DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions

Genomics

Volumn 89, Issue 1, 2007, Pages 10-21

  El Mogharbel, Nisrine ^a   Wakefield, Matthew ^a,b   Deakin, Janine E ^a   Tsend Ayush, Enkhjargal ^a,c   Grützner, Frank ^a,c   Alsop, Amber ^a   Ezaz, Tariq ^a   Marshall Graves, Jennifer A ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^c UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

CNGs; DMRT genes; DMRT1; Gene annotation; Platypus; Sex determination

Indexed keywords

DSX AND MAB 3 RELATED TRANSCRIPTION FACTOR 1; DSX AND MAB 3 RELATED TRANSCRIPTION FACTOR 2; DSX AND MAB 3 RELATED TRANSCRIPTION FACTOR 3; TRANSCRIPTION FACTOR;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; EXON; FEMALE; GENE CLUSTER; GENE DELETION; GENE ISOLATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC ORGANIZATION; GENETIC REGULATION; GENOME ANALYSIS; MALE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLATYPUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SEX CHROMOSOME; SEXUAL DEVELOPMENT; SPECIES COMPARISON; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONSERVED SEQUENCE; DNA; DNA PRIMERS; FEMALE; GENES, REGULATOR; GENOME; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PLATYPUS; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

MAMMALIA; MONOTREMATA; VERTEBRATA;

EID: 33845247095     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.07.017     Document Type: Article

References (56)

1. Zarkower D. Establishing sexual dimorphism: conservation amidst diversity?. Nat. Rev. Genet. 2 (2001) 175-185
2. Volff J.N., Zarkower D., Bardwell V.J., and Schartl M. Evolutionary dynamics of the DM domain gene family in metazoans. J. Mol. Evol. 57 Suppl. 1 (2003) S241-S249
3. Brunner B., Hornung U., Shan Z., Nanda I., Kondo M., Zend-Ajusch E., et al. Genomic organization and expression of the doublesex-related gene cluster in vertebrates and detection of putative regulatory regions for DMRT1. Genomics 77 (2001) 8-17
4. Nanda I., Shan Z., Schartl M., Burt D.W., Koehler M., Nothwang H., et al. 300 million years of conserved synteny between chicken Z and human chromosome 9. Nat. Genet. 21 (1999) 258-259
5. Grutzner F., Rens W., Tsend-Ayush E., El-Mogharbel N., O'Brien P.C., Jones R.C., et al. In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature 432 (2004) 913-917
6. Matsuda M., Nagahama Y., Shinomiya A., Sato T., Matsuda C., Kobayashi T., et al. DMY is a Y-specific DM-domain gene required for male development in the medaka fish. Nature 417 (2002) 559-563
7. Nanda I., Kondo M., Hornung U., Asakawa S., Winkler C., Shimizu A., et al. A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11778-11783
8. Kondo M., Nanda I., Hornung U., Asakawa S., Shimizu N., Mitani H., et al. Absence of the candidate male sex-determining gene dmrt1b(Y) of medaka from other fish species. Curr. Biol. 13 (2003) 416-420
9. Guo Y., Cheng H., Huang X., Gao S., Yu H., and Zhou R. Gene structure, multiple alternative splicing, and expression in gonads of zebrafish Dmrt1. Biochem. Biophys. Res. Commun. 330 (2005) 950-957
10. Ottolenghi C., Fellous M., Barbieri M., and McElreavey K. Novel paralogy relations among human chromosomes support a link between the phylogeny of doublesex-related genes and the evolution of sex determination. Genomics 79 (2002) 333-343
11. Kim S., Kettlewell J.R., Anderson R.C., Bardwell V.J., and Zarkower D. Sexually dimorphic expression of multiple doublesex-related genes in the embryonic mouse gonad. Gene Expression Patterns 3 (2003) 77-82
12. Raymond C.S., Kettlewell J.R., Hirsch B., Bardwell V.J., and Zarkower D. Expression of Dmrt1 in the genital ridge of mouse and chicken embryos suggests a role in vertebrate sexual development. Dev. Biol. 215 (1999) 208-220
13. Moniot B., Berta P., Scherer G., Sudbeck P., and Poulat F. Male specific expression suggests role of DMRT1 in human sex determination. Mech. Dev. 91 (2000) 323-325
14. Pask A.J., Behringer R.R., and Renfree M.B. Expression of DMRT1 in the mammalian ovary and testis-From marsupials to mice. Cytogenet. Genome Res. 101 (2003) 229-236
15. Smith C.A., McClive P.J., Western P.S., Reed K.J., and Sinclair A.H. Conservation of a sex-determining gene. Nature 402 (1999) 601-602
16. Shetty S., Kirby P., Zarkower D., and Graves J.A.M. DMRT1 in a ratite bird: evidence for a role in sex determination and discovery of a putative regulatory element. Cytogenet. Genome Res. 99 (2002) 245-251
17. Kettlewell J.R., Raymond C.S., and Zarkower D. Temperature-dependent expression of turtle Dmrt1 prior to sexual differentiation. Genesis 26 (2000) 174-178
18. Sreenivasulu K., Ganesh S., and Raman R. Evolutionarily conserved DMRT1 encodes alternatively spliced transcripts and shows dimorphic expression during gonadal differentiation in the lizard, Calotes versicolor. Gene Expression Patterns 2 (2002) 51-60
19. Aoyama S., Shibata K., Tokunaga S., Takase M., Matsui K., and Nakamura M. Expression of Dmrt1 protein in developing and in sex-reversed gonads of amphibians. Cytogenet. Genome Res. 101 (2003) 295-301
20. Osawa N., Oshima Y., and Nakamura M. Molecular cloning of Dmrt1 and its expression in the gonad of Xenopus. Zool. Sci. 22 (2005) 681-687
21. Guan G., Kobayashi T., and Nagahama Y. Sexually dimorphic expression of two types of DM (Doublesex/Mab-3)-domain genes in a teleost fish, the tilapia (Oreochromis niloticus). Biochem. Biophys. Res. Commun. 272 (2000) 662-666
22. Marchand O., Govoroun M., D'Cotta H., McMeel O., Lareyre J., Bernot A., et al. DMRT1 expression during gonadal differentiation and spermatogenesis in the rainbow trout, Oncorhynchus mykiss. Biochim. Biophys. Acta 1493 (2000) 180-187
23. Veith A.M., Froschauer A., Korting C., Nanda I., Hanel R., Schmid M., et al. Cloning of the dmrt1 gene of Xiphophorus maculatus: dmY/dmrt1Y is not the master sex-determining gene in the platyfish. Gene 317 (2003) 59-66
24. Raymond C.S., Parker E.D., Kettlewell J.R., Brown L.G., Page D.C., Kusz K., et al. A region of human chromosome 9p required for testis development contains two genes related to known sexual regulators. Hum. Mol. Genet. 8 (1999) 989-996
25. Wang Y., and Gu X. Evolutionary patterns of gene families generated in the early stage of vertebrates. J. Mol. Evol. 51 (2000) 88-96
26. Meng A., Moore B., Tang H., Yuan B., and Lin S. A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. Development 126 (1999) 1259-1268
27. Winkler C., Hornung U., Kondo M., Neuner C., Duschl J., Shima A., et al. Developmentally regulated and non-sex-specific expression of autosomal dmrt genes in embryos of the medaka fish (Oryzias latipes). Mech. Dev. 121 (2004) 997-1005
28. Saude L., Lourenco R., Goncalves A., and Palmeirim I. terra is a left-right asymmetry gene required for left-right synchronization of the segmentation clock. Nat. Cell Biol. 7 (2005) 918-920
29. Seo K.W., Wang Y., Kokubo H., Kettlewell J.R., Zarkower D.A., and Johnson R.L. Targeted disruption of the DM domain containing transcription factor Dmrt2 reveals an essential role in somite patterning. Dev. Biol. 290 (2006) 200-210
30. Ottolenghi C., and McElreavey K. Deletions of 9p and the quest for a conserved mechanism of sex determination. Mol. Genet. Metab. 71 (2000) 397-404
31. Smith C.A., Hurley T.M., McClive P.J., and Sinclair A.H. Restricted expression of DMRT3 in chicken and mouse embryos. Gene Expression Patterns 2 (2002) 69-72
32. Ottolenghi C., Veitia R., Quintana-Murci L., Torchard D., Scapoli L., Souleyreau-Therville N., et al. The region on 9p associated with 46,XY sex reversal contains several transcripts expressed in the urogenital system and a novel doublesex-related domain. Genomics 64 (2000) 170-178
33. Dermitzakis E.T., Reymond A., and Antonarakis S.E. Conserved non-genic sequences-An unexpected feature of mammalian genomes. Nat. Rev. Genet. 6 (2005) 151-157
34. Margulies E.H., Chen C.W., and Green E.D. Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons. Trends Genet. 22 (2006) 187-193
35. Dermitzakis E.T., Reymond A., Scamuffa N., Ucla C., Kirkness E., Rossier C., et al. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302 (2003) 1033-1035
36. Woolfe A., Goodson M., Goode D.K., Snell P., McEwen G.K., Vavouri T., et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3 (2005) e7
37. Thomas J.W., Touchman J.W., Blakesley R.W., Bouffard G.G., Beckstrom-Sternberg S.M., Margulies E.H., et al. Comparative analyses of multispecies sequences from targeted genomic regions. Nature 424 (2003) 788-793
38. Duret L., Dorkeld F., and Gautier C. Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in posttranscriptional regulation of gene expression. Nucleic Acids Res. 21 (1993) 2315-2322
39. Van Laere A.S., Nguyen M., Braunschweig M., Nezer C., Collette C., Moreau L., et al. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425 (2003) 832-836
40. Wakefield M.J., and Graves J.A.M. Marsupials and monotremes sort genome treasures from junk. Genome Biol. 6 (2005) 218
41. Yeh R.F., Lim L.P., and Burge C.B. Computational inference of homologous gene structures in the human genome. Genome Res. 11 (2001) 803-816
42. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
43. Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
44. Mayor C., Brudno M., Schwartz J.R., Poliakov A., Rubin E.M., Frazer K.A., et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16 (2000) 1046-1047
45. Brudno M., Do C.B., Cooper G.M., Kim M.F., Davydov E., Green E.D., et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13 (2003) 721-731
46. Brudno M., Poliakov A., Salamov A., Cooper G.M., Sidow A., Rubin E.M., et al. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 14 (2004) 685-692
47. Ovcharenko I., Nobrega M.A., Loots G.G., and Stubbs L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 32 (2004) W280-W286
48. Margulies E.H., Maduro V.V., Thomas P.J., Tomkins J.P., Amemiya C.T., Luo M., et al. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 3354-3359
49. Gilbert N., and Labuda D. Evolutionary inventions and continuity of CORESINEs in mammals. J. Mol. Biol. 298 (2000) 365-377
50. Mathe C., Sagot M.F., Schiex T., and Rouze P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30 (2002) 4103-4117
51. Watson J.M., Spencer J.A., Riggs A.D., and Graves J.A.M. The X chromosome of monotremes shares a highly conserved region with the eutherian and marsupial X chromosomes despite the absence of X chromosome inactivation. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 7125-7129
52. Grutzner F., Deakin J., Rens W., El-Mogharbel N., and Graves J.A.M. The monotreme genome: a patchwork of reptile, mammal and unique features?. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 136 (2003) 867-881
53. Gruetzner F., Ashley T., Rowell D.M., and Graves J.A.M. How did the platypus get its sex chromosome chain? A comparison of meiotic multiples and sex chromosomes in plants and animals. Chromosoma 115 (2006) 75-88
54. El-Mogharbel N., Deakin J., Tsend-Ayush E., Pask A., and Graves J.A.M. Assignment of the DMRT1 gene to tammar wallaby chromosome 3p by fluorescence in situ hybridization. Cytogenet. Genome Res. 108 (2005) 362
55. Nanda I., Zend-Ajusch E., Shan Z., Grutzner F., Schartl M., Burt D.W., et al. Conserved synteny between the chicken Z sex chromosome and human chromosome 9 includes the male regulatory gene DMRT1: a comparative (re)view on avian sex determination. Cytogenet. Cell Genet. 89 (2000) 67-78
56. McQueen H.A., McBride D., Miele G., Bird A.P., and Clinton M. Dosage compensation in birds. Curr. Biol. 11 (2001) 253-257