Phylogenetic Footprinting

Abstract

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 β‐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

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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 ε and γ 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

Phylofoot.org. Tools for phylogenetic footprinting purposes http://www.phylofoot.org/

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How to Cite close
Wasserman, Wyeth W, and Alkema, Wynand(Apr 2008) Phylogenetic Footprinting. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005091.pub2]