The chicken z chromosome is enriched for genes with preferential expression in ovarian somatic cells

Journal of Molecular Evolution

Volumn 70, Issue 2, 2010, Pages 129-136

  Mořkovský, Libor ^a   Storchová, Radka ^a   Plachý, Jiří ^b   Ivánek, Robert ^b   Divina, Petr ^b   Hejnar, Jiří ^b  

^a CHARLES UNIVERSITY   (Czech Republic)

^b INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

Author keywords

Birds; Gene expression; Meiotic sex chromosome inactivation; Oogenesis; Sexual antagonism; Z chromosome

Indexed keywords

ANIMAL; ANTIBODY SPECIFICITY; ARTICLE; CHI SQUARE DISTRIBUTION; CHICKEN; CYTOLOGY; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC SELECTION; GENETICS; GRANULOSA CELL; MEIOSIS; METABOLISM; MUTATION; OOCYTE DEVELOPMENT; OVARY; PHYSIOLOGY; SEX CHROMOSOME; STATISTICAL MODEL;

ANIMALS; CHI-SQUARE DISTRIBUTION; CHICKENS; DATABASES, GENETIC; DOSAGE COMPENSATION, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GRANULOSA CELLS; LINEAR MODELS; MEIOSIS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OOGENESIS; ORGAN SPECIFICITY; OVARY; SELECTION, GENETIC; SEX CHROMOSOMES;

AVES; MAMMALIA;

EID: 77649180491     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9315-5     Document Type: Article

References (48)

1. Arnold AP, Itoh Y, Melamed E (2008) A bird's-eye view of sex chromosome dosage compensation. Annu Rev Genom Hum Genet 9:109-127
2. Arunkumar KP, Mita K, Nagaraju J (2009) Silkworm Z chromosome is enriched in testis-specific genes. Genetics 182:493-501
3. Baker BS, Gorman M, Marin I (1994) Dosage compensation in Drosophila. Annu Rev Genet 28:491-521
4. Betran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12:1854-1859 (Pubitemid 35469934)
5. Connallon T, Knowles LL (2005) Intergenomic conflict revealed by patterns of sex-biased gene expression. Trends Genet 21:495-499 (Pubitemid 41132583)
6. Dai M, Wang P, Boyd AD, Rostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33:e175 (Pubitemid 41806403)
7. Divina P, Vlcek C, Strnad P, Paces V, Forejt J (2005) Global transcriptome analysis of the C57BL/6 J mouse testis by SAGE: Evidence for nonrandom gene order. BMC Genom 6:29
8. Elis S, Batellier F, Couty I, Balzergue S, Martin-Magniette ML, Monget P, Blesbois E, Govoroun MS (2008) Search for the genes involved in oocyte maturation and early embryo development in the hen. BMC Genom 9:110 (Pubitemid 351546721)
9. Ellegren H, Parsch J (2007) The evolution of sex-biased genes and sex-biased gene expression. Nat Rev Genet 8:689-698 (Pubitemid 47281991)
10. Ellegren H, Hultin-Rosenberg L, Brunstrom B, Dencker L, Kultima K, Scholz B (2007) Faced with inequality: Chicken do not have a general dosage compensation of sex-linked genes. BMC Biol 5:40 (Pubitemid 350226887)
11. Emerson JJ, Kaessmann H, Betran E, Long M. (2004) Extensive gene traffic on the mammalian X chromosome. Science 303:537-540 (Pubitemid 38120854)
12. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5:R80
13. Gurbich TA, Bachtrog D (2008) Gene content evolution on the X chromosome. Curr Opin Genet Dev 18:493-498
14. Hense W, Baines JF, Parsch J (2007) X chromosome inactivation during Drosophila spermatogenesis. PLoS Biol 5:e273
15. Hurst LD, Randerson JP (1999) An exceptional chromosome. Trends Genet 15:383-385
16. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264
17. Itoh Y, Melamed E, Yang X, Kampf K, Wang S, Yehya N, Van Nas A, Replogle K, Band MR, Clayton DF, Schadt EE, Lusis AJ, Arnold AP (2007) Dosage compensation is less effective in birds than in mammals. J Biol 6:2 (Pubitemid 46474683)
18. Kaiser VB, Ellegren H (2006) Nonrandom distribution of genes with sex-biased expression in the chicken genome. Evolution 60:1945-1951 (Pubitemid 44808243)
19. Kelly WG, Schaner CE, Dernburg AF, Lee MH, Kim SK, Villeneuve AM, Reinke V (2002) X-chromosome silencing in the germline of C. elegans. Development 129:479-492
20. Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD (2004) The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet 36:642-646
21. Lercher MJ, Urrutia AO, Hurst LD (2003) Evidence that the human X chromosome is enriched for male-specific but not femalespecific genes. Mol Biol Evol 20:1113-1116
22. Mank JE (2009) Sex chromosomes and the evolution of sexual dimorphism: Lessons from the genome. Am Nat 173:141-150
23. Mank JE, Ellegren H (2009a) All dosage compensation is local: Gene-by-gene regulation of sex-biased expression on the chicken Z chromosome. Heredity 102:312-320
24. Mank JE, Ellegren H (2009b) Sex-linkage of sexually antagonistic genes is predicted by female, but not male, effects in birds. Evolution 63:1464-1472
25. MAQC Consortium (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161
26. McKee BD, Handel MA (1993) Sex chromosomes, recombination, and chromatin conformation. Chromosoma 102:71-80
27. Melamed E, Arnold AP (2007) Regional differences in dosage compensation on the chicken Z chromosome. Genome Biol 8:R202 (Pubitemid 351895463)
28. Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JMA (2008) The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nat Genet 40:794-799
29. Namekawa SH, Lee JT (2009) XY and ZW: Is meiotic sex chromosome inactivation the rule in evolution? PLoS Genet 5 :e1000493
30. Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT (2006) Postmeiotic sex chromatin in the male germline of mice. Curr Biol 16:660-667
31. Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B (2003) Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299:697-700 (Pubitemid 36159482)
32. Potrzebowski L, Vinckenbosch N, Marques AC, Chalmel F, Jegou B, Kaessmann H (2008) Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol 6:e80 (Pubitemid 351649305)
33. Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL (2003) Sexdependent gene expression and evolution of the Drosophila transcriptome. Science 300:1742-1745 (Pubitemid 36712569)
34. Reinke V, Gil IS, Ward S, Kazmer K (2004) Genome-wide germlineenriched and sex-biased expression profiles in Caenorhabditis elegans. Development 131:311-323
35. RiceWR(1984)Sexchromosomesandtheevolutionofsexualdimorphism.Evolution38: 735-742(Pubitemid16277746)
36. Rogers DW, Carr M, Pomiankowski A (2003) Male genes: X-pelled or X-cluded? Bioessays 25:739-741
37. Saifi GM, Chandra HS (1999) An apparent excess of sex- and reproduction-related genes on the human X chromosome. Proc Biol Sci 266:203-209
38. Schoenmakers S, Wassenaar E, Hoogerbrugge JW, Laven JS, Grootegoed JA, Baarends WM (2009) Female meiotic sex chromosome inactivation in chicken. PLoS Genet 5:e1000466
39. Smyth G (2005) Limma: Linear models for microarray data. In: Gentleman R, Carey VJ, Huber W, Dudoit S, Irizarry RA (eds) Bioinformatics and computational biology solutions using R and bioconductor. Springer, New York, pp 397-420
40. Storchova R, Divina P (2006) Nonrandom representation of sexbiased genes on chicken Z chromosome. J Mol Evol 63:676-681 (Pubitemid 44833230)
41. Sturgill D, Zhang Y, Parisi M, Oliver B (2007) Demasculinization of X chromosomes in the Drosophila genus. Nature 450:238-241
42. Turner JM (2007) Meiotic sex chromosome inactivation. Development 134:1823-1831
43. van Doom GS (2009) Intralocus sexual conflict. Ann N Y Acad Sci 1168:52-71
44. Vibranovski MD, Zhang Y, Long M (2009) Out of the X chromosomal gene movement in the Drosophila genus. Genome Res 19:897-903
45. Vicoso B, Charlesworth B (2006) Evolution on the X chromosome: Unusual patterns and processes. Nat Rev Genet 7:645-653 (Pubitemid 44100521)
46. Vicoso B, Charlesworth B (2009) The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? J Mol Evol 68:576-583
47. Wang PJ, McCarrey JR, Yang F, Page DC (2001) An abundance of X-linked genes expressed in spermatogonia. Nat Genet 27: 422-426 (Pubitemid 32268424)
48. Zha X, Xia Q, Duan J, Wang C, He N, Xiang Z (2008) Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx morí. Insect Biochem Mol Biol 39:315-321