Bioinformatic Identification of Homing Endonucleases and Their Target Sites

  • Eyal Privman
Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1123)

Abstract

Homing endonuclease genes (HEGs) are a large, phylogenetically diverse superfamily of enzymes with high specificity for especially long target sites. The public genomic sequence databases contain thousands of HEGs. This is a large and diverse arsenal of potential genome editing tools. To make use of this natural resource, one needs to identify candidate HEGs. Due to their special relationship with a host gene, it is also possible to predict their cognate target sequences. Here I describe the HomeBase algorithm that was developed to this end. A detailed description of the computational pipeline is provided with emphasis on technical and methodological caveats of the approach.

Key words

Homing endonucleases Homology search Target-site prediction HomeBase 
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References

  1. 1.
    Barzel A, Privman E, Peeri M, Naor A, Shachar E, Burstein D, Lazary R, Gophna U, Pupko T, Kupiec M (2011) Native homing endonucleases can target conserved genes in humans and in animal models. Nucleic Acids Res 39: 6646–6659PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Gimble FS, Wang J (1996) Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing. J Mol Biol 263:163–180PubMedCrossRefGoogle Scholar
  3. 3.
    Kurokawa S, Bessho Y, Higashijima K, Shirouzu M, Yokoyama S, Watanabe KI, Ohama T (2005) Adaptation of intronic homing endonuclease for successful horizontal transmission. FEBS J 272:2487–2496PubMedCrossRefGoogle Scholar
  4. 4.
    Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) Coevolution of a homing endonuclease and its host target sequence. J Mol Biol 372:1305–1319PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Zhou Y, Lu C, Wu QJ, Wang Y, Sun ZT, Deng JC, Zhang Y (2008) GISSD: group I intron sequence and structure database. Nucleic Acids Res 36:D31–D37PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Perler FB (2002) InBase: the Intein Database. Nucleic Acids Res 30:383–384PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H et al (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611–1618PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Eyal Privman
    • 1
  1. 1.Institute of Evolution and Department of Evolutionary and Environmental BiologyUniversity of HaifaHaifaIsrael

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