Phylogenetic footprint

Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB. Dioxin-responsive AHRE-II gene battery identification by phylogenetic footprinting. Biochem Biophys Res Commun 2004 321 707-715. 

Cliften, P., Sudarsanam, P., Desikan. A., Fulton, L., Fulton, B., Majors, (.. Waterston, R., Cohen, B.A., and Johnston, M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71-76. 

Key Words Multiple sequence alignment anchored alignment DIALIGN gene prediction phylogenetic footprinting. 

Prohaska, S. J., Fried, C., Flamm, C., Wagner, G., and Stadler, P. F. (2004) Surveying phylogenetic footprints in large gene clusters applications to Hox cluster duplications. Mol. Phyl. Evol. 31, 581-604. 

Blanchette, M. and Tompa, M. (2002) Discovery of regulatory elements by a computationalmethod for phylogenetic footprinting. Genome Res. 12, 739-748. 

Chapman, M. A., Charchar, F. J., Kinston, S., et al. (2003) Comparative and functional analysis of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting. Genomics 81, 249-259. 

Key Words Transcriptional regulation pattern discovery pattern matching phylogenetic footprinting prokaryotes RSAT get-orthologs retrieve-seq dyad-analysis. 

McCue, F., Thompson, W., Carmack, C., et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29, 774-782. 

Key Words Phylogenetic footprinting noncoding functional DNA element Saccharomyces-, ribosomal DNA. 

We provide a practical example of how phylogenetic footprinting can reveal functional elements by using the ribosomal RNA gene repeats (rDNA) from a number of Saccharomyces yeast species. The rDNA repeats are maintained in most eukaryotes as multiple tandem repeats (see Fig. 1). Each repeat unit... 

The first consideration for a phylogenetic footprinting study is the species to use (see Note 1). To aid in species selection, a phylogeny showing the relationship of species related to the species of interest is useful. We used the phylogeny of the Saccharomyces yeasts presented in Kurtzman and Robnett (17) to select a number of species for analysis. The relationships of the species we used here are shown in Fig. 2. 

Ganley, A. R. D., Hayashi, K., Horiuchi, T., and Kobayashi, T. (2005) Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. USA 102, 11,787-11,792. 

An alternative approach is phylogenetic footprinting (e.g., refs. 11 and 12) which identifies significantly conserved segments in multiple alignments of orthologous intergenic sequences. One of the drawbacks of this approach is that it assumes that only conserved sequence is functional, which is often not a safe assumption (13,14). 

Using the Gibbs Motif Sampler for Phylogenetic Footprinting... 

Key Words Gibbs sampling phylogenetic footprinting transcription regulation. 

---