%0 Journal Article %A Alper Akay %A Tomas Di Domenico %A Kin M. Suen %A Amena Nabih %A Guillermo E. Parada %A Mark Larance %A Ragini Medhi %A Ahmet C. Berkyurek %A Xinlian Zhang %A Christopher J. Wedeles %A Ping Ma %A Angus I. Lamond %A Martin Hemberg %A Julie M. Claycomb %A Eric A. Miska %T The Aquarius/EMB-4 helicase licenses co-transcriptional gene silencing %D 2016 %R 10.1101/089763 %J bioRxiv %P 089763 %X Small RNAs (sRNAs) play an ancient role in genome defence against transposable elements. In animals, plants and fungi small RNAs guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. In animals the link between small RNA pathways and the transcriptional machinery remains unclear. Here we show that the Caenorhabditis elegans germline Argonaute HRDE-1 physically interacts with the conserved RNA helicase Aquarius/EMB-4. We demonstrate that the Aquarius/EMB-4 helicase activity is required to initiate small RNA-induced co-transcriptional gene silencing. HRDE-1 and Aquarius/EMB-4 are required to silence the transcription of overlapping sets of transposable elements. Surprisingly, removal of introns from a small RNA pathway target abolishes the requirement for Aquarius/EMB-4, but not HRDE-1, for gene silencing. We conclude that the Aquarius/EMB-4 helicase activity allows HRDE-1/sRNA complexes to efficiently engage nascent RNA transcripts - in competition with the general RNA processing machinery. We postulate that Aquarius/EMB-4 facilitates the surveillance of the nascent transcriptome to detect and silence transposable elements through small RNA pathways. %U https://www.biorxiv.org/content/biorxiv/early/2016/12/05/089763.full.pdf