- Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116:281–297
Article PubMed CAS Google Scholar
- Carlini DB, Genut JE (2006) Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 62:89–98
Article PubMed CAS Google Scholar
- Chamary JV, Hurst LD (2005a) Biased codon usage near intron-exon junctions: Selection on splicing enhancers, splice-site recognition or something else? Trends Genet 21:256–259
Article CAS Google Scholar
- Chamary JV, Hurst LD (2005b) Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol 6:R75
Article CAS Google Scholar
- Chamary J-V, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7:98–108
Article PubMed CAS Google Scholar
- Comeron JM (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167:1293–1304
Article PubMed CAS Google Scholar
- Doench JG, Sharp PA (2004) Specificity of microRNA target selection in translational repression. Genes Dev 18:504–511
Article PubMed CAS Google Scholar
- dos Reis M, Savva R, Wernisch L (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32:5036–5044
Article PubMed CAS Google Scholar
- Duan JB, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12:205–216
Article PubMed CAS Google Scholar
- Duret L (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12:640–649
Article PubMed CAS Google Scholar
- Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Article PubMed CAS Google Scholar
- Eskesen ST, Eskesen FN, Ruvinsky A (2004) Natural selection affects frequencies of AG and GT dinucleotides at the 5′ and 3′ ends of exons. Genetics 167:543–550
Article PubMed CAS Google Scholar
- Fairbrother WG, Holste D, Burge CB, Sharp PA (2004) Single nucleotide polymorphism–based validation of exonic splicing enhancers. PLoS Biol 2:E268
Article PubMed Google Scholar
- Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310:1817–1821
Article PubMed CAS Google Scholar
- Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32:D109–D111
Article PubMed CAS Google Scholar
- Hellmann I, Zollner S, Enard W, Ebersberger I, Nickel B, Paabo S (2003) Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13:831–837
Article PubMed CAS Google Scholar
- Hurst LD (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet 18:486–487
Article PubMed Google Scholar
- Hurst LD, Pal C (2001) Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet 17:62–65
Article PubMed CAS Google Scholar
- Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotech 21:635–637
Article CAS Google Scholar
- Keightley PD, Eyre-Walker A (2000) Deleterious mutations and the evolution of sex. Science 290:331–333
Article PubMed CAS Google Scholar
- Kondrashov AS (1998) Measuring spontaneous deleterious mutation process. Genetica 103:183–197
Article Google Scholar
- Kondrashov FA, Ogurtsov AY, Kondrashov AS (2006) Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J Theor Biol (in press)
- Kumar S, Subramanian S (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci USA 99:803–808
Article PubMed CAS Google Scholar
- Lavner Y, Kotlar D (2005) Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345:127–138
Article PubMed CAS Google Scholar
- Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798
Article PubMed CAS Google Scholar
- Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20
Article PubMed CAS Google Scholar
- Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99
Article PubMed CAS Google Scholar
- Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773
Article PubMed CAS Google Scholar
- Lu J, Wu CL (2005) Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci USA 102:4063–4067
Article PubMed CAS Google Scholar
- Nakamoto M, Jin P, O’Donnell WT, Warren ST (2005) Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum Mol Genet 14:3813–3821
Article PubMed CAS Google Scholar
- Pagani F, Raponi M, Baralle FE (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci USA 102:6368–6372
Article PubMed CAS Google Scholar
- Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10:271–281
PubMed CAS Google Scholar
- Parmley JL, Chamary JV, Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23:301–309
Article PubMed CAS Google Scholar
- Pond SK, Muse SV (2005) Site-to-site variation of synonymous substitution rates. Mol Biol Evol 22:2375–2385
Article PubMed CAS Google Scholar
- Robins H, Press WH (2005) Human microRNAs target a functionally distinct population of genes with AT-rich 3 ‘ UTRs. Proc Natl Acad Sci USA 102:15557–15562
Article PubMed CAS Google Scholar
- Sharp PM, Averof M, Lloyd AT, Matassi G, Peden JF (1995) DNA-sequence evolution: the sounds of silence. Phil Trans R Soc Lond B 349:241–247
CAS Google Scholar
- Smith NGC, Hurst LD (1999a) The causes of synonymous rate variation in the rodent genome: can substitution rates be used to estimate the sex bias in mutation rate? Genetics 152:661–673
CAS Google Scholar
- Smith NGC, Hurst LD (1999b) The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics 153:1395–1402
CAS Google Scholar
- Tamura K, Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol 19:1727–1736
PubMed CAS Google Scholar
- Urrutia AO, Hurst LD (2003) The signature of selection mediated by expression on human genes. Genome Res 13:2260–2264
Article PubMed CAS Google Scholar
- Willie E, Majewski J (2004) Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet 20:534–538
Article PubMed CAS Google Scholar
- Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals. Nature 434:338–345
Article PubMed CAS Google Scholar
- Yang ZH, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503
Article PubMed Google Scholar
- Zhao Y, Samal E, Srivastava D (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436:214–220
Article PubMed CAS Google Scholar
- Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Article PubMed CAS Google Scholar