Identification of novel ETn insertions in KRAB-ZFP cluster depleted mice

Genetic deletion of a large KRAB-ZFP gene cluster on chromosome 4 (Chr4-cl) leads to transcriptional reactivation of retrotransposons (mainly ETn elements) in ES cells. We therefore wanted to test whether ETn elements retrotranspose in Chr4-cl KO mice at higher frequency. For this we purified genomic DNA from WT and KO mice, enriched gDNA libraries using ETn capture probes and sequenced those libraries as paire-end reads. These reads were then used to identify novel ETn insertions that are not annotated in the reference genome or present in the germ line of their progenitors. Identification of novel retrotransposon insertons in mice by capture sequencing