GSE29116
Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species
Efforts to catalogue eukaryotic transcripts have uncovered a set of species derived from the termini and exon/intron boundaries of protein-coding loci. The biogenesis pathways of these small RNAs (sRNAs) are largely unknown, but a mechanism depending on backtracking of RNA polymerase II (RNAPII) has been suggested. Moreover, the functional relevance, if any, of these sRNAs remains elusive. By sequencing 12-100nt transcripts from cells depleted of major RNA degradation enzymes as well as RNAs associated with the effector-proteins Argonaute (AGO) 1/2, we provide mechanistic models for sRNA production and utilization. We suggest that neither splice site associated (SSa)- nor transcription start site associated (TSSa)-RNAs arise from RNAPII backtracking. Instead SSa-RNAs are largely degradation products of mRNA splicing intermediates, while TSSa-RNAs likely derive from nascent RNA protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs, including such derived from 3''ends of introns (5''tailed miRtrons) and from mRNA 3''UTRs. Interestingly, both appear to draw from non-canonical microRNA (miRNA) biogenesis pathways. Overall design: 10 samples all from HeLa in three size ranges: 12-20, 18-30 and 30-100. 1 from 12-20: nuclear; 6 from 18-30: WT, nuclear, RRP40 knockdown, Ago1&2 IP, RRP40 knockdown and Ago1&2 IP, XRN1&2 knockdown; 3 from 30-100: WT, of RRP40 knockdown, XRN1&2 knockdown.