Studying the evolution of promoter sequences: A waiting time problem

Journal of Computational Biology

Volumn 17, Issue 12, 2010, Pages 1591-1606

  Behrens, Sarah ^a   Vingron, Martin ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

evolution; gene regulation; Markov model; transcription factor binding sites; waiting times

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; BINDING SITE; BIOLOGICAL MODEL; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PROMOTER REGION; TIME;

ANIMALS; BASE SEQUENCE; BINDING SITES; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PAN TROGLODYTES; PROMOTER REGIONS, GENETIC; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 78650013855     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0084     Document Type: Article

References (19)

1. Arndt, P. F., Burge, C. B., and Hwa, T. 2003. DNA sequence evolution with neighbor-dependent mutation. J. Comput. Biol. 10, 313-322.
2. Arndt, P. F. and Hwa, T. 2005. Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21, 2322-2328.
3. Chaurasia, G., Iqbal, Y., Hänig, C., et al. 2007. UniHI: an entry gate to the human protein interactome. Nucleic Acids Res. 35.
4. Duret, L., and Arndt, P. F. 2008. The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4.
5. Durrett, R., and Schmidt, D. 2007. Waiting for regulatory sequences to appear. Annu. Appl. Probab. 17, 1-32.
6. Ewens, W. J. 2004. Mathematical Population Genetics, 2nd ed. Springer, New York.
7. Hobolth, A., Christensen, O. F., Mailund, T., et al. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3, e7+.
8. Karlin, S., and Taylor, H. M. 1975. A First Course in Stochastic Processes, 2nd ed. Academic Press, New York.
9. Kreitman, M., and Comeron, J. M. 1999. Coding sequence evolution. Curr. Opin. Genet. Dev. 9, 637-641.
10. MacArthur, S. and Brookfield, J. F. 2004. Expected rates and modes of evolution of enhancer sequences. Mol. Biol. Evol. 21, 1064-1073.
11. Nowak, M. A. 2006. Evolutionary Dynamics: Exploring the Equations of Life. Belknap Press of Harvard University Press, Cambridge, MA.
12. Odom, D. T., Dowell, R. D., Jacobsen, E. S., et al. 2007. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39, 730-732.
13. Portales-Casamar, E., Thongjuea, S., Kwon, A. T., et al. 2010. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105-D110.
14. Reinert, G., Schbath, S., and Waterman, M. S. 2000. Probabilistic and statistical properties of words: an overview. J. Comput. Biol. 7, 1-46.
15. Stone, J. R. and Wray, G. A. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Mol. Biol. Evol. 18, 1764-1770.
16. Taylor, M. S., Kai, C., Kawai, J., et al. 2006. Heterotachy in mammalian promoter evolution. PLoS Genet. 2, e30+.
17. Wang, D. G., Fan, J. B., Siao, C. J., et al. 1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-1082.
18. Wray, G. A., Hahn, M. W., Abouheif, E., et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20, 1377-1419.
19. Wunderlich, Z., and Mirny, L. A. 2009. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 25, 434-440.