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Sequence Analyses to Study the Evolutionary History and Cis-Regulatory Elements of Hedgehog Genes

  • Ferenc Müller
  • Anne-Gaelle Borycki
Part of the Methods Inmolecular Biology™ book series (MIMB, volume 397)

Abstract

Sequence analysis and comparative genomics are powerful tools to gain knowledge on multiple aspects of gene and protein regulation and function. These have been widely used to understand the evolutionary history and the biochemistry of Hedgehog (Hh) proteins, and the molecular control of Hedgehog gene expression. Here, we report on some of the methods available to retrieve protein and genomic sequences. We describe how protein sequence comparison can produce information on the evolutionary history of Hh proteins. Moreover, we describe the use of genomic sequence analysis including phylogenetic footprinting and transcription factor-binding site search tools, techniques that allow for the characterization of cis-regulatory elements of developmental genes such as the Hedgehog genes.

Key Words

Hedgehog sequence analysis evolution cis-regulatory element bioinformatics 

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Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Ferenc Müller
    • 1
  • Anne-Gaelle Borycki
    • 2
  1. 1.Institute of Toxicology and Genetics, ForschungszentrumKarlsruheGermany
  2. 2.Department of Biomedical ScienceUniversity of Sheffield, Centre for Developmental GeneticsSheffieldUK

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