Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans

Genome Research

Volumn 13, Issue 12, 2003, Pages 2651-2657

  Cutter, Asher D ^a   Payseur, Bret A ^a   Salcedo, Tovah ^a   Estes, Anne M ^a   Good, Jeffrey M ^a   Wood, Elizabeth ^a   Hartl, Thomas ^b   Maughan, Heather ^a   Strempel, Jannine ^a   Wang, Baomin ^a   Bryan, Anthony C ^a   Dellos, Melissa ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Arizona   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA;

AMINO ACID COMPOSITION; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; GENOTYPE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS;

ANIMALS; CAENORHABDITIS ELEGANS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENES, HELMINTH; GENOME; GENOTYPE; PHENOTYPE; RNA INTERFERENCE; RNA, HELMINTH;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; INVERTEBRATA; NEMATODA;

EID: 10744225908     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1659203     Document Type: Article

References (45)

1. Akashi, H. and Gojobori, T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. 99: 3695-3700.
2. Andersson, M. 1994. Sexual selection. Princeton University Press, Princeton, NJ.
3. Barnes, T.M., Kohara, Y., Coulson, A., and Hekimi, S. 1995. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141: 159-179.
4. Barrai, I., Volinia, S., and Scapoli, C. 1995. The usage of oligopeptides in proteins correlates negatively with molecular-weight. Int. J. Peptide Prot. Res. 45: 326-331.
5. Bird, A. 2002. DNA methylation patterns and epigenetic memory. Genes & Dev. 16: 6-21.
6. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
7. Carmi, I. and Meyer, B.J. 1999. The primary sex determination signal of Caenorhabditis elegans. Genetics 152: 999-1015.
8. Castillo-Davis, C.I. and Hartl, D.L. 2002. Genome evolution and developmental constraint in Caenorhabditis elegans. Mol. Biol. Evol. 19: 728-735.
9. Civetta, A. and Singh, R.S. 1998. Sex-related genes, directional sexual selection, and speciation. Mol. Biol. Evol. 15: 901-909.
10. Coulthart, M.B. and Singh, R.S. 1988. High-level of divergence of male-reproductive-tract proteins, between Drosophila melanogaster and its sibling species, Drosophila simulans. Mol. Biol. Evol. 5: 182-191.
11. Cutter, A.D. and Payseur, B.A. 2003. Selection at linked sites in the partial selfer Caenorhabditis elegans. Mol. Biol. Evol. 20: 665-673.
12. Dufton, M.J. 1997. Genetic code synonym quotas and amino acid complexity: Cutting the cost of proteins? J. Theor. Biol. 187: 165-173.
13. Ferris, P.J. Pavlovic, C., Fabry, S., and Goodenough, U.W. 1997. Rapid evolution of sex-related genes in Chlamydomonas. Proc. Natl. Acad. Sci. 94: 8634-8639.
14. Fire, A., Xu, S.Q., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
15. Fraser, A.G., Kamath, R.S., Zipperlen, P., Martinez-Campos, M., Sohrmann M., and Ahringer, J. 2000. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325-330.
16. Gonczy, P., Echeverri, C., Oegema, K., Coulson, A., Jones, S.J.M., Copley, R.R., Duperon, J., Oegema, J., Brehm, M., Cassin, E., et al. 2000. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408: 331-336.
17. Hill, A.A., Hunter, C.P., Tsung, B.T., Tucker-Kellogg, G., and Brown, E.L. 2000. Genomic analysis of gene expression in C. elegans. Science 290: 809-812.
18. Ikemura, T. 1985. Codon usage and transfer-RNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2: 13-34.
19. Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., et al. 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
20. Kimura, M. 1983. Rare variant alleles in the light of the neutral theory. Mol. Biol. Evol. 1: 84-93.
21. Koopman, P., Munsterberg, A., Capel, B., Vivian, N., and Lovellbadge, R. 1990. Expression of a candidate sex-determining gene during mouse testis differentiation. Nature 348: 450-452.
22. Lee, Y.H., Ota, T., and Vacquier, V.D. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12: 231-238.
23. Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
24. Li, W.-H., Wu, C.I., and Luo, C.C. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
25. Marais, G. and Duret, L. 2001. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J. Mol. Evol. 52: 275-280.
26. Marais, G., Mouchiroud, D., and Duret, L. 2001. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc. Natl. Acad. Sci. 98: 5688-5692.
27. Moriyama, E.N. and Powell, J.R. 1998. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26: 3188-3193.
28. Pamilo, P. and Bianchi, N.O. 1993. Evolution of the zft and zfy genes - Rates and interdependence between the genes. Mol. Biol. Evol. 10: 271-281.
29. Rice, W.R. and Holland, B. 1997. The enemies within: Intergenomic conflict, interlocus contest evolution (ICE), and the intraspecific Red Queen. Behav. Ecol. Sociobiol. 41: 1-10.
30. Rivera, M.C., Jain, R., Moore, J.E., and Lake, J.A. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. 95: 6239-6244.
31. Sayre, F.W., Hansen, E.L., and Yarwood, E.A. 1963. Biochemical aspects of nutrition of Caenorhabditis briggsae. Exp. Parasitol. 13: 98-107.
32. Seligmann, H. 2003. Cost-minimization of amino acid usage. J. Mol. Evol. 56: 151-161.
33. Sharp, P.M. and Bradnam, K.R. 1997. Codon usage in C. elegans. In C. elegans II (ed. D.L. Riddle, T. Blumenthal, B.J. Meyer, and J.R. Priess), pp. 1053-1057. Cold Spring Harbor Laboratory Press, New York.
34. Stenico, M., Lloyd, A.T., and Sharp, P.M. 1994. Codon usage in Caenorhabditis elegans - Delineation of translational selection and mutational biases. Nucleic Acids Res. 22: 2437-2446.
35. Subramanian, S. and Kumar, S. 2003. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13: 838-844.
36. Swanson, W.J. and Vacquier, V.D. 2002. The rapid evolution of reproductive proteins. Nat. Rev. Genet. 3: 137-144.
37. Swanson, W.J., Zhang, Z.H., Wolfner, M.F., and Aquadro, C.F. 2001. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. 98: 2509-2514.
38. Timmons, L. and Fire, A. 1998. Specific interference by ingested dsRNA. Nature 395: 854.
39. Torshin, I.Y. 2001. Clustering amino acid contents of protein domains: Biochemical functions of proteins and implications for origin of biological macromolecules. Front. Biosci. 6: A1-A12.
40. Vanfleteren, J.R. 1973. Amino-acid requirements of free-living nematode Caenorhabditis briggsae. Nematologica 19: 93-99.
41. Walhout, A.J.M., Reboul, J., Shtanko, O., Bertin, N., Vaglio, P., Ge, H., Lee, H., Doucette-Stamm, L., Gunsalus, K.C., Schetter, A.J., et al. 2002. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12: 1952-1958.
42. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
43. Wilson, A.C., Carlson, S.S., and White, T.J., 1977. Biochemical evolution. Annu. Rev. Biochem. 46: 573-639.
44. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
45. Wyckoff, G.J., Wang, W., and Wu, C.I. 2000. Rapid evolution of male reproductive genes in the descent of man. Nature 403: 304-309.