Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility

G3 : Genes - Genomes - Genetics
Pavle VrljicakKaruna Sampath

Abstract

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 germ-line 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 the integration of heterologous DNA in genomes, and have implications for targeted genome engineering.

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Citations

Jan 31, 2018·G3 : Genes - Genomes - Genetics·Kevin MielichReinhard Kunze
Mar 20, 2019·Frontiers in Cell and Developmental Biology·Kaili LiuGaurav K Varshney
Jan 11, 2018·ACS Synthetic Biology·Christine A MerrickSusan J Rosser

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Methods Mentioned

BETA
transgenic
PCR
RNA-seq
protein trap
transgenics

Software Mentioned

custom
Ensembl
weblogo
UCSC browser
GeIST
BEDTools
Python script
Bowtie
BLAT
DAVID

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