GSE50595
Argonaute-bound small RNAs from promoter-proximal RNA Polymerase II
Argonaute (Ago) proteins mediate post-transcriptional gene repression by binding  guide microRNAs (miRNAs) to regulate targeted RNAs. To confidently assess Agobound  small RNAs, we adapted a mouse embryonic stem cell system to express a single  inducible epitope-tagged Ago protein. Here, we report the small RNA profile of Agodeficient  cells and determine Ago-dependent stability is a common feature of mammalian  miRNAs. Considering both in vivo Ago-dependence for stability and Ago2 binding as  defined by immunopurification, we have identified a novel class of non-canonical  miRNAs derived from protein-coding gene promoters, which we name transcriptional  start site miRNAs (TSS-miRNAs). A subset of promoter-proximal RNA polymerase II  complexes produce hairpin RNAs that are processed in a DGCR8/Drosha-independent,  but Dicer-dependent manner. TSS-miRNA activity is detectable endogenously, upon  transfection of a mimic or by mRNA overexpression. Finally, we present evidence of  differential expression and conservation in humans, suggesting important roles in gene  regulation. Overall design: Examination of Ago immunoprecipitations and mESC without Ago proteins