No accelerated evolution of 3′UTR region in human for brain-expressed genes

Gene

Volumn 383, Issue , 2006, Pages 38-42

  Li, Yi ^a,b,c   Su, Bing ^a,b  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c QUJING NORMAL UNIVERSITY   (China)

Author keywords

Gene expression; Neutral evolution; Rhesus monkey; Substitution rates

Indexed keywords

3' UNTRANSLATED REGION; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN; BRAIN DEVELOPMENT; COGNITION; CONTROLLED STUDY; DNA DETERMINATION; DNA LIBRARY; EVOLUTION; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; MALE; MOUSE; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREFRONTAL CORTEX; PRIORITY JOURNAL; RHESUS MONKEY; STATISTICAL SIGNIFICANCE;

3' UNTRANSLATED REGIONS; ANIMALS; BRAIN; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE LIBRARY; HUMANS; MACACA MULATTA; PAN TROGLODYTES; PRIMATES; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY;

MACACA MULATTA; PAN; PAN TROGLODYTES; PRIMATES;

EID: 33750086359     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.06.024     Document Type: Article

References (42)

1. Arriza J.L., Fairman W.A., Wadiche J.I., Murdoch G.H., Kavanaugh M.P., and Amara S.G. Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex. J. Neurosci. 14 (1994) 5559-5569
2. Bashirullah A., Cooperstock R.L., and Lipshitz H.D. Spatial and temporal control of RNA stability. Proc. Natl. Acad. Sci. 98 (2001) 7025-7028
3. Caceres M., et al. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl. Acad. Sci. 100 (2003) 13030-13035
4. Chen F.C., and Li W.-H. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68 (2001) 444-456
5. Dorus S., et al. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119 (2004) 1027-1040
6. Duret L., and Mouchiroud D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17 (2000) 68-74
7. Ebersberger I., Metzler D., Schwarz C., and Paabo S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70 (2002) 1490-1497
8. Enard W., et al. Intra- and interspecific variation in primate gene expression patterns. Science 296 (2002) 340-343
9. Ewa A.G., Wilczynska A., and Siedlecki J.A. Regulatory Functions of 3′UTRs. Biochem. Biophys. Res. Commun. 288 (2001) 291-295
10. Fujiyama A., et al. Construction and analysis of a human-chimpanzee comparative clone map. Science 295 (2002) 131-134
11. Gavis E.R., Lunsford L., Bergsten S.E., and Lehmann R. A conserved 90 nucleotide element mediates translational repression of nanosRNA. Development 122 (1996) 2791-2800
12. Goldberg-Cohen I., Furneauxb H., and Levy A.P. A 40-bp RNA element that mediates stabilization of vascular endothelial growth factor mRNA by HuR. J. Biol. Chem. 277 16 (2002) 13635-13640
13. Goodman M., et al. Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9 (1998) 585-598
14. Gu J., and Gu X. Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 19 (2003) 63-65
15. Hellmann I., Zollner S., Enard W., Ebersberger I., Nickel B., and Paabo S. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13 (2003) 831-837
16. Jansen R.P. mRNA localization: message on the move. Nat. Rev., Mol. Cell Biol. 2 (2001) 247-256
17. Kawamura S., Tanabe H., Watanabe Y., Kurosaki K., Saitou N., and Ueda S. Evolutionary rate of immunoglobulin alpha noncoding region is greater in hominoids than in Old World monkeys. Mol. Biol. Evol. 8 (1991) 743-752
18. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
19. King M.C., and Wilson A.C. Evolution at two levels in humans and chimpanzees. Science 188 (1975) 107-116
20. Kuersten S., and Goodwin E.B. The power of the 3′ UTR: translational control and development. Nat. Rev., Genet. 4 (2003) 626-637
21. Kumar S., and Hedges S.B. A molecular timescale for vertebrate evolution. Nature 392 (1998) 917-920
22. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
23. Li W.-H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
24. Li W.-H. Molecular Evolution (1997), Sinauer Associates, Sunderland, Mass
25. Makalowski W., and Boguski M.S. Evolutionary parameters of the transcribed mammalian genome: an analysis of 2820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. 95 (1998) 9407-9412
26. Mignone F., Gissi C., Liuni S., and Pesole G. Untranslated regions of mRNAs. Genome Biol. 3 (2002) 0004.1-0004.10
27. Osada N., et al. Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. BMC Genomics 3 (2002) 36
28. Osada N., et al. Substitution rate and structural divergence of 5′UTR evolution: comparative analysis between human and cynomolgus monkey cDNAs. Mol. Biol. Evol. 22 10 (2005) 1976-1982
29. Pamilo P., and Bianchi N.O. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol. Biol. Evol. 10 (1993) 271-281
30. Pruitt K.D., Tatusova T., and Maglott D.R. NCBI Reference Sequence project: update and current status. Nucleic Acids Res. 31 (2003) 34-37
31. Savatier P., Trabuchet G., Chebloune Y., Faure C., Verdier G., and Nigon V.M. Nucleotide sequence of the deltabeta-globin intergenic segment in the macaque: structure and evolutionary rates in higher primates. J. Mol. Evol. 24 (1987) 297-308
32. Springer M.S., Murphy W.J., Eizirik E., and O'Brien S.J. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. 100 (2003) 1056-1061
33. Stauffer R.L., Walker A., Ryder O.A., Lyons-Weiler M., and Hedges S.B. Human and ape molecular clocks and constraints on paleontological hypotheses. J. Heredity 92 (2002) 469-474
34. Tajima F. Statistical analysis of DNA polymorphism. J. Genet. 68 (1993) 567-595
35. Thompson J.D., Higgins D.G., and 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. 22 (1994) 4673-4680
36. Van Der Velden A.W., and Thomas A.A. The role of the 5′ untranslated region of an mRNA in translation regulation during development. Int. J. Biochem. Cell Biol. 31 (1999) 87-106
37. Wang H.Y., Tang H., Shen C.K., and Wu C.-I. Rapidly evolving genes in human. I. The glycophorins and their possible role in evading malaria parasites. Mol. Biol. Evol. 20 (2003) 1795-1804
38. Wittkopp P.J., Haerum B.K., and Clark A.G. Evolutionary changes in cis and trans gene regulation. Nature 430 (2004) 85-88
39. Xia X., and Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Heredity 92 (2001) 371-373
40. Yu, X.J., Zheng H.K., Wang, J., Wang, W., Su, B., in press. Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. Genomics.
41. Zhang L., and Li W.-H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21 2 (2004) 236-239
42. Zhang J.Z., Webb D.M., and Podlaha O. Accelerated protein evolution and origins of human-specific features: FOXP2 as an example. Genetics 162 (2002) 1825-1835