Developmental staging of male murine embryonic gonad by SAGE analysis

Journal of Genetics and Genomics

Volumn 36, Issue 4, 2009, Pages 215-227

  Lee, Tin Lap ^a   Li, Yunmin ^b   Alba, Diana ^a   Vong, Queenie P ^a   Wu, Shao Ming ^a   Baxendale, Vanessa ^a   Rennert, Owen M ^a   Lau, Yun Fai Chris ^b   Chan, Wai Yee ^a,c  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c GEORGETOWN UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

chromosome; cluster analysis; male gonads gene tag; novel transcripts; SAGE; transcription hotspot; transcriptome

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; CHROMOSOME MAP; CHROMOSOME POSITIONING; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENOMICS; GONAD DEVELOPMENT; MALE; MOUSE; NONHUMAN; SERIAL ANALYSIS OF GENE EXPRESSION;

ANIMALS; CHROMOSOME MAPPING; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MALE; MICE; MOLECULAR SEQUENCE DATA; TESTIS; TRANSCRIPTION, GENETIC;

MURINAE;

EID: 64349106794     PISSN: 16738527     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1673-8527(08)60109-5     Document Type: Article

References (50)

1. Abba M.C., Drake J.A., Hawkins K.A., Hu Y., Sun H., Notcovich C., Gaddis S., Sahin A., Baggerly K., and Aldaz C.M. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression. Breast Cancer Res. 6 (2004) R499-R513
2. Anisimov S.V. Serial Analysis of Gene Expression (SAGE): 13 years of application in research. Curr. Pharm. Biotechnol. 9 (2008) 338-350
3. Awad I.A., Rees C.A., Hernandez-Boussard T., Ball C.A., and Sherlock G. Caryoscope: An open source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 5 (2004) 151
4. Baggerly K.A., Deng L., Morris J.S., and Aldaz C.M. Differential expression in SAGE: Accounting for normal between-library variation. Bioinformatics 19 (2003) 1477-1483
5. Beverdam A., and Koopman P. Expression profiling of purified mouse gonadal somatic cells during the critical time window of sex determination reveals novel candidate genes for human sexual dysgenesis syndromes. Hum. Mol. Genet. 15 (2006) 417-431
6. Blake J., Schwager C., Kapushesky M., and Brazma A. ChroCoLoc: An application for calculating the probability of co-localization of microarray gene expression. Bioinformatics 22 (2006) 765-767
7. Bouma G.J., Hart G.T., Washburn L.L., Recknagel A.K., and Eicher E.M. Using real time RT-PCR analysis to determine multiple gene expression patterns during XX and XY mouse fetal gonad development. Gene Expr. Patterns 5 (2004) 141-149
8. Bowles J., Bullejos M., and Koopman P. A subtractive gene expression screen suggests a role for vanin-1 in testis development in mice. Genesis 27 (2000) 124-135
9. Brennan J., and Capel B. One tissue, two fates: Molecular genetic events that underlie testis versus ovary development. Nat. Rev. Genet. 5 (2004) 509-521
10. Capel B., Albrecht K.H., Washburn L.L., and Eicher E.M. Migration of mesonephric cells into the mammalian gonad depends on Sry. Mech. Dev. 84 (1999) 127-131
11. Cederroth C.R., Pitetti J.L., Papaioannou M.D., and Nef S. Genetic programs that regulate testicular and ovarian development. Mol. Cell Endocrinol. 265-266 (2007) 3-9
12. Chan W.Y., Lee T.L., Wu S.M., Ruszczyk L., Alba D., Baxendale V., and Rennert O.M. Transcriptome analyses of male germ cells with serial analysis of gene expression (SAGE). Mol. Cell Endocrinol. 250 (2006) 8-19
13. Chan W.Y., Wu S.M., Ruszczyk L., Law E., Lee T.L., Baxendale V., Lap-Yin Pang A., and Rennert O.M. The complexity of antisense transcription revealed by the study of developing male germ cells. Genomics 87 (2006) 681-692
14. Cotinot C., Pailhoux E., Jaubert F., and Fellous M. Molecular genetics of sex determination. Semin. Reprod. Med. 20 (2002) 157-168
15. De Preter K., Barriot R., Speleman F., Vandesompele J., and Moreau Y. Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res. 36 (2008) e43
16. Diehn M., Sherlock G., Binkley G., Jin H., Matese J.C., Hernandez-Boussard T., Rees C.A., Cherry J.M., Botstein D., Brown P.O., and Alizadeh A.A. SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31 (2003) 219-223
17. DiNapoli L., and Capel B. SRY and the standoff in sex determination. Mol. Endocrinol. 22 (2008) 1-9
18. Gassei K., and Schlatt S. Testicular morphogenesis: Comparison of in vivo and in vitro models to study male gonadal development. Ann. N. Y. Acad. Sci. 1120 (2007) 152-167
19. Gattiker A., Niederhauser-Wiederkehr C., Moore J., Hermida L., and Primig M. The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. Nucleic Acids Res. 35 (2007) D457-D462
20. Ge X., and Wang S.M. Identifying nonspecific SAGE tags by context of gene expression. Methods Mol. Biol. 387 (2008) 199-204
21. Ge X., Jung Y.C., Wu Q., Kibbe W.A., and Wang S.M. Annotating nonspecific SAGE tags with microarray data. Genomics 87 (2006) 173-180
22. Getz G., Levine E., and Domany E. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. USA 97 (2000) 12079-12084
23. Grimmond S., Van Hateren N., Siggers P., Arkell R., Larder R., Soares M.B., de Fatima Bonaldo M., Smith L., Tymowska-Lalanne Z., Wells C., and Greenfield A. Sexually dimorphic expression of protease nexin-1 and vanin-1 in the developing mouse gonad prior to overt differentiation suggests a role in mammalian sexual development. Hum. Mol. Genet. 9 (2000) 1553-1560
24. Hosack D.A., Dennis Jr. G., Sherman B.T., Lane H.C., and Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol. 4 (2003) R70
25. Hu Y., Sun H., Drake J., Kittrell F., Abba M.C., Deng L., Gaddis S., Sahin A., Baggerly K., Medina D., and Aldaz C.M. From mice to humans: Identification of commonly deregulated genes in mammary cancer via comparative SAGE studies. Cancer Res. 64 (2004) 7748-7755
26. Huang da W., Sherman B.T., Tan Q., Kir J., Liu D., Bryant D., Guo Y., Stephens R., Baseler M.W., Lane H.C., and Lempicki R.A. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35 (2007) W169-W175
27. Lau Y.F., and Zhang J. Sry interactive proteins: Implication for the mechanisms of sex determination. Cytogenet. Cell Genet. 80 (1998) 128-132
28. Lee T.L., Alba D., Baxendale V., Rennert O.M., and Chan W.Y. Application of transcriptional and biological network analyses in mouse germ-cell transcriptomes. Genomics 88 (2006) 18-33
29. Lee T.L., Cheung H.H., Claus J., Sastry C., Singh S., Vu L., Rennert O., and Chan W.Y. GermSAGE: A comprehensive SAGE database for transcript discovery on male germ cell development. Nucleic Acids Res. 37 (2009) D891-D897
30. Lu H., Huang X., Zhang L., Guo Y., Cheng H., and Zhou R. Multiple alternative splicing of mouse Dmrt1 during gonadal differentiation. Biochem. Biophys. Res. Commun. 352 (2007) 630-634
31. McClive P.J., Hurley T.M., Sarraj M.A., van den Bergen J.A., and Sinclair A.H. Subtractive hybridisation screen identifies sexually dimorphic gene expression in the embryonic mouse gonad. Genesis 37 (2003) 84-90
32. McLaren A. Primordial germ cells in the mouse. Dev. Biol. 262 (2003) 1-15
33. Menke D.B., and Page D.C. Sexually dimorphic gene expression in the developing mouse gonad. Gene Expr. Patterns 2 (2002) 359-367
34. Morrish B.C., and Sinclair A.H. Vertebrate sex determination: Many means to an end. Reproduction 124 (2002) 447-457
35. Nef S., and Parada L.F. Hormones in male sexual development. Genes Dev. 14 (2000) 3075-3086
36. Nef S., Schaad O., Stallings N.R., Cederroth C.R., Pitetti J.L., Schaer G., Malki S., Dubois-Dauphin M., Boizet-Bonhoure B., Descombes P., Parker K.L., and Vassalli J.D. Gene expression during sex determination reveals a robust female genetic program at the onset of ovarian development. Dev. Biol. 287 (2005) 361-377
37. Neidhardt L., Gasca S., Wertz K., Obermayr F., Worpenberg S., Lehrach H., and Herrmann B.G. Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech. Dev. 98 (2000) 77-94
38. Nikolova G., and Vilain E. Mechanisms of disease: Transcription factors in sex determination-relevance to human disorders of sex development. Nat. Clin. Pract. Endocrinol. Metab. 2 (2006) 231-238
39. Palmer S.J., and Burgoyne P.S. In situ analysis of fetal, prepuberal and adult XX-XY chimaeric mouse testes: Sertoli cells are predominantly, but not exclusively, XY. Development 112 (1991) 265-268
40. Small C.L., Shima J.E., Uzumcu M., Skinner M.K., and Griswold M.D. Profiling gene expression during the differentiation and development of the murine embryonic gonad. Biol. Reprod. 72 (2005) 492-501
41. Smith L., Van Hateren N., Willan J., Romero R., Blanco G., Siggers P., Walsh J., Banerjee R., Denny P., Ponting C., and Greenfield A. Candidate testis-determining gene, Maestro (Mro), encodes a novel HEAT repeat protein. Dev. Dyn. 227 (2003) 600-607
42. Tohonen V., Osterlund C., and Nordqvist K. Testatin: A cystatin-related gene expressed during early testis development. Proc. Natl. Acad. Sci. USA 95 (1998) 14208-14213
43. van Ruissen F., Ruijter J.M., Schaaf G.J., Asgharnegad L., Zwijnenburg D.A., Kool M., and Baas F. Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics 6 (2005) 91
44. Velculescu V.E., Zhang L., Vogelstein B., and Kinzler K.W. Serial analysis of gene expression. Science 270 (1995) 484-487
45. Vong Q.P., Li Y., Lau Y.F., Dym M., Rennert O.M., and Chan W.Y. Structural characterization and expression studies of Dby and its homologs in the mouse. J. Androl. 27 (2006) 653-661
46. Wang H., Zheng H., and Azuaje F. Poisson-based self-organizing feature maps and hierarchical clustering for serial analysis of gene expression data. IEEE/ACM Trans Comput. Biol. Bioinform. 4 (2007) 163-175
47. Wang H., Zheng H., and Azuaje F. Clustering-based approaches to SAGE data mining. BioData Min. 1 (2008) 5
48. Wertz K., and Herrmann B.G. Large-scale screen for genes involved in gonad development. Mech. Dev. 98 (2000) 51-70
49. Wride M.A., Mansergh F.C., Adams S., Everitt R., Minnema S.E., Rancourt D.E., and Evans M.J. Expression profiling and gene discovery in the mouse lens. Mol. Vis. 9 (2003) 360-396
50. Wu S.M., Baxendale V., Chen Y., Pang A.L., Stitely T., Munson P.J., Leung M.Y., Ravindranath N., Dym M., Rennert O.M., and Chan W.Y. Analysis of mouse germ-cell transcriptome at different stages of spermatogenesis by SAGE: Biological significance. Genomics 84 (2004) 971-981