title: Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  The results provide clues for more comprehensive evaluation of the risks of using ΦC31 integrase in human gene therapy and for drug discovery.
authors: Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
authors: Zhi-peng
authors: ZP
authors: Hu
authors: Lu-sheng
authors: LS
authors: Chen
authors: Cai-yan
authors: CY
authors: Jia
authors: Huan-zhang
authors: HZ
authors: Zhu
authors: Wei
authors: W
authors: Wang
authors: Jiang
authors: J
authors: Zhong
mesh_terms: D001287:Attachment Sites, Microbiological / Q000235:genetics*; D001435:Bacteriophages / Q000201:enzymology* / Q000235:genetics*; D001665:Binding Sites; D002877:Chromosomes, Human; D017124:Conserved Sequence; D015316:Genetic Therapy; D015894:Genome, Human; D006801:Humans; D019426:Integrases / Q000235:genetics*; D013302:Streptomyces / Q000821:virology*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors; D019426:Integrases