5-methylcytosine promotes mRNA export \u2014 NSUN2 as the methyltransferase and ALYREF as an m5C reader

Xin Yang,Jiawei Xu ,Weiyi Lai ,Samir Adhikari,Yingpu Sun ,Hui Sun ,Yongliang Zhao ,Chih-Hsien Huang ,Ang Li,Wen Xiao,Hailin Wang ,Bao‐Fa Sun ,Guibin Jiang ,Yu‐Sheng Chen ,Xing Wang,Devi Prasad Bhattarai,Haili Ma ,Bing Zhang,Niu Huang,Qin Zhu,Ying Yang,Yajuan Hao ,Min Sun,Yun‐Gui Yang

doi:10.1038/cr.2017.55

Abstract

5-methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that m5C modification is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, m5C formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and m5C is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive m5C profiles of mammalian transcriptomes and suggests an essential role for m5C modification in mRNA export and post-transcriptional regulation.

Highlights

The identification of fat mass and obesity-associated (FTO) as the first discovered RNA m6A demethylase [1] established the reversible nature of m6A modification
This has revealed the main features of m5C modifications: their prevalence and unique distribution along transcripts and their tissue-specific and dynamic nature in mRNA
We further demonstrated that m5C is recognized by the mRNA export adaptor ALYREF in experiments in vitro and in vivo

Summary

Introduction

The identification of fat mass and obesity-associated (FTO) as the first discovered RNA m6A demethylase [1] established the reversible nature of m6A modification. Since accumulating lines of evidence have pointed to a broad effect of m6A on mRNA metabolism [2,3,4,5,6,7,8,9,10,11,12,13,14] Another two RNA modifications, pseudouridine (ψ) [15,16,17] and N1-methyladenosine (m1A) [18, 19], have been shown to play a vital role in posttranscriptional gene regulation. All these lines of emerging evidence point to the logical speculation that reversible RNA modifications may serve as novel epigenetic markers with profound biological significance in RNA metabolism. It is crucial to clarify how m5C modifications are distributed on mRNAs in different cell types, tissues, and organisms, and to identify and characterize the roles of the protein factors responsible for adding/removing/reading these modifications in order to gain better understanding of the potential significance of m5C modification for RNA metabolism

Methods

Results

Conclusion