Structural and functional basis of mammalian microRNA biogenesis by Dicer

• Published in: Molecular cell Vol. 82; no. 21; pp. 4064 - 4079.e13
• Main Authors: Zapletal, David, Taborska, Eliska, Pasulka, Josef, Malik, Radek, Kubicek, Karel, Zanova, Martina, Much, Christian, Sebesta, Marek, Buccheri, Valeria, Horvat, Filip, Jenickova, Irena, Prochazkova, Michaela, Prochazka, Jan, Pinkas, Matyas, Novacek, Jiri, Joseph, Diego F., Sedlacek, Radislav, Bernecky, Carrie, O’Carroll, Dónal, Stefl, Richard, Svoboda, Petr
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 03-11-2022; Cell Press
• Subjects: Animals; Carrier Proteins - metabolism; cryo-EM; DExD; Dicer; dsRBD; dsRNA; helicase; Mammals - metabolism; Mice; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; mirtron; PKR; Ribonuclease III - metabolism; RNA Interference; RNAi; TARBP2; dsRNA; DExD; mirtron; RNAi; dsRBD; Dicer; PKR; miRNA; helicase; cryo-EM; TARBP2
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2022.10.010

MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.
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•Structures of mouse Dicer⋅pre-miRNA complexes show pre-cleavage and cleavage states•Dicer’s DExD/H domain is essential in mice and has structural, not enzymatic role•Dicer’s DExD/H domain assures high fidelity of miRNA biogenesis in vivo•Mammalian Dicer is committed to miRNA pathway through DExD/H-RNase IIIb interaction
Zapletal et al. provide structural and functional in vivo analyses of murine RNase III Dicer variants, which (1) explain how Dicer variants recognize and cleave substrates in mammalian miRNA and RNAi pathways and (2) show ATP-independent essential structural role of the DExD/H helicase domain in committing mammalian Dicer to high-fidelity miRNA biogenesis.