Structure-based prediction of insertion-site preferences of transposons into chromosomes

Mobile genetic elements with the ability to integrate genetic information into chromosomes can cause disease over short periods of time and shape gen-omes over eons. These elements can be used for functional genomics, gene transfer and human gene therapy. However, their integration-site prefer-ences, which are critically important for these uses, are poorly understood. We analyzed the insertion sites of several transposons and retroviruses to detect patterns of integration that might be useful for prediction of preferred integration sites. Initially we found that a mathematical description of DNA-deformability, called Vstep, could be used to distin-guish preferential integration sites for Sleeping Beauty (SB) transposons into a particular 100 bp region of a plasmid [G. Liu, A. M. Geurts, K. Yae