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PMID: 17903288 Published · epublish English Journal Article Review

From biophysics to evolutionary genetics: statistical aspects of gene regulation.

BMC bioinformatics ·Vol. 8 Suppl 6 ·2007-09-27 ·Pages S7

Lässig M

Abstract

This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by genomic analysis, and these undergo a stochastic evolution process governed by selection, mutations, and genetic drift. We focus on the links between the biophysical function and the evolution of regulatory elements. In particular, we infer fitness landscapes of binding sites from genomic data, leading to a quantitative evolutionary picture of regulation.

MeSH Terms
Algorithms Biophysics/trends Computational Biology/methods Computer Simulation Data Interpretation, Statistical Evolution, Molecular Gene Expression Profiling/methods Gene Expression Regulation/physiology Models, Genetic Models, Statistical Oligonucleotide Array Sequence Analysis/methods Proteome/metabolism Signal Transduction/physiology Transcription Factors/metabolism Transcription, Genetic/physiology
Chemicals
Proteome Transcription Factors
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Lässig Michael
Institut für Theoretische Physik, Universität zu Köln, Zülpicher Str, 77, 50937 Köln, Germany. [email protected]
References (48)
48 references, click to expand
  1. Identification of conserved regulatory elements by comparative genome analysis.
    J Biol. 2003;2(2):13 PMID: 12760745
  2. Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution.
    Evol Dev. 2001 Nov-Dec;3(6):397-407 PMID: 11806635
  3. MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Genome Biol. 2004;5(12):R98 PMID: 15575972
  4. Physical constraints and functional characteristics of transcription factor-DNA interaction.
    Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12015-20 PMID: 12218191
  5. The application of statistical physics to evolutionary biology.
    Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9541-6 PMID: 15980155
  6. A biophysical approach to transcription factor binding site discovery.
    Genome Res. 2003 Nov;13(11):2381-90 PMID: 14597652
  7. The origins of genome complexity.
    Science. 2003 Nov 21;302(5649):1401-4 PMID: 14631042
  8. Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli.
    Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2404-9 PMID: 14983022
  9. Identification and measurement of neighbor-dependent nucleotide substitution processes.
    Bioinformatics. 2005 May 15;21(10):2322-8 PMID: 15769841
  10. Evolution of transcriptional regulation.
    Curr Opin Genet Dev. 2000 Oct;10(5):575-9 PMID: 10980438
  11. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
    Bioinformatics. 1999 Jul-Aug;15(7-8):563-77 PMID: 10487864
  12. On the specificity of DNA-protein interactions.
    Proc Natl Acad Sci U S A. 1986 Mar;83(6):1608-12 PMID: 3456604
  13. Turnover of binding sites for transcription factors involved in early Drosophila development.
    Gene. 2003 May 22;310:215-20 PMID: 12801649
  14. Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically.
    Proc Natl Acad Sci U S A. 1989 Sep;86(17):6513-7 PMID: 2771938
  15. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons.
    Genome Res. 2002 Feb;12(2):298-308 PMID: 11827949
  16. Quantitative specificity of the Mnt repressor.
    J Mol Biol. 1997 Aug 15;271(2):178-94 PMID: 9268651
  17. On schemes of combinatorial transcription logic.
    Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5136-41 PMID: 12702751
  18. The evolutionary demography of duplicate genes.
    J Struct Funct Genomics. 2003;3(1-4):35-44 PMID: 12836683
  19. Evidence for stabilizing selection in a eukaryotic enhancer element.
    Nature. 2000 Feb 3;403(6769):564-7 PMID: 10676967
  20. The Average Number of Generations until Fixation of a Mutant Gene in a Finite Population.
    Genetics. 1969 Mar;61(3):763-71 PMID: 17248440
  21. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
    J Mol Biol. 1998 Nov 27;284(2):241-54 PMID: 9813115
  22. Adaptations to fluctuating selection in Drosophila.
    Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2277-82 PMID: 17287357
  23. The evolution of transcriptional regulation in eukaryotes.
    Mol Biol Evol. 2003 Sep;20(9):1377-419 PMID: 12777501
  24. On the probability of fixation of mutant genes in a population.
    Genetics. 1962 Jun;47:713-9 PMID: 14456043
  25. Identifying protein-binding sites from unaligned DNA fragments.
    Proc Natl Acad Sci U S A. 1989 Feb;86(4):1183-7 PMID: 2919167
  26. Selection and gene duplication: a view from the genome.
    Genome Biol. 2002;3(5):reviews1012 PMID: 12049669
  27. Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain.
    J Mol Biol. 1998 Feb 27;276(3):571-90 PMID: 9551098
  28. On the selection and evolution of regulatory DNA motifs.
    J Mol Evol. 2002 Oct;55(4):386-400 PMID: 12355260
  29. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
    Biophys J. 2004 Dec;87(6):4021-35 PMID: 15465864
  30. Position specific variation in the rate of evolution in transcription factor binding sites.
    BMC Evol Biol. 2003 Aug 28;3:19 PMID: 12946282
  31. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.
    Proc Natl Acad Sci U S A. 2002 May 28;99(11):7323-8 PMID: 12032281
  32. Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies.
    Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15936-41 PMID: 16236723
  33. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.
    Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80 PMID: 16317069
  34. Specificity, free energy and information content in protein-DNA interactions.
    Trends Biochem Sci. 1998 Mar;23(3):109-13 PMID: 9581503
  35. Expected rates and modes of evolution of enhancer sequences.
    Mol Biol Evol. 2004 Jun;21(6):1064-73 PMID: 15014138
  36. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.
    Biochemistry. 1981 Nov 24;20(24):6929-48 PMID: 7317363
  37. Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor--operator interaction: equilibrium measurements.
    Biochemistry. 1981 Nov 24;20(24):6948-60 PMID: 6274381
  38. Conservation and evolution of cis-regulatory systems in ascomycete fungi.
    PLoS Biol. 2004 Dec;2(12):e398 PMID: 15534694
  39. A view from the genome: spatial control of transcription in sea urchin development.
    Curr Opin Genet Dev. 1999 Oct;9(5):530-41 PMID: 10508696
  40. Adaptive evolution of transcription factor binding sites.
    BMC Evol Biol. 2004 Oct 28;4:42 PMID: 15511291
  41. Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803.
    FEBS Lett. 2004 Apr 9;563(1-3):55-8 PMID: 15063722
  42. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.
    Biochemistry. 1981 Nov 24;20(24):6961-77 PMID: 7032584
  43. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.
    Development. 1998 Mar;125(5):949-58 PMID: 9449677
  44. Analysis and function of transcriptional regulatory elements: insights from Drosophila.
    Annu Rev Entomol. 2003;48:579-602 PMID: 12359740
  45. Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology.
    Microbiol Mol Biol Rev. 2001 Mar;65(1):151-85 PMID: 11238990
  46. Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.
    Mol Biol Evol. 2003 May;20(5):703-14 PMID: 12679540
  47. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.
    Mol Biol Evol. 1998 Jul;15(7):910-7 PMID: 9656490
  48. Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci.
    J Exp Zool. 2002 Oct 15;294(3):285-99 PMID: 12362434
Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-8-S6-S7
Email
[email protected]
Published
2007-09-27
Epub
2007-00-27
Pages
S7
Language
English
Region
England
NLM ID
100965194
PMCID
PMC1995540
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2105-8-S6-S7 PMC Full Text View journal details
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