Screening of potential pseudo att sites of Streptomyces phage φC31 integrase in the human genome

• Published in: Acta pharmacologica Sinica Vol. 34; no. 4; pp. 561 - 569
• Main Authors: Hu, Zhi-peng, Chen, Lu-sheng, Jia, Cai-yan, Zhu, Huan-zhang, Wang, Wei, Zhong, Jiang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-04-2013; Nature Publishing Group
• Subjects: ATT; Attachment Sites, Microbiological - genetics; Bacteriophages - enzymology; Bacteriophages - genetics; Binding Sites; Biomedical and Life Sciences; Biomedicine; Chromosomes, Human; Conserved Sequence; Genetic Therapy; Genome, Human; Humans; Immunology; Integrases - genetics; Internal Medicine; Medical Microbiology; Original; original-article; Pharmacology/Toxicology; Streptomyces; Streptomyces - virology; Transcription Factors - genetics; Vaccine; 人类基因组; 位点特异性重组; 噬菌体; 整合酶; 筛选; 网站; 链霉菌; P; drug discovery; human genome; motif finding; gene therapy; ΦC31 integrase; pseudo
• ISSN: 1671-4083; 1745-7254
• DOI: 10.1038/aps.2012.173

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 （I）C31 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.