Control of noncoding RNA production and histone levels by a 5' tRNA fragment

Small RNAs derived from mature tRNAs, referred to as tRNA fragments or “tRFs”, are an emerging class of regulatory RNAs with poorly understood functions in cellular regulation. We recently identified a role for one specific tRF – 5' tRF-Gly-GCC, or tRF-GG – in repression of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs normally synthesized in Cajal bodies. Among these noncoding RNAs, tRF-GG regulation of the U7 snRNA modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, activity of a histone 3' UTR reporter, and ultimately on MERVL regulation could all be suppressed by the U7 RNA. We show that the related RNA-binding proteins hnRNPF and H bind directly to tRF-GG, and are required for Cajal body biogenesis. Together, our data reveal a conserved mechanism for 5' tRNA fragment control of noncoding RNA biogenesis and, consequently, in global chromatin organization. Overall design: Mouse embryonic stem cells were transfected with tRNA fragments, LNA sequences against tRNA fragments, snRNAs, or siRNAs. Changes in gene expression were quantified using RNAseq and metabolic labeling. Changes in ribosomal rRNA methylation were quantified using Ribomethseq. Changes in chromatin architecture were probed with ATAC-seq. E14 mESCs were transfected with LNA-containing oligos antisense to tRF-GG or Mock transfected. iClip libraries were constructed against hnRNPF/H using sc-32310 antibody, with protocol from Zarnegar et al. 2016 Nat Methods.