<p>(A) In this model, dCAP-D3/Condensin II (green circles) organizes gene clusters that it transcriptionally regulates (orange) into a rigid and possibly looped structure (shown on the left). This would serve to position retrotransposon sequences within the cluster (purple) in a manner that is inhibitory to recombination with the homologous chromosome. A decrease in dCAP-D3 levels would result in increased DNA double strand breaks (DSBs) within retrotransposon sequence and an opening of the chromatin structure. This would then allow retrotransposon sequences to more frequently contact the homologous chromosome (magnified image of dCAP-D3 regulated gene cluster shown on the right). While having only minor effects on regions that normally pair at high frequencies (blue), the increased frequency of contacts between repeats flanking retrotransposon sequences on homologous chromosomes combined with increased double strand breaks could lead to unequal crossover events and/or repair by single strand annealing. This would then result in loss of locus-specific retrotransposon sequence and gain of sequence in a separate place. (B) It is also possible that, at some retrotransposon containing dCAP-D3 regulated gene clusters, the opening of chromatin and slight increase in retrotransposon transcription seen following decreased dCAP-D3 expression could lead to generation of RNA intermediates and retrotransposition of new copies to other places in the genome.</p
