Sequestration of microRNA-mediated target repression by the Ago2-associated RNA-binding protein FAM120A

Timothy J. Kelly; Hiroshi I. Suzuki; Jesse R. Zamudio; Megumu Suzuki; Phillip A. Sharp

doi:10.1261/rna.071621.119

Sequestration of microRNA-mediated target repression by the Ago2-associated RNA-binding protein FAM120A

¹David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
²Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
³Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

Corresponding author: sharppa{at}mit.edu

↵4 These authors contributed equally to this work.

↵5 Present address: Cardiovascular and Metabolic Disease, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts 02139, USA

Abstract

Argonaute (Ago) proteins interact with various binding partners and play a pivotal role in microRNA (miRNA)-mediated silencing pathways. By utilizing immunoprecipitation followed by mass spectrometry to determine cytoplasmic Ago2 protein complexes in mouse embryonic stem cells (mESCs), we identified a putative RNA-binding protein FAM120A (also known as OSSA/C9ORF10) as an Ago2 interacting protein. Individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) analysis revealed that FAM120A binds to homopolymeric tracts in 3′-UTRs of about 2000 mRNAs, particularly poly(G) sequences. Comparison of FAM120A iCLIP and Ago2 iCLIP reveals that greater than one-third of mRNAs bound by Ago2 in mESCs are co-bound by FAM120A. Furthermore, such FAM120A-bound Ago2 target genes are not subject to Ago2-mediated target degradation. Reporter assays suggest that the 3′-UTRs of several FAM120A-bound miRNA target genes are less sensitive to Ago2-mediated target repression than those of FAM120A-unbound miRNA targets and FAM120A modulates them via its G-rich target sites. These findings suggest that Ago2 may exist in multiple protein complexes with varying degrees of functionality.

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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.071621.119.

Received April 29, 2019.
Accepted July 1, 2019.

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