Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites

Nucleic Acids Res. 2018 Jun 20;46(11):5737-5752. doi: 10.1093/nar/gky306.

Abstract

MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5' 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5' extensions up to 39 nt long. The 5'-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5' extension does not block Dicer processing. Rather, Dicer directly cleaves 5'-extended pre-miRNAs by recognizing its 3' end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5'-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cell Line
  • Exportin 1 Protein
  • Guanine / analogs & derivatives
  • Karyopherins / metabolism
  • Mice
  • MicroRNAs / chemistry
  • MicroRNAs / metabolism*
  • Protein Domains
  • RNA Caps
  • RNA Cleavage
  • RNA Interference
  • RNA Polymerase II / metabolism
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism*
  • RNA Processing, Post-Transcriptional
  • RNA Transport
  • RNA, Double-Stranded / chemistry
  • RNA, Double-Stranded / metabolism
  • Receptors, Cytoplasmic and Nuclear / metabolism
  • Ribonuclease III / chemistry
  • Ribonuclease III / metabolism*
  • Transcription Initiation Site*

Substances

  • Karyopherins
  • MicroRNAs
  • RNA Caps
  • RNA Precursors
  • RNA, Double-Stranded
  • Receptors, Cytoplasmic and Nuclear
  • Guanine
  • 7-methylguanine
  • RNA Polymerase II
  • Ribonuclease III