Intron length and accelerated 3′ gene evolution

Genomics

Volumn 88, Issue 6, 2006, Pages 682-689

  Tang, Clara S ^a   Zhao, Yong Z ^a   Smith, David K ^b   Epstein, Richard J ^a  

^a Department of Medicine   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Comparative genomics; CpG suppression; Molecular evolution

Indexed keywords

3' UNTRANSLATED REGION; AMINO ACID SUBSTITUTION; ARTICLE; CPG ISLAND; EVOLUTION; EXON; GENE MUTATION; GENETIC TRANSCRIPTION; GENOME; HUMAN; INTRON; METHYLATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

3' UNTRANSLATED REGIONS; ANIMALS; CAENORHABDITIS ELEGANS; CPG ISLANDS; DINUCLEOSIDE PHOSPHATES; DNA METHYLATION; DNA REPAIR; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENES; HUMANS; INTRONS; MICE; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC; ZEBRAFISH;

EID: 33750954198     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.06.017     Document Type: Article

References (28)

1. Aburomia R., Khaner O., and Sidow A. Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail. J. Struct. Funct. Genomics 3 1-4 (2003) 45-52
2. Gregory T.R. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol. Rev. Camb. Philos. Soc. 76 1 (2001) 65-101
3. Fedorova L., and Fedorov A. Introns in gene evolution. Genetica 118 2-3 (2003) 123-131
4. Comeron J.M., and Kreitman M. The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces. Genetics 156 3 (2000) 1175-1190
5. Mattick J.S., and Gagen M.J. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 18 9 (2001) 1611-1630
6. Beutler E., et al. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc. Natl. Acad. Sci. USA 86 1 (1989) 192-196
7. Jabbari K., and Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 333 (2004) 143-149
8. Smith N.G., and Hurst L.D. Molecular evolution of an imprinted gene: repeatability of patterns of evolution within the mammalian insulin-like growth factor type II receptor. Genetics 150 2 (1998) 823-833
9. Epstein R.J., Lin K., and Tan T.W. A functional significance for codon third bases. Gene 245 2 (2000) 291-298
10. Lin K., et al. Nonrandom intragenic variations in patterns of codon bias implicate a sequential interplay between transitional genetic drift and functional amino acid selection. J. Mol. Evol. 57 5 (2003) 538-545
11. Cooper G.M., et al. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 14 4 (2004) 539-548
12. Green P., et al. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33 4 (2003) 514-517
13. Majewski J. Dependence of mutational asymmetry on gene-expression levels in the human genome. Am. J. Hum. Genet. 73 3 (2003) 688-692
14. Castillo-Davis C.I., et al. Selection for short introns in highly expressed genes. Nat. Genet. 31 4 (2002) 415-418
15. Robinson P.N., et al. Gene-Ontology analysis reveals association of tissue-specific 5′ CpG-island genes with development and embryogenesis. Hum. Mol. Genet. 13 17 (2004) 1969-1978
16. Schorderet D.F., and Gartler S.M. Analysis of CpG suppression in methylated and nonmethylated species. Proc. Natl. Acad. Sci. USA 89 3 (1992) 957-961
17. Mahadevan M., et al. Myotonic dystrophy mutation: an unstable CTG repeat in the 3′ untranslated region of the gene. Science 255 5049 (1992) 1253-1255
18. Biousse V., et al. Frequency of the 20210 G→A mutation in the 3′-untranslated region of the prothrombin gene in 35 cases of cerebral venous thrombosis. Stroke 29 7 (1998) 1398-1400
19. Ishikawa K., et al. An autosomal dominant cerebellar ataxia linked to chromosome 16q22.1 is associated with a single-nucleotide substitution in the 5′ untranslated region of the gene encoding a protein with spectrin repeat and Rho guanine-nucleotide exchange-factor domains. Am. J. Hum. Genet. 77 2 (2005) 280-296
20. Malumbres M., et al. Hypermethylation of the cell cycle inhibitor p15INK4b 3′-untranslated region interferes with its transcriptional regulation in primary lymphomas. Oncogene 18 2 (1999) 385-396
21. Touchon M., et al. Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res. 32 17 (2004) 4969-4978
22. Kremenskoy M., et al. Genome-wide analysis of DNA methylation status of CpG islands in embryoid bodies, teratomas, and fetuses. Biochem. Biophys. Res. Commun. 311 4 (2003) 884-890
23. Monk M. Epigenetic programming of differential gene expression in development and evolution. Dev. Genet. 17 3 (1995) 188-197
24. Zinser E.R., et al. Bacterial evolution through the selective loss of beneficial Genes. Trade-offs in expression involving two loci. Genetics 164 4 (2003) 1271-1277
25. Stone E.A., Cooper G.M., and Sidow A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu. Rev. Genomics Hum. Genet. 6 (2005) 143-164
26. Karolchik D., Hinrichs A.S., Furey T.S., Roskin K.M., Sugnet C.W., Haussler D., and Kent W.J. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32 Suppl 1 (2004) D493-D496
27. Touchon M., et al. Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett. 555 3 (2003) 579-582
28. Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 5 (1994) 725-736