Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome
- Isioma I.I. Enwerem1,
- Nathan D. Elrod2,
- Chung-Te Chang3,
- Ai Lin2,
- Ping Ji2,
- Jennifer A. Bohn4,
- Yevgen Levdansky3,
- Eric J Wagner2,
- Eugene Valkov3 and
- Aaron Goldstrohm1,5
- 1 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
- 2 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA;
- 3 Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany;
- 4 Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- ↵* Corresponding author; email: agoldstr{at}umn.edu
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 co-regulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved N-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 N-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.
Keywords
- Received November 17, 2020.
- Accepted December 28, 2020.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
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