Phylogenetic Footprinting

Wyeth W Wasserman, University of British Columbia, Vancouver, British Columbia, Canada
Wynand Alkema, Karoliniska Institutet, Stockholm, Sweden

Published online: May 2008

DOI: 10.1002/9780470015902.a0005091.pub2

Phylogenetic footprinting is a method for the comparative analysis of orthologous gene sequences. Based on the expectation that sequences under selective pressure will be conserved over moderate periods of evolutionary time, phylogenetic footprinting is one means to identify gene segments with a specific function.

Keywords: phylogenetic footprinting; evolution; sequence comparison; transcription

Figure 1. Use of phylogenetic footprinting to discover regulatory elements in the upstream sequence of the human -globin gene. When no evolutionary filter is applied, a search for binding sites for the GATA transcription factors produces a large number of hits in the human sequence (lower panel). This number is greatly reduced when a phylogenetic filter is applied by aligning the human sequence to an orthologous mouse sequence (middle panel). The true sites, given in the box, now stand out even in a search in which motifs for all known transcription factors are used. When the orthologous chicken sequence is used as a filter, no conserved binding sites are observed any more, indicating that the evolutionary distance between human and chicken is too large to allow phylogenetic footprinting for this sequence (upper panel).
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 References
    Aparicio S, Hawker K, Cottage A et al. (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nature Genetics 16: 79–83.
    Blackwood EM and Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281: 61–63.
    Blanchette M and Tompa M (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 12: 739–748.
    book Davidson EH (2001) Genomic Regulatory Systems: Development and Evolution. New York: Academic Press.
    Duret L and Bucher P (1997) Searching for regulatory elements in human non-coding sequences. Current Opinion in Structural Biology 7: 399–406.
    Loots GG, Locksley RM, Blankespoor CM et al. (2000) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136–140.
    McCue L, Thompson W, Carmack C et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Research 29: 774–782.
    Schwartz S, Zhang Z, Frazer KA et al. (2000) PipMaker: a Web server for aligning two genomic DNA sequences. Genome Research 10: 577–586.
    Stormo G (2000) DNA binding sites: representation and discovery. Bioinformatics 16: 16–23.
    Tagle DA, Koop BF, Goodman M et al. (1988) Embryonic and globin genes of a prosimian primate (Galago crassicaudatus). Journal of Molecular Biology 203: 439–455.
    Wasserman WW, Palumbo M, Thompson W, Fickett JW and Lawrence CE (2000) Human–mouse genome comparisons to locate regulatory sites. Nature Genetics 26: 225–228.
    Wiehe T, Gebauer-Jung S, Mitchell-Olds T and Guigo R (2001) SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Research 11: 1574–1583.
 Further Reading
    Duret L and Bucher P (1997) Searching for regulatory elements in human noncoding sequences. Current Opinion in Structural Biology 7(3): 399–406.
    Parra G, Agarwal P, Abril JF et al. (2003) Comparative gene prediction in human and mouse. Genome Research 13(1): 108–117.
    Tagle DA, Koop BF, Goodman M et al. (1988) Embryonic and globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. Journal of Molecular Biology 203(2): 439–455.
    Zhang Z and Gerstein M (2003) Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. Journal of Biology 2: 11.
 Web Links
    ePath Phylofoot.org. Tools for phylogenetic footprinting purposes http://www.phylofoot.org/

Related Sub-Topics:

Evolutionary Genomics | Molecular Evolution | Techniques and Tools in Molecular Biology | Evolution of Coding and Functional Modules
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Article Title: Phylogenetic Footprinting
 
How to Cite close
Wasserman, Wyeth W, and Alkema, Wynand(May 2008) Phylogenetic Footprinting. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005091.pub2]