RNAi mediates allele-specific epigenetic inheritance of heterochromatin [ncRNA-seq]

We tested the ability of trans siRNAs to establish a silent allele of endogenous ade6+ or an ade6+ transgene inserted within euchromatic loci. We found that a silent ade6-OFF epi-allele that grows red on low adenine medium could be established in several mutant backgrounds (mlo3∆, leo1∆) in the presence of ectopic siRNAs. Furthermore, we found that the silent ade6-OFF epi-allele could be meiotically inherited to wildtype progeny lacking the establishing mutation or ectopic siRNAs. Here, we sequenced genome-wide small RNAs and found widespread generation of secondary siRNAs at genes surrounding the ade6-OFF locus in cells expressing the ectopic siRNAs source cen::ade6. In wildtype meiotic progeny lacking the driver cen::ade6 siRNAs, we observed establishment of a local siRNA producing locus at genes adjacent to the endogenous ade6-OFF or at a kanMX-ade6-OFF transgene inserted within euchromatic loci. In contrast, spreading of secondary siRNAs was limited or nonexistent in ade6-ON cells. Finally, we found that spreading of secondary siRNAs at the endogenous ade6 locus was limited when an ade6 hairpin construct served as the ectopic siRNA driver locus instead of cen::ade6. Non-coding RNA profiling by high throughput sequencing