DICER cleavage fidelity is governed by 5′-end binding pockets
Nature
by Minh Khoa NgoMarch 4, 2026
RNA interference (RNAi) depends on DICER, an essential enzyme that processes RNA precursors into small regulatory RNAs. DICER cleaves RNA precursors according to the 5′-end counting rule, in which RNA length is measured from the 5′-end1–3. Previous work proposed a single 5′-end binding pocket that disfavours guanosine (5′-G), leading to cleavage inaccuracies4. Here we show that 5′-G promotes precise cleavage for many substrates. Using massively parallel dicing assays and cryo-electron microscopy, we identify a conserved guanosine-favoured (G-favoured) binding pocket in DICER, distinct from the previously described uridine-favoured (U-favoured) pocket. Together, these pockets influence the alignment between 21-nucleotide and 22-nucleotide cleavage registers, expanding the mechanism of small-RNA biogenesis in metazoan DICERs. We also find that conflicts between 5′-end binding and RNA-motif recognition can trigger RNA conformational adjustments that preserve accurate cleavage-site selection. In addition, conformational adjustments of the double-stranded RNA-binding domain (dsRBD) and PAZ domain help to align substrates with the catalytic centres for precise double-strand cleavage. These results show that the DICER cleavage mechanism integrates dual 5′-end binding pockets, RNA-motif influence and domain motions, advancing our understanding of microRNA biogenesis. Cryo-electron microscopy and massively parallel assays shed light on the mechanism by which DICER, a key enzyme in the RNase III family, cleaves RNA at precise locations to produce small RNAs.
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Originally published on Nature on 3/4/2026