Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome

Isioma I.I. Enwerem, Nathan D. Elrod, Chung Te Chang, Ai Lin, Ping Ji, Jennifer A. Bohn, Yevgen Levdansky, Eric J. Wagner, Eugene Valkov, Aaron C. Goldstrohm

Research output: Contribution to journalArticlepeer-review

Abstract

Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad coregulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved amino-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the mRNA decapping enzyme, DCP2, has an important role in repression by PUM1&2 amino-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent mRNA decay pathway.

Original languageEnglish (US)
Pages (from-to)445-464
Number of pages20
JournalRNA
Volume27
Issue number4
DOIs
StatePublished - Apr 2021

Keywords

  • CCR4-NOT
  • Deadenylation
  • mRNA decay
  • Pumilio
  • Translational repression

ASJC Scopus subject areas

  • Molecular Biology

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