ZFIN ID: ZDB-PUB-160129-15
Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility
Vrljicak, P., Tao, S., Varshney, G.K., Quach, H.N., Joshi, A., LaFave, M.C., Burgess, S.M., Sampath, K.
Date: 2016
Source: G3 (Bethesda)   6(4): 805-17 (Journal)
Registered Authors: Burgess, Shawn, Joshi, Adita, Quach, Helen Ngoc Bao, Sampath, Karuna, Tao, Shijie, Varshney, Gaurav, Vrljicak, Pavle
Keywords: transposon, Ac/Ds, genome-wide analysis, integrations, gene targeting, genome engineering, functional genomics, Tol2, retrovirus, MMLV, mouse, ES cells, vertebrate genomes, zebrafish
MeSH Terms:
  • Animals
  • Base Sequence
  • DNA Transposable Elements*
  • Gene Targeting
  • Genetic Engineering
  • Genome*
  • Genome-Wide Association Study*
  • Genomics*/methods
  • Mice
  • Moloney murine leukemia virus/genetics
  • Mutagenesis, Insertional
  • Nucleotide Motifs
  • Repetitive Sequences, Nucleic Acid
  • Retroviridae/genetics*
  • Virus Integration*
  • Zebrafish/genetics
PubMed: 26818075 Full text @ G3 (Bethesda)
DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germline transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish, with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence integration of heterologous DNA in genomes, and have implications for targeted genome engineering.