Examples of novel cis-NAT-siRNA loci annotated in this study. (A) The convergent genes lig and Vps28 have 3′ UTRs that are not annotated to overlap; however, the specific accumulation of abundant siRNAs between these gene models suggests that their 3′ UTRs indeed overlap in several cell lines. This is bolstered by the presence of overlap siRNAs in AGO2-IP data (21-nt read coverage shown in color; coverage over all read sizes shown in gray). (B) Example of alternative 3′ UTRs generating distinct genomic limits of siRNAs. The limits of siRNAs from the ref(2)P/CG10337 pair in OSC cells and S2R+ cells (here showing AGO2-IP data) strictly obey the overlap limits of their annotated gene models. In contrast, the genomic extent of siRNA accumulation is greatly expanded in mbn2 cells. (C) An especially abundant and expansive cis-NAT-siRNA locus in the intron of eIF5B (overlapping one alternative exon) is expressed specifically in mbn2 cells. (D) Highly expressed siRNAs emanate from the 3′ region of CG34126, including both exons and introns, potentially suggesting that the siRNA substrate involves an unprocessed form of this gene.
