Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: Evidence for nonrandom gene order

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Divina, Petr ^a   Vlček, Čestmír ^a   Strnad, Petr ^a   Pačes, Václav ^a   Forejt, Jiří ^a  

^a INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE MAPPING; GENE ORDER; GENETIC ANALYSIS; GERM CELL; INTERMETHOD COMPARISON; MALE; MEIOSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; SERIAL ANALYSIS OF GENE EXPRESSION; SOMATIC CELL; TESTIS CELL; THEORY; TISSUE SPECIFICITY; X CHROMOSOME INACTIVATION; X CHROMOSOME LINKAGE;

EID: 25444465171     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-29     Document Type: Article

References (59)

1. Doolittle WF, Sapienza C: Selfish genes, the phenotype paradigm and genome evolution. Nature 1980, 284:601-603.
2. Orgel LE, Crick FH, Sapienza C: Selfish DNA. Nature 1980, 288:645-646.
3. Watson D, Jacombs AS, Loebel DA, Robinson ES, Johnston PG: Single nucleotide primer extension (SNuPE) analysis of the G6PD gene in somatic cells and oocytes of a kangaroo (Macropus robustus). Genet Res 2000, 75:269-274.
4. Handel MA, Hunt PA: Sex-chromosome pairing and activity during mammalian meiosis. Bioessays 1992, 14:817-822.
5. McCarrey JR, Watson C, Atencio J, Ostermeier GC, Marahrens Y, Jaenisch R, Krawetz SA: X-chromosome inactivation during spermatogenesis is regulated by an Xist/Tsix-independent mechanism in the mouse. Genesis 2002, 34:257-266.
6. Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD: The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet 2004, 36:642-646.
7. Lifschytz E, Lindsley DL: The role of X-chromosome inactivation during spermatogenesis (Drosophila-allocycly-chromosome evolution-male sterility-dosage compensation). Proc Natl Acad Sci U S A 1972, 69:182-186.
8. Davis TL, Yang GJ, McCarrey JR, Bartolomei MS: The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet 2000, 9:2885-2894.
9. Liu J, Yu S, Litman D, Chen W, Weinstein LS: Identification of a methylation imprint mark within the mouse Gnas locus. Mol Cell Biol 2000, 20:5808-5817.
10. Cooke HJ, Saunders PT: Mouse models of male infertility. Nat Rev Genet 002, 3:790-801.
11. de Rooij DG, de Boer P: Specific arrests of spermatogenesis in genetically modified and mutant mice. Cytogenet Genome Res 2003, 103:267-276.
12. Ashley T: X-Autosome translocations, meiotic synapsis, chromosome evolution and speciation. Cytogenet Genome Res 2002, 96:33-39.
13. Forejt J: Hybrid sterility in the mouse. Trends Genet 1996, 12:412-417.
14. Orr HA, Presgraves DC: Speciation by postzygotic isolation: forces, genes and molecules. Bioessays 2000, 22:1085-1094.
15. Storchova R, Gregorova S, Buckiova D, Kyselova V, Divina P, Forejt J: Genetic analysis of X-linked hybrid sterility in the house mouse. Mammalian Genome 2004, 15:515-524.
16. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 1995, 270:484-487.
17. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, et al.: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
18. Singer JB, Hill AE, Burrage LC, Olszens KR, Song J, Justice M, O'Brien WE, Conti DV, Witte JS, Lander ES, Nadeau JH: Genetic dissection of complex traits with chromosome substitution strains of mice. Science 2004, 304:445-448.
19. O'Shaughnessy PJ, Fleming L, Baker PJ, Jackson G, Johnston H: Identification of Developmentally-Regulated Genes in the Somatic Cells of the Mouse Testis Using Serial Analysis of Gene Expression. Biol Reprod 2003, 69:797-808.
20. NCBI Gene Expression Omnibus [http://www.ncbi.nlm.nih.gov/geo/]
21. Mouse SAGE Site [http://mouse.biomed.cas.cz/sage/]
22. Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF: SAGEmap: a public gene expression resource. Genome Res 2000, 10:1051-1060.
23. SAGEmap database [ftp://ftp.ncbi.nlm.nih.gov/pub/sage/]
24. Divina P, Forejt J: The Mouse SAGE Site: database of public mouse SAGE libraries. Nucleic Acids Res 2004, 32:D482-3.
25. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32 (Database issue):D258-61.
26. Gene Ontology Project [http://www.geneontology.org/]
27. Sutcliffe MJ, Darling SM, Burgoyne PS: Spermatogenesis in XY, XYSxra and XOSxra mice: a quantitative analysis of spermatogenesis throughout puberty. Mol Reprod Dev 1991, 30:81-89.
28. Baross A, Schertzer M, Zuyderduyn SD, Jones SJ, Marra MA, Lansdorp PM: Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer 2004, 39:298-310.
29. Lercher MJ, Urrutia AO, Hurst LD: Evidence that the human X chromosome is enriched for male-specific but not femalespecific genes. Mol Biol Evol 2003, 20:1113-1116.
30. Wang PJ, McCarrey JR, Yang F, Page DC: An abundance of Xlinked genes expressed in spermatogonia. Nat Genet 2001, 27:422-426.
31. Huminiecki L, Lloyd AT, Wolfe KH: Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases. BMC Genomics 2003, 4:31.
32. Yao J, Chiba T, Sakai J, Hirose K, Yamamoto M, Hada A, Kuramoto K, Higuchi K, Mori M: Mouse testis transcriptome revealed using serial analysis of gene expression. Mamm Genome 2004, 15:433-451.
33. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004, 101:6062-6067.
34. GNF Mouse Atlas v2 [http://symatlas.gnf.org/]
35. Pravenec M, Zidek V, Landa V, Simakova M, Mlejnek P, Kazdova L, Bila V, Krenova D, Kren V: Genetic analysis of "metabolic syndrome" in the spontaneously hypertensive rat. Physiol Res 2004, 53 Suppl 1:S15-22.
36. Farrall M: Quantitative genetic variation: a post-modern view. Hum Mol Genet 2004, 13 Spec No 1:R1-7.
37. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE: Using the transcriptome to annotate the genome. Nat Biotechnol 2002, 20:508-512.
38. Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y: 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 2004, 101:11701-6.
39. Hurst LD, Pal C, Lercher MJ: The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 2004, 5:299-310.
40. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000, 18:630-634.
41. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, Kim SK: A global profile of germline gene expression in C. elegans. Mol Cell 2000, 6:605-616.
42. Betran E, Thornton K, Long M: Retroposed new genes out of the X in Drosophila. Genome Res2002, 12:1854-1859.
43. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI: Large clusters of co-expressed genes in the Drosophila genome. Nature 2002, 420:666-669.
44. Forejt J: X-Y involvment in male sterility caused by autosome translocations - a hypothesis. In Genetic control of Gamete Production and Function Edited by: Fraccaro M and Rubin B. , Academic Press, New York; 1982:135-151.
45. Turner JM, Mahadevaiah SK, Elliott DJ, Garchon HJ, Pehrson JR, Jaenisch R, Burgoyne PS: Meiotic sex chromosome inactivation in male mice with targeted disruptions of Xist. J Cell Sci 2002, 115:4097-4105.
46. Handel MA: The XY body: a specialized meiotic chromatin domain. Exp Cell Res 2004, 296:57-63.
47. Rice WR: Sex-Chromosomes and the Evolution of Sexual Dimorphism. Evolution 1984, 38:735-742.
48. Spellman PT, Rubin GM: Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 2002, 1:5.
49. Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH: The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.b] Genome Res 2003, 13:1998-2004.
50. Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31:180-183.
51. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291:1289-1292.
52. Lercher MJ, Urrutia AO, Pavlicek A, Hurst LD: A unification of mosaic structures in the human genome. Hum Mol Genet 2003, 12:2411-2415.
53. SAGE method homepage [http://www.sagenet.org/]
54. Patefield WM: An efficient method of generating random RxC tables with given row and column totals. Applied Statistics 1981, 30:91-97.
55. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
56. UCSC Genome Browser expression database [http://hgdownload.cse.ucsc.edu/goldenPath/hgFixed/database/]
57. NCBI mouse genome assembly [ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/maps/mapview/]
58. NCBI mouse Reference Sequences [ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_prot/]
59. The R Project for Statist [http://www.r-project.org/]