Julian, Andrea Marian (2003-12). Use of bioinformatics to investigate and analyze transposable element insertions in the genomes of caenorhabditis elegans and drosophila melanogaster, and into the target plasmid pGDV1. Master's Thesis. Thesis uri icon

abstract

  • Transposable elements (TEs) are utilized for the creation of a wide range of transgenic organisms. However, in some systems, this technique is not very efficient due to low transposition frequencies and integration into unstable or transcriptionally inactive genomic regions. One approach to ameliorate this problem is to increase knowledge of how transposons move and where they integrate into target genomes. Most transposons do not insert randomly into their host genome, with class II TEs utilizing target sequences of between 2 ? 8 bp in length, which are duplicated upon insertion. Furthermore, amongst insertion sites, certain sites are preferred for insertion and hence are classified as hot spots, while others not targeted by TEs are referred to as cold spots. The hypothesis tested in this analysis is that in addition to the primary consensus target sequence, secondary and tertiary DNA structures have a significant influence on TE target site preference. Bioinformatics was used to predict and analyze the structure of the flanking DNA around known insertion sites and cold spots for various TEs, to understand why insertion sites are used preferentially to cold spots for element integration. Hidden Markov Models were modeled and trained to analyze datasets of insertions of the P element in the Drosophila melanogaster genome, the Tc1 element in the Caenorhabditis elegans genome, and insertions of the Mos1, piggyBac and Hermes transposons into the target plasmid pGDV1. Analysis of the DNA structural profiles of the insertion sites for the P element and Hermes transposons revealed that both transposons targeted regions of DNA with a relatively high degree of bendability/flexibility at the insertion site. However, similar trends were not observed for the Tc1, Mos1 or piggyBac transposons. Hence, it is believed that the secondary structural features of DNA can contribute to target site preference for some, but not all transposable elements.
  • Transposable elements (TEs) are utilized for the creation of a wide range of transgenic organisms. However, in some systems, this technique is not very efficient due to low transposition frequencies and integration into unstable or transcriptionally inactive genomic regions. One approach to ameliorate this problem is to increase knowledge of how transposons move and where they integrate into target genomes. Most transposons do not insert randomly into their host genome, with class II TEs utilizing target sequences of between 2 ? 8 bp in length, which are duplicated upon insertion. Furthermore, amongst insertion sites, certain sites are preferred for insertion and hence are classified as hot spots, while others not targeted by TEs are referred to as cold spots.

    The hypothesis tested in this analysis is that in addition to the primary consensus target sequence, secondary and tertiary DNA structures have a significant influence on TE target site preference. Bioinformatics was used to predict and analyze the structure of the flanking DNA around known insertion sites and cold spots for various TEs, to understand why insertion sites are used preferentially to cold spots for element integration. Hidden Markov Models were modeled and trained to analyze datasets of insertions of the P element in the Drosophila melanogaster genome, the Tc1 element in the Caenorhabditis elegans genome, and insertions of the Mos1, piggyBac and Hermes transposons into the target plasmid pGDV1. Analysis of the DNA structural profiles of the insertion sites for the P element and Hermes transposons revealed that both transposons targeted regions of DNA with a relatively high degree of bendability/flexibility at the insertion site. However, similar trends were not observed for the Tc1, Mos1 or piggyBac transposons. Hence, it is believed that the secondary structural features of DNA can contribute to target site preference for some, but not all transposable elements.

publication date

  • December 2003