2. Academic Validation
  3. Isoform characterization of m6A in single cells identifies its role in RNA surveillance

Isoform characterization of m6A in single cells identifies its role in RNA surveillance

  • Nat Commun. 2025 Jul 1;16(1):5828. doi: 10.1038/s41467-025-60869-0.
Zhijun Ren # 1 2 3,  Jialiang He # 1 2,  Xiang Huang # 1 2 3,  Yan Gao # 1 2 4,  Chuanchuan Wei # 1 2 3,  Zehong Wu 1 2,  Wenbing Guo 1 2 3,  Feng Wang 4 5 6,  Qingquan Zhao 7,  Xiang Sun 1 2,  Jie Zhang 1 2,  Nan Cao 1 2,  Lan Lin 8 9 10,  Jinkai Wang 11 12,  Yixian Cun 13 14
Affiliations

Affiliations

  • 1 Department of Histoembryology and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
  • 2 Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.
  • 3 Medical College of Jiaying University, Meizhou, China.
  • 4 Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 5 Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
  • 6 Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • 7 Center of Translational Medicine, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
  • 8 Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. linlan@chop.edu.
  • 9 Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. linlan@chop.edu.
  • 10 Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. linlan@chop.edu.
  • 11 Department of Histoembryology and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. wangjk@mail.sysu.edu.cn.
  • 12 Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China. wangjk@mail.sysu.edu.cn.
  • 13 Department of Histoembryology and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. cunyx3@mail.sysu.edu.cn.
  • 14 Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China. cunyx3@mail.sysu.edu.cn.
  • # Contributed equally.
PMID: 40593665 DOI: 10.1038/s41467-025-60869-0
Abstract

The distribution of m6A across various RNA isoforms and its heterogeneity within single cells are still not well understood. Here, we develop m6A-isoSC-seq, which employs both Oxford Nanopore long-read and Illumina short-read Sequencing on the same 10x Genomics single-cell cDNA library with APOBEC1-YTH induced C-to-U mutations near m6A sites. Through m6A-isoSC-seq on a pooled sample of three cell line origins, we unveil a profound degree of m6A heterogeneity at both the isoform and single-cell levels. Through comparisons across single cells, we identify widespread specific m6A methylation on certain RNA isoforms, usually those misprocessed RNA isoforms. Compared to the coding isoforms of the same genes, the expression of highly methylated misprocessed RNA isoforms is more sensitive to METTL3 depletion. These misprocessed RNAs tend to have excessive m6A sites in coding regions, which are targets of CDS-m6A decay (CMD). This study offers undocumented insights into the role of m6A in RNA surveillance.

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