A Non-Canonical Nuclear Activity Triggered by Small RNAs and Argonaute Proteins in Human Cells. Homo sapiens

In this study we report the discovery of an unexpected nuclear activity of small RNAs that target an ~8.6 megabase chromosomal domain located on the telomeric q-arm of chromosome 5 from an unbiased genome-wide RNAi screen. Short-hairpin RNAs that target genes within this large domain induce trans-activation of CREB signaling transcriptional reporters and induce an endogenous gene expression signature that includes CREB-target and neuronal-fate genes. Furthermore, CRISPR-guided deletion of AGO-1 and -2 demonstrate their mutually redundant roles in this mechanism, which we named Chromosomally Induced Trans Activation by RNAi (CITAR). Overall design: We sequenced the transcriptome of HEK293 cells undergoing Chromosomally-Induced Trans Activation by RNAi (CITAR), as measured by transcriptional activation of a CRE-Luciferase reporter (pGL4.29), by shRNAs targeting Chr5q35 loci (TSPAN17 at Chr5:176,074,388, TMED9 at Chr5:177,019,213 and N4BP3 at Chr5:177,540,556), as well as two negative control shRNAs to account for infection (non-hairpin) and for engagement of the RNAi pathway (ASNA1 encoded on Chr19).