Abstract

N6-methyladenosine (m6A) is enriched in 3′untranslated region (3′UTR) and near stop codon of mature polyadenylated mRNAs in mammalian systems and has regulatory roles in eukaryotic mRNA transcriptome switch. Significantly, the mechanism for this modification preference remains unknown, however. Herein we report a characterization of the full m6A methyltransferase complex in HeLa cells identifying METTL3/METTL14/WTAP/VIRMA/HAKAI/ZC3H13 as the key components, and we show that VIRMA mediates preferential mRNA methylation in 3′UTR and near stop codon. Biochemical studies reveal that VIRMA recruits the catalytic core components METTL3/METTL14/WTAP to guide region-selective methylations. Around 60% of VIRMA mRNA immunoprecipitation targets manifest strong m6A enrichment in 3′UTR. Depletions of VIRMA and METTL3 induce 3′UTR lengthening of several hundred mRNAs with over 50% targets in common. VIRMA associates with polyadenylation cleavage factors CPSF5 and CPSF6 in an RNA-dependent manner. Depletion of CPSF5 leads to significant shortening of 3′UTR of over 2800 mRNAs, 84% of which are modified with m6A and have increased m6A peak density in 3′UTR and near stop codon after CPSF5 knockdown. Together, our studies provide insights into m6A deposition specificity in 3′UTR and its correlation with alternative polyadenylation.

Details

Title
VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation
Author
Yue, Yanan 1 ; Liu, Jun 2 ; Cui, Xiaolong 2 ; Cao, Jie 1 ; Luo, Guanzheng 2   VIAFID ORCID Logo  ; Zhang, Zezhou 1 ; Cheng, Tao 1 ; Gao, Minsong 1 ; Xiao Shu 1 ; Ma, Honghui 2 ; Wang, Fengqin 3 ; Wang, Xinxia 3 ; Shen, Bin 4 ; Wang, Yizhen 3 ; Feng, Xinhua 5 ; He, Chuan 2   VIAFID ORCID Logo  ; Liu, Jianzhao 6   VIAFID ORCID Logo 

1  MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China 
2  Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA 
3  College of Animal Sciences, Key Laboratory of Molecular Nutrition, Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China 
4  State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, Jiangsu, China 
5  Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China 
6  MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, China; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China 
Pages
1-17
Publication year
2018
Publication date
Feb 2018
Publisher
Springer Nature B.V.
e-ISSN
20565968
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41421-018-0019-0
ProQuest document ID
2008351761
Copyright
© 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.