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

doi:10.1261/rna.078436.120

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

¹Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
²Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
³Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
⁴Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA

Corresponding author: agoldstr{at}umn.edu

↵5 Present address: Department of Biochemical Engineering, Emory University, Atlanta, GA 30322, USA
↵6 Present address: Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
↵7 Present address: Rockefeller University, Laboratory of Retrovirology, New York, NY 10065, USA
↵8 Present address: Messenger RNA Regulation and Decay Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA

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.

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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.078436.120.

Received November 17, 2020.
Accepted December 28, 2020.

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