study of mice genome dynamics in the context of Trex1 KO.
We present genomic sequencing data from two experiments, which might be relevant for people interested in genome dynamics in the context of Trex-1 KO mutant, especially people interested in repetitive elements: > a) we have successfully bred two parallel lines of Trex1-/- mice and we have the sequence of one individual from each line after inbreeding (one brother-sister) of 7 and 11 generations respectively, A7 and B11. > b) we also sequenced Trex1-/- ku80-/- animals from a double heterozygous cross. We sequenced the 4 genotypes from the cross (one generation only because the double homozygote is sterile): double heterozygote (T+K+), single heterozygote for one gene and double for the other (T-K+ and T+K-), and double homozygote (T-K-).    There are arguments from comparative genome analysis during evolution that some organisms loose their introns. All current models of intron loss involve reverse transcription products generated from spliced mRNAs that can serve as a template for gene conversion-type recombination events that can eliminate introns at the genomic level. In Trex1-/- mice, these reverse transcription products accumulate in such large quantities that they activate cytoplasmic surveillance mechanisms that induce an interferon response. The central hypothesis of this work is that the accumulation of these reverse transcription products in the cells will have important genomic consequences, such as intron loss. In order to maintain healthy Trex1 homozygous KO mice, we balanced the Trex1 mutation with a deficiency in the Zap70 gene that prevents T cell activation. The Trex1-/- Zap70-/- double KO mice can reproduce in the laboratory.  Our project was to sequence the genome of these mice after about 10 generations of inbreeding. The fertility of these inbred families is low and the litters are small, but we were able to continue our experiment of propagating a genome in a Trex1 deficient context. At the seventh generation, we sacrificed an individual in order to prepare genomic DNA and sequence the genome (Illumina, 125 bp, paired) and also of an individual from another independent family at generation 11. Our research must have been good because we identified new copies lacking introns, but which corresponded to pseudogenes inserted after reverse transcription compared to the mouse reference genome we were using (despite the numerous backcrosses on C57Bl6, there remain some regions of line 129) . However, we have shown that they were in fact pre-existing the Trex1 KO in the animals we used To increase the chance of observing an intron loss event by increasing the frequency of homologous recombination, we also constructed a double KO line: Trex1-/- and Ku80-/-, a gene required for non-homologous recombination (NHEJ). The Ku80- homozygous individuals are viable but not fertile, this time we sequenced mices of 4 possible genotypes from a double heterozygous Trex+/-, Ku80+/- cross: double heterozygous Trex+/-, Ku80+/-, double homozygous Trex-/-, Ku80-/- as well as the respective single homozygotes Trex-/-, Ku+/- and Trex+/-, Ku80-/-. Unfortunately for our hypothesis, no intron deletion events were detected after genotype analysis of the double homozygous individual vs. the other 3. You are welcome to use the data. Clement Mettling (clement.mettling@cnrs.fr), Aubin Thomas (aubin.thomas@cnrs.fr) and Georges Lutfalla (georges.lutfalla@umontpellier.fr)