Screening of potential pseudo att sites of Streptomycesphage ΦC31 integrase in the human genome
Abstract
Zhi-peng HU1, Lu-sheng CHEN2, Cai-yan JIA2, Huan-zhang ZHU3, Wei WANG4, *, Jiang ZHONG1, *
1Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; 2Intelligent Information Processing Lab, Department of Computer Science, Fudan University, Shanghai 200433, China; 3State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China; 4Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
Aim: ΦC31 integrase mediates site-specific recombination between two short sequences, attP and attB, in phage and bacterial genomes, which is a promising tool in gene regulation-based therapy since the zinc finger structure is probably the DNA recognizing domain that can further be engineered. The aim of this study was to screen potential pseudo att sites of ΦC31 integrase in the human genome, and evaluate the risks of its application in human gene therapy.
Methods: TFBS (transcription factor binding sites) were found on the basis of reported pseudo att sites using multiple motif-finding tools, including AlignACE, BioProspector, Consensus, MEME, and Weeder. The human genome with the proposed motif was scanned to find the potential pseudo att sites of ΦC31 integrase.
Results: The possible recognition motif of ΦC31 integrase was identified, which was composed of two co-occurrence conserved elements that were reverse complement to each other flanking the core sequence TTG. In the human genome, a total of 27924 potential pseudo att sites of ΦC31 integrase were found, which were distributed in each human chromosome with high-risk specificity values in the chromosomes 16, 17, and 19. When the risks of the sites were evaluate more rigorously, 53 hits were discovered, and some of them were just the vital functional genes or regulatory regions, such as ACYP2, AKR1B1, DUSP4, etc.
Conclusion: The results provide clues for more comprehensive evaluation of the risks of using ΦC31 integrase in human gene therapy and for drug discovery.
Keywords: gene therapy; ΦC31 integrase; pseudo attP; human genome; motif finding; drug discovery
We thank Fei WANG from the Intelligent Information Processing Lab, Department of Computer Science of Fudan University for her kindly offering of related materials. We also thank Rodolf FLEISCHER, also from Department of Computer Science of Fudan University, for his improvement of the manuscript.
* To whom correspondence should be addressed.
E-mail ww6@bcm.edu (Wei WANG); jzhong@fudan.edu.cn (Jiang ZHONG)
Received 2012-08-08 Accepted 2012-11-27
Keywords:
1Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; 2Intelligent Information Processing Lab, Department of Computer Science, Fudan University, Shanghai 200433, China; 3State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China; 4Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
Aim: ΦC31 integrase mediates site-specific recombination between two short sequences, attP and attB, in phage and bacterial genomes, which is a promising tool in gene regulation-based therapy since the zinc finger structure is probably the DNA recognizing domain that can further be engineered. The aim of this study was to screen potential pseudo att sites of ΦC31 integrase in the human genome, and evaluate the risks of its application in human gene therapy.
Methods: TFBS (transcription factor binding sites) were found on the basis of reported pseudo att sites using multiple motif-finding tools, including AlignACE, BioProspector, Consensus, MEME, and Weeder. The human genome with the proposed motif was scanned to find the potential pseudo att sites of ΦC31 integrase.
Results: The possible recognition motif of ΦC31 integrase was identified, which was composed of two co-occurrence conserved elements that were reverse complement to each other flanking the core sequence TTG. In the human genome, a total of 27924 potential pseudo att sites of ΦC31 integrase were found, which were distributed in each human chromosome with high-risk specificity values in the chromosomes 16, 17, and 19. When the risks of the sites were evaluate more rigorously, 53 hits were discovered, and some of them were just the vital functional genes or regulatory regions, such as ACYP2, AKR1B1, DUSP4, etc.
Conclusion: The results provide clues for more comprehensive evaluation of the risks of using ΦC31 integrase in human gene therapy and for drug discovery.
Keywords: gene therapy; ΦC31 integrase; pseudo attP; human genome; motif finding; drug discovery
We thank Fei WANG from the Intelligent Information Processing Lab, Department of Computer Science of Fudan University for her kindly offering of related materials. We also thank Rodolf FLEISCHER, also from Department of Computer Science of Fudan University, for his improvement of the manuscript.
* To whom correspondence should be addressed.
E-mail ww6@bcm.edu (Wei WANG); jzhong@fudan.edu.cn (Jiang ZHONG)
Received 2012-08-08 Accepted 2012-11-27