Antagonistic actions of two human Pan3 isoforms on global mRNA turnover

RNA. 2017 Sep;23(9):1404-1418. doi: 10.1261/rna.061556.117. Epub 2017 May 30.

Abstract

Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does. Pan2 deadenylase activity is enhanced by Pan3S but suppressed by Pan3L. Knocking down individual Pan3 isoforms has opposing effects on the global poly(A) tail length profile, P-body formation, and different mRNA decay pathways. Transcriptome-wide analysis of Pan3 knockdown effects on mRNA turnover shows that depleting either Pan3 isoform causes profound and extensive changes in mRNA stability globally. These results reveal a new fundamental step governing mammalian mRNA metabolism. We propose that the first phase of deadenylation, coordinated through the interplay among the two Pan3 isoforms, Pan2, and PABP, represents a cytoplasmic mRNA maturation step important for proper mRNA turnover.

Keywords: P-body; Pan2-Pan3 complex; deadenylation; mRNA turnover; transcriptome regulation.

Publication types

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

MeSH terms

  • Animals
  • Carrier Proteins / chemistry
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism*
  • Cell Line
  • Cell Proliferation
  • Exoribonucleases / chemistry
  • Exoribonucleases / metabolism
  • Gene Expression Regulation
  • Gene Knockdown Techniques
  • Humans
  • Mice
  • MicroRNAs / genetics
  • Mutation
  • Poly A
  • Polyadenylation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Isoforms
  • RNA Stability
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism*
  • Transcriptome

Substances

  • Carrier Proteins
  • MicroRNAs
  • PAN3 protein, human
  • Protein Isoforms
  • RNA, Messenger
  • Poly A
  • Exoribonucleases
  • PAN2 protein, human