J. and Walsh, C. A. (2005). Targeted disruption of Tgif, the mouse ortholog of a human holoprosencephaly gene, does not result in holoprosencephaly in mice. Mol Cell Biol 25, 3639-47.

• Kusumi, K., Sun, E. S., Kerrebrock, A. W., Bronson, R. T., Chi, D. C., Bulotsky, M. S., Spencer, J. B., Birren, B. W., Frankel, W. N. and Lander, E. S. (1998). The mouse pudgy mutation disrupts Delta homologue Dll3 and initiation of early somite boundaries. Nat Genet 19, 274-8.
• Bulman, M. P., Kusumi, K., Frayling, T. M., McKeown, C., Garrett, C., Lander, E. S., Krumlauf, R., Hattersley, A. T., Ellard, S. and Turnpenny, P. D. (2000). Mutations in the human delta homologue, DLL3, cause axial skeletal defects in spondylocostal dysostosis. Nat Genet 24, 438-41.
• Katsube, K. and Sakamoto, K. (2005). Notch in vertebrates--molecular aspects of the signal. Int J Dev Biol 49, 369-74. Nat Genet 24, 438-41.

• Lopes, S., Lewis, A., Hajkova, P., Dean, W., Oswald, J., Forne, T., Murrell, A., Constancia, M., Bartolomei, M., Walter, J. et al. (2003). Epigenetic modifications in an imprinting cluster are controlled by a hierarchy of DMRs suggesting long-range chromatin interactions. Hum Mol Genet 12, 295-305.
• Sparago, A., Cerrato, F., Vernucci, M., Ferrero, G. B., Silengo, M. C. and Riccio, A. (2004). Microdeletions in the human H19 DMR result in loss of IGF2 imprinting and Beckwith-Wiedemann syndrome. Nat Genet 36, 958-60.

• Breau, M.A., Pietri, T., Eder, O., Blanche, M., Brakebusch, C., Fassler, R., Thiery, J.P. and Dufour, S. (2006) Lack of beta1 integrins in enteric neural crest cells leads to a Hirschsprung-like phenotype. Development 133, 1725-34.
• Brakebusch, C. and Fassler, R. (2005) beta 1 integrin function in vivo: adhesion, migration and more. Cancer Metastasis Rev 24, 403-11.

• Ray, A. (2005) Plant genetics: RNA cache or genome trash? Nature 437, E1-2; discussion E2.
• Lolle, S.J., Victor, J.L., Young, J.M. and Pruitt, R.E. (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. Nature 434, 505-9.
• Chaudhury, A. (2005) Plant genetics: hothead healer and extragenomic information. Nature 437, E1; discussion E2.

10.  Epigenetics B: Mouse
Rassoulzadegan, M., Grandjean, V., Gounon, P., Vincent, S., Gillot, I. and Cuzin, F. (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441, 469-74.
Soloway, P.D. (2006) Genetics: paramutable possibilities. Nature 441, 413-4.

11.  Epigenetics C: Demethylation

• Ueda, Y., Okano, M., Williams, C., Chen, T., Georgopoulos, K. and Li, E. (2006) Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 133, 1183-92.
• El-Osta, A. (2003) DNMT cooperativity--the developing links between methylation, chromatin structure and cancer. Bioessays 25, 1071-84.

12.  Epigenetics D: Ubiquitination

• Alkuraya, F.S., Saadi, I., Lund, J.J., Turbe-Doan, A., Morton, C.C. and Maas, R.L. (2006) SUMO1 haploinsufficiency leads to cleft lip and palate. Science 313, 1751.
• Abdelhak, S., Kalatzis, V., Heilig, R., Compain, S., Samson, D., Vincent, C., Levi-Acobas, F., Cruaud, C., Le Merrer, M., Mathieu, M., Konig, R., Vigneron, J., Weissenbach, J., Petit, C. and Weil, D. (1997) Clustering of mutations responsible for branchio-oto-renal (BOR) syndrome in the eyes absent homologous region (eyaHR) of EYA1. Hum Mol Genet 6, 2247-55.

13.  Limb Evolution A: Fins

• Freitas, R., Zhang, G. and Cohn, M.J. (2006) Evidence that mechanisms of fin development evolved in the midline of early vertebrates. Nature 442, 1033-7.
• Shubin, N.H., Daeschler, E.B. and Jenkins, F.A., Jr. (2006) The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440, 764-71.

• Ahlberg, P.E. and Clack, J.A. (2006) Palaeontology: a firm step from water to land. Nature 440, 747-9.
• Daeschler, E.B., Shubin, N.H. and Jenkins, F.A., Jr. (2006) A Devonian tetrapod-like fish and the evolution of the tetrapod body plan.Nature 440, 757-63.

15.  Limb Evolution C: Hox Genes and Molecular Controls

• Capellini, T.D., Di Giacomo, G., Salsi, V., Brendolan, A., Ferretti, E., Srivastava, D., Zappavigna, V. and Selleri, L. (2006) Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression. Development 133, 2263-73.
• Tarchini, B., Duboule, D. and Kmita, M. (2006) Regulatory constraints in the evolution of the tetrapod limb anterior-posterior polarity. Nature 443, 985-8.

16.  Segmentation A: Controlling the Segmentation Clock

• Dequeant, M.L., Glynn, E., Gaudenz, K., Wahl, M., Chen, J., Mushegian, A. and Pourquie, O. (2006) A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 314, 1595-8.
• Pourquie, O. (2003) Vertebrate somitogenesis: a novel paradigm for animal segmentation? Int J Dev Biol 47, 597-603.

• Iimura, T. and Pourquie, O. (2006) Collinear activation of Hoxb genes during gastrulation is linked to mesoderm cell ingression. Nature 442, 568-71.
• Zakany, J., Kmita, M., Alarcon, P., de la Pompa, J.L. and Duboule, D. (2001) Localized and transient transcription of Hox genes suggests a link between patterning and the segmentation clock. Cell 106, 207-17.

18.  Stem Cells : Alternative Sources

• Chung, Y., Klimanskaya, I., Becker, S., Marh, J., Lu, S.J., Johnson, J., Meisner, L. and Lanza, R. (2006) Embryonic and extraembryonic stem cell lines derived from single mouse blastomeres. Nature 439, 216-9.
• Klimanskaya, I., Chung, Y., Becker, S., Lu, S.J. and Lanza, R. (2006) Human embryonic stem cell lines derived from single blastomeres. Nature 444, 481-5.
• Pearson, H. (2006) Early embryos can yield stem cells... and survive. Nature 442, 858.

19.  Stem Cells: Therapeutic Cloning and Ethics

• Meissner, A. and Jaenisch, R. (2006) Generation of nuclear transfer-derived pluripotent ES cells from cloned Cdx2-deficient blastocysts. Nature 439, 212-5.
• Dennis, C. and Check, E. (2005) 'Ethical' routes to stem cells highlight political divide. Nature 437, 1076-7.
• Tolkunova, E., Cavaleri, F., Eckardt, S., Reinbold, R., Christenson, L.K., Scholer, H.R. and Tomilin, A. (2006) The caudal-related protein cdx2 promotes trophoblast differentiation of mouse embryonic stem cells. Stem Cells 24, 139-44.

20.  Neuron Guidance

• Luo, L. (2006) Developmental neuroscience: two gradients are better than one. Nature 439, 23-4.
• Schmitt, A.M., Shi, J., Wolf, A.M., Lu, C.C., King, L.A. and Zou, Y. (2006) Wnt-Ryk signalling mediates medial-lateral retinotectal topographic mapping. Nature 439, 31-7.

21.  Alzheimer’s
A Prion Disorder?
 

• Meyer-Luehmann, M., Coomaraswamy, J., Bolmont, T., Kaeser, S., Schaefer, C., Kilger, E., Neuenschwander, A., Abramowski, D., Frey, P., Jaton, A.L., Vigouret, J.M., Paganetti, P., Walsh, D.M., Mathews, P.M., Ghiso, J., Staufenbiel, M., Walker, L.C. and Jucker, M. (2006) Exogenous induction of cerebral beta-amyloidogenesis is governed by agent and host. Science 313, 1781-4.
• Riek, R. (2006) Cell biology: infectious Alzheimer's disease?Nature 444, 429-31.

22.  Cardiac Transcription Factors: GATA4, FOG2
Syndrome: Tetralogy of Fallot

• Nemer, G., Fadlalah, F., Usta, J., Nemer, M., Dbaibo, G., Obeid, M. and Bitar, F. (2006) A novel mutation in the GATA4 gene in patients with Tetralogy of Fallot. Hum Mutat 27, 293-4.
• Pizzuti, A., Sarkozy, A., Newton, A.L., Conti, E., Flex, E., Digilio, M.C., Amati, F., Gianni, D., Tandoi, C., Marino, B., Crossley, M. and Dallapiccola, B. (2003) Mutations of ZFPM2/FOG2 gene in sporadic cases of tetralogy of Fallot. Hum Mutat 22, 372-7.
• Jay, P.Y., Bielinska, M., Erlich, J.M., Mannisto, S., Pu, W.T., Heikinheimo, M. and Wilson, D.B. (2006) Impaired mesenchymal cell function in Gata4 mutant mice leads to diaphragmatic hernias and primary lung defects. Dev Biol.

23.  Hedgehog Pathway: Pancreas Development and Cancer

• Pasca di Magliano, M., Sekine, S., Ermilov, A., Ferris, J., Dlugosz, A.A. and Hebrok, M. (2006) Hedgehog/Ras interactions regulate early stages of pancreatic cancer. Genes Dev 20, 3161-73.
• Lau, J., Kawahira, H. and Hebrok, M. (2006) Hedgehog signaling in pancreas development and disease. Cell Mol Life Sci 63, 642-52.
• Hebrok, M. (2003) Hedgehog signaling in pancreas development. Mech Dev 120, 45-57.

24.  Human Developmental Evolution B. Ancient (Primate Evolution)

• Green, R.E., Krause, J., Ptak, S.E., Briggs, A.W., Ronan, M.T., Simons, J.F., Du, L., Egholm, M., Rothberg, J.M., Paunovic, M. and Paabo, S. (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444, 330-6.
• Lambert, D.M. and Millar, C.D. (2006) Evolutionary biology: ancient genomics is born. Nature 444, 275-6.
• Noonan, J.P., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., Chen, F., Platt, D., Paabo, S., Pritchard, J.K. and Rubin, E.M. (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314, 1113-8.

25.  Human Developmental Evolution A: Modern (Race and Individual Variation)

• Redon, R., et al., (2006) Global variation in copy number in the human genome. Nature 444, 444-54.
• Spielman, R.S., Bastone, L.A., Burdick, J.T., Morley, M., Ewens, W.J. and Cheung, V.G. (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet.
• Shianna, K.V. and Willard, H.F. (2006) Human genomics: in search of normality. Nature 444, 428-9.