YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex.

Hao Du,Ya Zhao,Jinqiu He,Hairui Xi,Yao Zhang,Jinbiao Ma,Ligang Wu,Mofang Liu

doi:10.1038/ncomms12626

Abstract

Methylation at the N6 position of adenosine (m6A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions. YT521-B homology domain family (YTHDF) proteins are the readers of m6A, the binding of which results in the alteration of the translation efficiency and stability of m6A-containing RNAs. However, the mechanism by which YTHDF proteins cause the degradation of m6A-containing RNAs is poorly understood. Here we report that m6A-containing RNAs exhibit accelerated deadenylation that is mediated by the CCR4–NOT deadenylase complex. We further show that YTHDF2 recruits the CCR4–NOT complex through a direct interaction between the YTHDF2 N-terminal region and the SH domain of the CNOT1 subunit, and that this recruitment is essential for the deadenylation of m6A-containing RNAs by CAF1 and CCR4. Therefore, we have uncovered the mechanism of YTHDF2-mediated degradation of m6A-containing RNAs in mammalian cells.

Highlights

Methylation at the N6 position of adenosine (m6A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions
In this study, we have demonstrated that expedited poly(A) shortening is the initiation step of the decay of m6A-containing RNAs, and that CAF1 and CCR4A/B of the CCR4–NOT complex are the key deadenylases responsible for the accelerated deadenylation
We have shown that the CCR4–NOT complex is recruited to m6A-containing RNAs through a direct interaction between the N-terminal region of YTHDF2, the reader of m6A and the superfamily homology (SH) domain of CNOT1, the scaffolding subunit of the CCR4–NOT complex

Summary

Introduction

Methylation at the N6 position of adenosine (m6A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions. We have uncovered the mechanism of YTHDF2-mediated degradation of m6A-containing RNAs in mammalian cells It is well-known that chemical modifications occur on genomic DNA and histone proteins, and that these modifications affect gene expression and have critical biological functions[1,2,3,4]. On receiving a degradation signal, the RNA molecule is subjected to one of the following pathways: the deadenylation-dependent decay pathway that starts with the shortening of the poly(A) tail, the deadenylation-independent decay pathway that starts with the removal of the 50-cap structure or the endonuclease-mediated decay pathway that is initiated by internal cleavage of the RNA. We present evidence that the m6A reader protein YTHDF2 recruits the CCR4–NOT deadenylase complex by directly interacting with the superfamily homology (SH) domain of CNOT1, the scaffolding subunit of the complex, to initiate deadenylation and decay of m6A-containing mRNAs

Methods

Findings

Conclusion