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Phylogenetic Footprinting to Find Functional DNA Elements

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Comparative Genomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 395))

Summary

Phylogenetic footprinting is powerful technique for finding functional elements from sequence data. Functional elements are thought to have greater sequence constraint than nonfunctional elements, and, thus, undergo a slower rate of sequence change through time. Phylogenetic footprinting uses comparisons of homologous sequences from closely related organisms to identify “phylogenetic footprints,” regions with slower rates of sequence change than background. This does not require prior characterization of the sequence in question, therefore, it can be used in a wide range of applications. In particular, it is useful for the identification of functional elements in noncoding DNA, which are traditionally difficult to detect. Here, we describe in detail how to perform a simple yet powerful phylogenetic footprinting analysis. As an example, we use ribosomal DNA repeat sequences from various Saccharomyces yeasts to find functional noncoding DNA elements in the intergenic spacer, and explain critical considerations in performing phylogenetic footprinting analyses, including the number of species and species range, and some of the available software. Our methods are broadly applicable and should appeal to molecular biologists with little experience in bioinformatics.

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Acknowledgments

This work was supported by grants 13141205, 17080010, and 17370065 from the Ministry of Education, Science and Culture, Japan, and by a Human Frontier Science Program grant.

Author information

Authors and Affiliations

  1. Division of Cytogenetics, National Institute of Genetics and Department of Genetics, Sokendai, USA

    Austen R.D. Ganley

  2. Division of Cytogenetics, National Institute of Genetics and Department of Genetics, Sokendai, USA

    Takehiko Kobayashi

Authors
  1. Austen R.D. Ganley
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  2. Takehiko Kobayashi
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Editor information

Editors and Affiliations

  1. Bioinformatics Program and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI

    Nicholas H. Bergman

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© 2007 Humana Press Inc.

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Ganley, A.R., Kobayashi, T. (2007). Phylogenetic Footprinting to Find Functional DNA Elements. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_23

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  • DOI: https://doi.org/10.1007/978-1-59745-514-5_23

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-693-1

  • Online ISBN: 978-1-59745-514-5

  • eBook Packages: Springer Protocols

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