Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

Genomics, Proteomics and Bioinformatics

Volumn 10, Issue 1, 2012, Pages 4-10

  Cui, Peng ^a   Ding, Feng ^a   Lin, Qiang ^a   Zhang, Lingfang ^a   Li, Ang ^b   Zhang, Zhang ^a   Hu, Songnian ^a   Yu, Jun ^a  

^a China National Center for Bioinformation   (China)

^b KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

Author keywords

Genetic variation; Mutational pressure; Replication; Transcription

Indexed keywords

DNA;

ARTICLE; DENSITY; DNA REPLICATION; GENE EXPRESSION; GENE MUTATION; GENETIC PARAMETERS; GENETIC TRANSCRIPTION; GENOME; HOUSEKEEPING GENE; HUMAN; HUMAN TISSUE; MUTATION RATE VARIATION; PRESSURE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS;

DNA REPLICATION; GENES, ESSENTIAL; GENOME, HUMAN; HELA CELLS; HUMANS; MUTATION RATE; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84863346336     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/S1672-0229(11)60028-4     Document Type: Article

References (24)

1. Arnheim N., Calabrese P. Understanding what determines the frequency and pattern of human germline mutations. Nat. Rev. Genet. 2009, 10:478-488.
2. Baer C.F., et al. Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat. Rev. Genet. 2007, 8:619-631.
3. Ellegren H., et al. Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 2003, 13:562-568.
4. Hellmann I., et al. Why do human diversity levels vary at a megabase scale?. Genome Res. 2005, 15:1222-1231.
5. Smith N.G., et al. Deterministic mutation rate variation in the human genome. Genome Res. 2002, 12:1350-1356.
6. Chen C.L., et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res. 2010, 20:447-457.
7. Stamatoyannopoulos J.A., et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 2009, 41:393-395.
8. Comeron J.M. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 2004, 167:1293-1304.
9. Green P., et al. Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 2003, 33:514-517.
10. Hanawalt P.C., Spivak G. Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 2008, 9:958-970.
11. Klapacz J., Bhagwat A.S. Transcription promotes guanine to thymine mutations in the non-transcribed strand of an Escherichia coli gene. DNA Repair (Amst.) 2005, 4:806-813.
12. Majewski J. Dependence of mutational asymmetry on gene-expression levels in the human genome. Am. J. Hum. Genet. 2003, 73:688-692.
13. Polak P., Arndt P.F. Transcription induces strand-specific mutations at the 5' end of human genes. Genome Res. 2008, 18:1216-1223.
14. Fujimori S., et al. GC-compositional strand bias around transcription start sites in plants and fungi. BMC Genomics 2005, 6:26.
15. Sherry S.T., et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308-311.
16. Wang E.T., et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
17. Zhu J., et al. On the nature of human housekeeping genes. Trends Genet. 2008, 24:481-484.
18. Watanabe Y., et al. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum. Mol. Genet. 2002, 11:13-21.
19. Wang D.P., et al. Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol. Direct. 2009, 4:20.
20. Pruitt K.D., et al. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35:D61-D65.
21. Kent W.J., et al. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
22. Li H., et al. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18:1851-1858.
23. Mortazavi A., et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods. 2008, 5:621-628.
24. Ramskold D., et al. An abundance of ubiquitously expressed genes revealed by tissue transcriptomesequence data. PLoS Comput. Biol. 2009, 5:e1000598.