Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing
Zihe Xu,
Xiaoqi Zheng,
Jiajun Fan,
Yuting Jiao,
Sihao Huang,
Yingyuan Xie,
Shunlan Xu,
Yi Lu,
Anrui Liu,
Runzhou Liu,
Ying Yang,
Guan-Zheng Luo,
Tao Pan,
Xiaoyun Wang
Affiliations
Zihe Xu
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
Xiaoqi Zheng
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
Jiajun Fan
School of Life Sciences, South China Normal University, Guangzhou 510631, China
Yuting Jiao
School of Life Sciences, South China Normal University, Guangzhou 510631, China
Sihao Huang
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
Yingyuan Xie
MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
Shunlan Xu
School of Life Sciences, South China Normal University, Guangzhou 510631, China
Yi Lu
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
Anrui Liu
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China
Runzhou Liu
School of Life Sciences, South China Normal University, Guangzhou 510631, China
Ying Yang
CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
Guan-Zheng Luo
MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
Tao Pan
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
Xiaoyun Wang
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; School of Life Sciences, South China Normal University, Guangzhou 510631, China; University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding author
Summary: It has been widely recognized that the microbiota has the capacity to shape host gene expression and physiological functions. However, there remains a paucity of comprehensive study revealing the host transcriptional landscape regulated by the microbiota. Here, we comprehensively examined mRNA landscapes in mouse tissues (brain and cecum) from specific-pathogen-free and germ-free mice using nanopore direct RNA sequencing. Our results show that the microbiome has global influence on a host’s RNA modifications (m6A, m5C, Ψ), isoform generation, poly(A) tail length, and transcript abundance in both brain and cecum tissues. Moreover, the microbiome exerts tissue-specific effects on various post-transcriptional regulatory processes. In addition, the microbiome impacts the coordination of multiple RNA modifications in host brain and cecum tissues. In conclusion, we establish the relationship between microbial regulation and gene expression. Our results help the understanding of the mechanisms by which the microbiome reprograms host gene expression.
