Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production

J Cell Biol. 2008 Jul 14;182(1):61-76. doi: 10.1083/jcb.200803111.

Abstract

MicroRNAs (miRNAs) are noncoding RNAs with important roles in regulating gene expression. In studying the earliest nuclear steps of miRNA biogenesis, we observe that primary miRNA (pri-miRNA) transcripts retained at transcription sites due to the deletion of 3'-end processing signals are converted more efficiently into precursor miRNAs (pre-miRNAs) than pri-miRNAs that are cleaved, polyadenylated, and released. Flanking exons, which also increase retention at transcription sites, likewise contribute to increased levels of intronic pri-miRNAs. Consistently, efficiently processed endogenous pri-miRNAs are enriched in chromatin-associated nuclear fractions. In contrast, pri-miRNAs that accumulate to high nuclear levels after cleavage and polyadenylation because of the presence of a viral RNA element (the ENE of the Kaposi's sarcoma-associated herpes virus polyadenylated nuclear RNA) are not efficiently processed to precursor or mature miRNAs. Exogenous pri-miRNAs unexpectedly localize to nuclear foci containing splicing factor SC35; yet these foci are unlikely to represent sites of miRNA transcription or processing. Together, our results suggest that pri-miRNA processing is enhanced by coupling to transcription.

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

  • Chromatin / genetics
  • Exons / genetics
  • HeLa Cells
  • Humans
  • Introns / genetics
  • MicroRNAs / biosynthesis*
  • MicroRNAs / genetics*
  • Nuclear Proteins / metabolism
  • Polyadenylation
  • RNA Polymerase III / metabolism
  • RNA Processing, Post-Transcriptional
  • RNA Transport
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Viral / genetics
  • Regulatory Sequences, Nucleic Acid / genetics
  • Ribonucleoproteins / metabolism
  • Sequence Deletion
  • Serine-Arginine Splicing Factors
  • Subcellular Fractions
  • Transcription, Genetic*
  • mRNA Cleavage and Polyadenylation Factors / metabolism

Substances

  • Chromatin
  • MicroRNAs
  • Nuclear Proteins
  • RNA, Messenger
  • RNA, Viral
  • Ribonucleoproteins
  • mRNA Cleavage and Polyadenylation Factors
  • SRSF2 protein, human
  • Serine-Arginine Splicing Factors
  • RNA Polymerase III