Gene conversions in the growth hormone gene family of primates: Stronger homogenizing effects in the Hominidae lineage

Genomics

Volumn 98, Issue 3, 2011, Pages 173-181

  Petronella, Nicholas ^a   Drouin, Guy ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Gene conversion; Growth hormone genes; Human; Primates; Selective constraints

Indexed keywords

GROWTH HORMONE;

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; CSH1 GENE; CSH2 GENE; CSHL1 GENE; EXON; GC RICH SEQUENCE; GENE; GENE CONVERSION; GH1 GENE; GH2 GENE; HOMINID; HUMAN; INTRON; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RHESUS MONKEY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; GENE CONVERSION; GENOME, HUMAN; GROWTH HORMONE; HUMANS; MACACA MULATTA; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PAN TROGLODYTES; PHYLOGENY; PRIMATES; SEQUENCE ANALYSIS, DNA;

HOMINIDAE; PRIMATES;

EID: 80052145027     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.06.001     Document Type: Article

References (50)

1. Chen E.Y., Liao Y.C., Smith D.H., Barrera-Saldaña H.A., Gelinas R.E., Seeburg P.H. The human growth hormone locus: nucleotide sequence, biology, and evolution. Genomics 1989, 4:479-497.
2. Krawczak M., Chuzhanova N.A., Cooper D.N. Evolution of the proximal promoter region of the mammalian growth hormone gene. Gene 1999, 237:143-151.
3. Revol De Mendoza A., Esquivel Escobedo D., Martínez Dávila I., Barrera Saldaña H. Expansion and divergence of the GH locus between spider monkey and chimpanzee. Gene 2004, 336:185-193.
4. González Alvarez R., Revol de Mendoza A., Esquivel Escobedo D., Corrales Félix G., Rodríguez Sánchez I., González V., Dávila G., Cao Q., de Jong P., Fu Y.-X., Barrera Saldaña H.A. Growth hormone locus expands and diverges after the separation of New and Old World Monkeys. Gene 2006, 380:38-45.
5. Steiper M.E., Young N.M. Primate molecular divergence dates. Mol. Phylogenet. Evol. 2006, 41:384-394.
6. Wallis O.C., Zhang Y.P., Wallis M. Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change. J. Mol. Endocrinol. 2001, 26:249-258.
7. Wallis O.C., Wallis M. Characterisation of the GH gene cluster in a new-world monkey, the marmoset (Callithrix jacchus). J. Mol. Endocrinol. 2002, 29:87-89.
8. Adkins R.M., Nekrutenko A., Li W.H. Bushbaby growth hormone is much more similar to nonprimate growth hormone than to rhesus monkey and human growth hormones. Mol. Biol. Evol. 2001, 18:55-60.
9. Li Y., Ye C., Shi P., Zou X.J., Xiao R., Gong Y.Y., Zhang Y.P. Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids. J. Mol. Endocrinol. 2005, 35:399-409.
10. Ye C., Li Y., Shi P., Zhang Y.P. Molecular evolution of growth hormone gene family in old world monkeys and hominoids. Gene 2005, 350:183-192.
11. Chen J.M., Cooper D.N., Chuzhanova N., Férec C., Patrinos G.P. Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 2007, 8:762-775.
12. Bischof J.M., Chiang A.P., Scheetz T.E., Stone E.M., Casavant T.L., Sheffield V.C., Braun T.A. Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum. Mutat. 2006, 27:545-552.
13. Misra-Press A., Cooke N.E., Liebhaber S.A. Complex alternative splicing partially inactivates the human chorionic somatomammotropin-like (hCS-L) gene. J. Biol. Chem. 1994, 269:23220-23229.
14. Giordano M., Marchetti C., Chiorboli G.B., Richiardi P.M. Evidence for gene conversion in the generation of extensive polymorphism in the promoter of the growth hormone gene. Hum. Genet. 1997, 100:249-255.
15. Untergasser G., Hermann M., Rumpold H., Berger P. Complex alternative splicing of the GH-V gene in the human testis. Eur. J. Endocrinol. 1998, 139:424-427.
16. Harvey S., Kakebeeke M., Murphy A.E., Sanders E.J. Growth hormone in the nervous system: autocrine or paracrine roles in retinal function?. Can. J. Physiol. Pharmacol. 2003, 81:371-384.
17. Millar D.S., Lewis M.D., Horan M., Newsway V., Easter T.E., Gregory J.W., Fryklund L., Norin M., Crowne E.C., Davies S.J., Edwards P., Kirk J., Waldron K., Smith P.J., Phillips J.A., Scanlon M.F., Krawczak M., Cooper D.N., Procter A.M. Novel mutations of the growth hormone 1 (GH1) gene disclosed by modulation of the clinical selection criteria for individuals with short stature. Hum. Mutat. 2003, 21:424-440.
18. Sedman L., Padhukasahasram B., Kelgo P., Laan M. Complex signatures of locus-specific selective pressures and gene conversion on human growth hormone/chorionic somatomammotropin genes. Hum. Mutat. 2008, 29:1181-1193.
19. Wolf A., Millar D.S., Caliebe A., Horan M., Newsway V., Kumpf D., Steinmann K., Chee I.S., Lee Y.H., Mutirangura A., Pepe G., Rickards O., Schmidtke J., Schempp W., Chuzhanova N., Kehrer-Sawatzki H., Krawczak M., Cooper D.N. A gene conversion hotspot in the human growth hormone (GH1) gene promoter. Hum. Mutat. 2009, 30:239-247.
20. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
21. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
22. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
23. Sawyer S. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1989, 6:526-538.
24. Drouin G., Prat F., Ell M., Clarke G.D.P. Detecting and characterizing gene conversions between multigene family members. Mol. Biol. Evol. 1999, 16:1369-1390.
25. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:13757-13762.
26. Posada D. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol. Biol. Evol. 2002, 19:708-717.
27. Jeffreys J.A., May C.A. Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat. Genet. 2004, 36:151-156.
28. Graur D., Li W.-H. Fundamentals of molecular evolution 2000, Sinauer Associates, Sunderland. 2nd ed.
29. Hirt H., Kimelman J., Birnbaum M.J., Chen E.Y., Seeburg P.H., Eberhardt N.L., Barta A. The human growth hormone gene locus: structure, evolution, and allelic variations. DNA 1987, 6:59-70.
30. Shen P., Huang H.V. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 1986, 112:441-457.
31. Waldman A.S., Liskay R.M. Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology. Mol. Cell. Biol. 1988, 8:5350-5357.
32. Drouin G. Characterization of the gene conversions between the multigene family members of the yeast genome. J. Mol. Evol. 2002, 55:14-23.
33. Elliott B., Richardson C., Winderbaum J., Nickoloff J.A., Jasin M. Gene conversion tracts from double-strand break repair in mammalian cells. Mol. Cell. Biol. 1998, 18:93-101.
34. Lukacsovich T., Waldman A.S. Suppression of intrachromosomal gene conversion in mammalian cells by small degrees of sequence divergence. Genetics 1999, 151:1559-1568.
35. Shyue S.K., Li L., Chang B.H., Li W.-H. Intronic gene conversion in the evolution of human X-linked color vision genes. Mol. Biol. Evol. 1994, 11:548-551.
36. Noonan J.P., Grimwood J., Schmutz J., Dickson M., Myers R.M. Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res. 2004, 14:354-366.
37. Verrelli B.C., Tishkoff S.A. Signatures of selection and gene conversion associated with human color vision variation. Am. J. Hum. Genet. 2004, 75:363-375.
38. Benovoy D., Morris R.T., Morin A., Drouin G. Ectopic gene conversions increase the G+ C content of duplicated yeast and Arabidopsis genes. Mol. Biol. Evol. 2005, 22:1865-1868.
39. Morris R.T., Drouin G. Ectopic gene conversions in bacterial genomes. Genome 2007, 50:975-984.
40. Goldman A.S., Lichten M. The efficiency of meiotic recombination between dispersed sequences in Saccharomyces cerevisiae depends upon their chromosomal location. Genetics 1996, 144:43-55.
41. Fink G.R. Pseudogenes in yeast?. Cell 1987, 49:5-6.
42. Derr L.K., Strathern J.N., Garfinkel D.J. RNA-mediated recombination in S. cerevisiae. Cell 1991, 67:355-364.
43. Mourier T., Jeffares D.C. Eukaryotic intron loss. Science 2003, 300:1393.
44. Watahiki M., Yamamoto M., Yamakawa M., Tanaka M., Nakashima K. Conserved and unique amino acid residues in the domains of the growth hormones. Flounder growth hormone deduced from the cDNA sequence has the minimal size in the growth hormone prolactin gene family. J. Biol. Chem. 1989, 264:312-316.
45. Somers W., Ultsch M., De Vos A.M., Kossiakoff A.A. The X-ray structure of a growth hormone-prolactin receptor complex. Nature 1994, 372:478-481.
46. Procter A.M., Phillips J.A., Cooper D.N. The molecular genetics of growth hormone deficiency. Hum. Genet. 1998, 103:255-272.
47. Prager S., Wollmann H.A., Mergenthaler S., Mavany M., Eggermann K., Ranke M.B., Eggermann T. Characterization of genomic variants in CSH1 and GH2, two candidate genes for Silver-Russell syndrome in 17q24-q25. Genet. Test. 2003, 7:259-263.
48. Cacciari E., Pirazzoli P., Gualandi S., Baroncini C., Baldazzi L., Trevisani B., Capelli M., Zucchini S., Balsamo A., Cicognani A., Bernardi F. Molecular study of human growth hormone gene cluster in three families with isolated growth hormone deficiency and similar phenotype. Eur. J. Pediatr. 1994, 153:635-641.
49. Alsat E., Guibourdenche J., Luton D., Frankenne F., Evain-Brion D. Human placental growth hormone. Am. J. Obstet. Gynecol. 1997, 177:1526-1534.
50. McIntyre H.D., Serek R., Crane D.I., Veveris-Lowe T., Parry A., Johnson S., Leung K.C., Ho K.K., Bougoussa M., Hennen G., Igout A., Chan F.Y., Cowley D., Cotterill A., Barnard R. Placental growth hormone (GH), GH-binding protein, and insulin-like growth factor axis in normal, growth-retarded, and diabetic pregnancies: correlations with fetal growth. J. Clin. Endocrinol. Metab. 2000, 85:1143-1150.