Widespread occurrence of microRNA-mediated target cleavage on membrane-bound polysomes

Genome Biol. 2021 Jan 5;22(1):15. doi: 10.1186/s13059-020-02242-6.


Background: Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action.

Results: We investigate the cytoplasmic partitioning of sRNAs and their targets globally in maize (Zea mays, inbred line "B73") and rice (Oryza sativa, cv. "Nipponbare") by high-throughput sequencing of polysome-associated sRNAs and 3' cleavage fragments, and find that both miRNAs and a subset of 21-nucleotide (nt)/22-nt siRNAs are enriched on membrane-bound polysomes (MBPs) relative to total polysomes (TPs) across different tissues. Most of the siRNAs are generated from transposable elements (TEs), and retrotransposons positively contributed to MBP overaccumulation of 22-nt TE-derived siRNAs (TE-siRNAs) as opposed to DNA transposons. Widespread occurrence of miRNA-mediated target cleavage is observed on MBPs, and a large proportion of these cleavage events are MBP-unique. Reproductive 21PHAS (21-nt phasiRNA-generating) and 24PHAS (24-nt phasiRNA-generating) precursors, which were commonly considered as noncoding RNAs, are bound by polysomes, and high-frequency cleavage of 21PHAS precursors by miR2118 and 24PHAS precursors by miR2275 is further detected on MBPs. Reproductive 21-nt phasiRNAs are enriched on MBPs as opposed to TPs, whereas 24-nt phasiRNAs are nearly completely devoid of polysome occupancy.

Conclusions: MBP overaccumulation is a conserved pattern for cytoplasmic partitioning of sRNAs, and endoplasmic reticulum (ER)-bound ribosomes function as an independent regulatory layer for miRNA-induced gene silencing and reproductive phasiRNA biosynthesis in maize and rice.

Keywords: Membrane-bound polysome; Oryza sativa; PARE; Target cleavage; Zea mays; miRNA; phasiRNA; siRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • DNA Transposable Elements
  • Endoplasmic Reticulum
  • Gene Expression Regulation, Plant*
  • Gene Silencing
  • Genes, Plant
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism*
  • Nucleotides
  • Oryza / genetics
  • Oryza / metabolism
  • Polyribosomes / metabolism*
  • RNA, Plant / genetics*
  • RNA, Plant / metabolism*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • Zea mays / genetics
  • Zea mays / metabolism


  • DNA Transposable Elements
  • MicroRNAs
  • Nucleotides
  • RNA, Plant
  • RNA, Small Interfering