Gene expression in pharyngeal arch 1 during human embryonic development

Human Molecular Genetics

Volumn 14, Issue 7, 2005, Pages 903-912

  Cai, Juanliang ^a   Ash, David ^a   Kotch, Lori E ^a   Jabs, Ethylin Wang ^a   Atti Bitach, Tania ^b   Auge, Joelle ^b   Mattei, Geraldine ^b   Etchevers, Heather ^b   Vekemans, Michel ^b   Korshunova, Yulia ^c   Tidwell, Rose ^c   Messina, David N ^c   Winston, Julia B ^c   Lovett, Michael ^c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b HÔPITAL NECKER ENFANTS MALADES   (France)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BIOSYNTHESIS; BIRTH DEFECT; CATALYSIS; CLEFT FACE; CLEFT LIP; CONTROLLED STUDY; CRANIOFACIAL DEVELOPMENT; CRANIOFACIAL MALFORMATION; CRANIOFACIAL MORPHOLOGY; DNA MICROARRAY; EMBRYO; EMBRYO DEVELOPMENT; EMBRYONIC STRUCTURES; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC TRANSCRIPTION; HUMAN; IN SITU HYBRIDIZATION; JAW; MICRODISSECTION; MICROGNATHIA; MOLECULAR LIBRARY; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PALATE; PHARYNX ARCH; PRIORITY JOURNAL; PROTEIN BINDING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION; UNINDEXED SEQUENCE;

ANIMALS; BRANCHIAL REGION; CATALYSIS; CRANIOFACIAL ABNORMALITIES; DISEASE MODELS, ANIMAL; DNA, COMPLEMENTARY; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; HUMANS; IN SITU HYBRIDIZATION; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY; TIME FACTORS;

EID: 20244374082     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddi083     Document Type: Article

References (42)

1. Gorlin, R.J., Cohen, M.M., Jr and Hennekam, R.C.M. (2001) Syndromes of the Head and Neck. Oxford University Press, New York.
2. Graham, A. and Smith, A. (2001) Patterning the pharyngeal arches. Bioessays, 23, 54-61.
3. Neubuser, A., Peters, H., Balling, R. and Martin, G.R. (1997) Antagonistic interactions between FGF and BMP signaling pathways: a mechanism for positioning the sites of tooth formation. Cell, 90 247-255.
4. Lievre, C.L. (1974) Role of mesectodermal cells arising from the cephalic neural crest in the formation of the branchial arches and visceral skeleton. J. Embryol. Exp. Morphol., 31, 453-477.
5. Noden, D.M. (1983) The role of the neural crest in patterning of avian cranial skeletal, connective, and muscle tissues. Dev. Biol. 96, 144-165.
6. Trainor, P. and Krumlauf, R. (2000) Plasticity in mouse neural crest cells reveals a new patterning role for cranial mesoderm. Nat. Cell Biol., 2, 96-102.
7. Graham, A., Francis-West, P., Brickell, P. and Lumsden, A. (1994) The signalling molecule BMP4 mediates apoptosis in the rhombencephalic neural crest. Nature, 372, 684-686.
8. Winograd, J., Reilly, M.P., Roe, R., Lutz, J., Laughner, E., Xu, X., Hu, L., Asakura, T., van der Kolk, C., Strandberg, J.D. et al. (1997) Perinatal lethality and multiple craniofacial malformations in MSX2 transgenic mice. Hum. Mol. Genet., 6, 369-379.
9. Veitch, E., Begbie, J., Schilling, T.F., Smith, M.M. and Graham, A. (1999) Pharyngeal arch patterning in the absence of neural crest. Curr. Biol., 9, 1481-1484.
10. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
11. Richards, M., Tan, S.P., Tan, J.H., Chan, W.K. and Bongso, A. (2004) The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells, 22, 51-64.
12. Sperger, J.M., Chen, X., Draper, J.S., Antosiewicz, J.E., Chon, C.H., Jones, S.B., Brooks, J.D., Andrews, P.W., Brown, P.O. and Thomson, J.A. (2003) Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc. Natl Acad. Sci. USA, 100, 13350-13355.
13. Cai, J., Ash, D. and Jabs, E.W. (2002) SAGE analysis from 1 μg of total RNA. In Yamada, K.M. (ed.), Current Protocols in Cell Biology. John Wiley & Sons, Inc., Vol. 2.
14. Margulies, E.H. and Innis, J.W. (2000) eSAGE: managing and analysing data generated with serial analysis of gene expression (SAGE). Bioinformatics, 16, 650-651.
15. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E., Jr, Hieter, P., Vogelstein, B. and Kinzler, K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
16. Velculescu, V.E., Madden, S.L., Zhang, L., Lash, A.E., Yu, J., Rago, C., Lal, A., Wang, C.J., Beaudry, G.A., Ciriello, K.M. et al. (1999) Analysis of human transcriptomes. Nat. Genet., 23 387-388.
17. Margulies, E.H., Kardia, S.L. and Innis, J.W. (2001) A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). Genome Res. 11, 1686-1698.
18. Zhou, G., Chen, J., Lee, S., Clark, T., Rowley, J.D. and Wang, S.M. (2001) The pattern of gene expression in human CD34(+) stem/progenitor cells. Proc. Natl Acad. Sci. USA, 98, 13966-13971.
19. Li, C. and Wong, W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
20. Audic, S. and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res., 7, 986-995.
21. Beissbarth, T. and Speed, T.P. (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics, 20, 1464-1465.
22. Avantaggiato, V., Orlandini, M., Acampora, D., Oliviero, S. and Simeone, A. (1998) Embryonic expression pattern of the murine figf gene, a growth factor belonging to platelet-derived growth factor/vascular endothelial growth factor family. Mech. Dev., 73 221-224.
23. Pilia, G., Hughes-Benzie, R.M., MacKenzie, A., Baybayan, P., Chen, E.Y., Huber, R., Neri, G., Cao, A., Forabosco, A. and Schlessinger, D. (1996) Mutations in GPC3, a glypican gene, cause the Simpson-Golabi-Behmel overgrowth syndrome. Nat. Genet., 12, 241-247.
24. Veugelers, M., Cat, B.D., Muyldermans, S.Y., Reekmans, G., Delande, N., Frints, S., Legius, E., Fryns, J.P., Schrander-Stumpel, C., Weidle, B. et al. (2000) Mutational analysis of the GPC3/GPC4 glypican gene cluster on Xq26 in patients with Simpson-Golabi-Behmel syndrome: identification of loss-of-function mutations in the GPC3 gene. Hum. Mol. Genet., 9, 1321-1328,
25. Joutel, A., Vahedi, K., Corpechot, C., Troesch, A., Chabriat, H., Vayssiere, C., Cruaud, C., Maciazek, J., Weissenbach, J., Bousser, M.G. et al. (1997) Strong clustering and stereotyped nature of Notch3 mutations in CADASIL patients. Lancet, 350, 1511-1515.
26. Pai, S.I., Wu, G.S., Ozoren, N., Wu, L., Jen, J., Sidransky, D. and El-Deiry, W.S. (1998) Rare loss-of-function mutation of a death receptor gene in head and neck cancer. Cancer Res., 58, 3513-3518.
27. Howard, T.D., Paznekas, W.A., Green, E.D., Chiang, L.C., Ma, N., Ortiz de Luna, R.I., Garcia Delgado, C., Gonzalez-Ramos, M., Kline, A.D. and Jabs, E.W. (1997) Mutations in TWIST, a basic helix-loop-helix transcription factor, in Saethre-Chotzen syndrome. Nat. Genet., 15, 36-41.
28. Bourgeois, P., Bolcato-Bellemin, A.L., Danse, J.M., Bloch-Zupan, A., Yoshiba, K., Stoetzel, C. and Perrin-Schmitt, F. (1998) The variable expressivity and incomplete penetrance of the twist-null heterozygous mouse phenotype resemble those of human Saethre-Chotzen syndrome. Hum. Mol. Genet., 7, 945-957.
29. The Treacher Collins Syndrome Collaborative Group (1996) Positional cloning of a gene involved in the pathogenesis of Treacher Collins syndrome. Nat. Genet., 12, 130-136.
30. Dixon, J., Brakebusch, C., Fassler, R. and Dixon, M.J. (2000) Increased levels of apoptosis in the prefusion neural folds underlie the craniofacial disorder, Treacher Collins syndrome. Hum. Mol. Genet., 9, 1473-1480.
31. von Lindern, M., van Baal, S., Wiegant, J., Raap, A., Hagemeijer, A. and Grosveld, G. (1992) Can, a putative oncogene associated with myeloid leukemogenesis, may be activated by fusion of its 3′ half to different genes: characterization of the set gene. Mol. Cell. Biol., 12, 3346-3355.
32. Sevigny, G., Joly, E.C., Bibor-Hardy, V. and Lemieux, N. (1994) Assignment of the human homologue of the mTRiC-P5 gene (TRIC5) to band 1q23 by fluorescence in situ hybridization. Genomics 22, 634-636.
33. Wilcoxon, F. (1945) Individual comparisons by ranking methods. Biometrics Bull., 1, 80-83.
34. Li, H., Chen, Y., Jiang, Y., Bittner, M., Meltzer, P., Trent, J., Yamada, K. and Yamada, Y. (1999) Profiling expression patterns of 2214 unigenes in mouse craniofacial development by CDNA microarray analysis. Nat. Genet., 23, 57-58.
35. Neuhauss, S.C., Solnica-Krezel, L., Schier, A.F., Zwartkruis, F., Stemple, D.L., Malicki, J., Abdelilah, S., Stainier, D.Y. and Driever, W. (1996) Mutations affecting craniofacial development in zebrafish. Development, 123, 357-367.
36. Fowles, L.F., Bennetts, J.S., Berkman, J.L., Williams, E., Koopman, P., Teasdale, R.D. and Wicking, C. (2003) Genomic screen for genes involved in mammalian craniofacial development. Genesis, 35, 73-87.
37. Ishii, M., Hashimoto, S., Tsutsumi, S., Wada, Y., Matsushima, K., Kodama, T. and Aburatani, H. (2000) Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics, 68, 136-143.
38. Haverty, P.M., Hsiao, L.L., Gullans, S.R., Hansen, U. and Weng, Z. (2004) Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinformatics, 20, 3431-3441.
39. Lu, J., Lal, A., Merriman, B., Nelson, S. and Riggins, G. (2004) A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics, 84, 631-636.
40. Cai, J., Goodman, B.K., Patel, A.S., Mulliken, J.B., van Maldergem, L., Hoganson, G.E., Paznekas, W.A., Ben-Neriah, Z., Sheffer, R., Cunningham, M.L. et al. (2003) Increased risk for developmental delay in Saethre-Chotzen syndrome is associated with TWIST deletions: an improved strategy for TWIST mutation screening. Hum. Genet., 114 68-76.
41. Henrique, D., Adam, J., Myat, A., Chitnis, A., Lewis, J. and Ish-Horowicz, D. (1995) Expression of a delta homologue in prospective neurons in the chick. Nature, 375, 787-790.
42. Zeeberg, B.R., Feng, W., Wang, G., Wang, M.D., Fojo, A.T., Sunshine, M., Narasimhan, S., Kane, D.W., Reinhold, W.C., Lababidi, S. et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol., 4, R28.