Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

We report on the function of the D. dictyostelium argonaute proteins AgnA and AgnB in the silencing mechanism of the retrotransposon DIRS-1. By deep sequencing analysis we found that AgnA is involved in the accumulation of DIRS-1 siRNAs since in respective knockout strains siRNAs are strongly reduced. This was verified by northern blots. Reduction of siRNAs was accompanied by increased transcript accumulation and the appearance of an extrachromosomal single stranded DIRS-1 cDNA. In contrast, disruption of the closely related agnB gene had no effect on DIRS-1 siRNAs. agnA-/agnB- double knockouts suggested positively regulator effects by the AgnB protein on DIRS-1. Small RNA profiles of the Ax2 wildtype and different mutant strains were generated by deep sequencing on an Illumina platform.