Small fitness effect of mutations in highly conserved non-coding regions

Human Molecular Genetics

Volumn 14, Issue 15, 2005, Pages 2221-2229

  Kryukov, Gregory V ^a   Schmidt, Steffen ^a   Sunyaev, Shamil ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL LINEAGE; CONTROLLED STUDY; GENE FREQUENCY; GENE MUTATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC EPISTASIS; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN; HUMAN VERSUS NONHUMAN DATA; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; POPULATION SIZE; PRIMATE; PRIORITY JOURNAL; RODENT; UNTRANSLATED REGION;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; GENOME; HUMANS; INTRONS; MICE; MODELS, GENETIC; MUTATION; PAN TROGLODYTES; POLYMORPHISM, GENETIC; RATS; SELECTION (GENETICS);

PRIMATES; RODENTIA;

EID: 26444606420     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddi226     Document Type: Article

References (41)

1. Mouse Genome Sequencing Consortium. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
2. Kondrashov, A.S. and Shabalina, S.A. (2002) Classification of common conserved sequences in mammmalian intergenic regions. Hum. Mol. Genet., 11, 669-674.
3. Dermitzakis, E.T., Kirkness, E., Schwarz, S., Birney, E., Reymond, A. and Antonarakis, S.E. (2004) Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Res., 14, 852-859.
4. Bejerano, G., Haussler, D. and Blanchette, M. (2004) Into the heart of darkness: Large-scale clustering of human non-coding DNA. Bioinformatics, 20, i40-i48.
5. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S. and Haussler D. (2004) Ultraconserved elements in the human genome. Science, 304, 1321-1325.
6. Keightley, P.D. and Gaffney, D.J. (2003) Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc. Natl Acad. Sci. USA, 100, 13402-13406.
7. Boffelli, D., Nobrega, M.A. and Rubin, E.M. (2004) Comparative genomics at the vertebrate extremes. Nat. Rev. Genet., 5, 456-465.
8. Kimura, M. (1994) Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers. The University of Chicago Press, Chicago, IL, pp. 69-72.
9. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
10. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
11. Rat Genome Sequencing Project Consortium. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428, 493-521.
12. Haldane, J.B.S. (1924) A mathematical theory of natural and artificial selection. Proc. Camb. Philos. Soc., 23, 838-844.
13. Sawyer, S.A. and Hartl, D.L. (1992) Population genetics of polymorphism and divergence. Genetics, 132, 1161-1176.
14. West, S.A., Peters, A.D. and Barton, N.H. (1998) Testing for epistasis between deleterious mutations. Genetics, 149, 435-444.
15. Eyre-Walker, A., Keightley, P.D., Smith, N.G. and Gaffney, D. (2002) Quantifying the slightly deleterious mutation model of molecular evolution. Mol. Biol. Evol., 19, 2142-2149.
16. Keightley, P.D., Lercher, M.J. and Eyre-Walker, A. (2005) Evidence for widespread degradation of gene control regions in hominid genomes. PloS Biol., 3, 282-288.
17. McDonald, J.H. and Kreitman, M. (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654.
18. Sunyaev, S., Ramensky, V., Koch, I., Lathe, W., III and Kondrashov, A.S. (2001) Prediction of deleterious human alleles. Hum. Mol. Genet., 10, 591-597.
19. Fay, J.C., Wyckoff, G.J. and Wu, C.I. (2001) Positive and negative selection on the human genome. Genetics, 158, 1227-1234.
20. Tamura, K. and Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol., 10, 512-526.
21. Akashi, H. (1995) Quantifying the slightly deleterious mutation model of molecular evolution. Genetics, 139, 1067-1076.
22. Akashi. H. (1996) Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics, 144, 1297-1307.
23. Jones, P.W. and Smith, P. (2001) Stochastic Processes: An Introduction. Arnold Publishers, London, UK, pp. 133-141.
24. Berg, J., Willman, S. and Lässig, M. (2004) Adaptive evolution of transcription factor binding sites. BMC Evol. Biol., 4, 42.
25. Botstein, D. and Risch, N. (2003) Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat. Genet., 33, 228-237.
26. Ramensky, V., Bork, P. and Sunyaev, S. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res., 30, 3894-3900.
27. Cowles, C.R., Hirschhorn, J.N., Altshuler, D. and Lander E.S. (2002) Detection of regulatory variation in mouse genes. Nat. Genet., 32, 432-437.
28. Morley, M., Molonv, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S. and Cheung, V.G. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
29. Wittkopp, P.J., Haerum, B.K. and Clark, A.G. (2004) Evolutionary changes in cis and trans gene regulation. Nature, 430, 85-88.
30. Hudson, T.J. (2003) Wanted: Regulatory SNPs. Nat. Genet., 33 439-440.
31. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D. et al. (2004) Aligning multiple genomic sequences with threaded blockset aligner. Genome Res. 14, 708-715.
32. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54.
33. Pruitt, K.D. and Maglott, D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
34. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E, Martin, M.J., Michoud, K., O'Donovan, C., Phan, I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
35. Parra, G., Blanco, E. and Guigo, R. (2000) GeneID in Drosophila. Genome Res., 10, 511-515.
36. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
37. Li, W.H. (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA, pp. 59-62.
38. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
39. Hirakawa, M., Tanaka, T., Hashimoto, Y., Kuroda, M., Takagi, T. and Nakamura, Y. (2002) JSNP: A database of common gene variations in the Japanese population. Nucleic Acids Res., 30, 158-162.
40. Nachman, M.W. (1997) Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics, 147, 1303-1316.
41. Takahata, N., Satta, Y. and Klein, J. (1995) Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol., 48, 198-221.