Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry

Genome Biology

Jitender Cheema¹  Yiliang Ding¹  Azahara C. Martín²  Ricardo Ramirez-Gonzalez²  Cristobal Uauy²  Ji Li³  Bao Liu³  Wenqing Sun³  Huakun Zhang³  Ling Ding³  Haopeng Yu⁴  Xiaofei Yang⁴  Xuebo Zhao⁵  Fei Lu⁵ 

[1] Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK;Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK;Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, 130024, Changchun, China;Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, 130024, Changchun, China;Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK;State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China;University of Chinese Academy of Sciences, Beijing, China;CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China;

关键词: Polyploidy;    Wheat;    Translational regulation;    Homoeologous asymmetry;    RNA structure;    riboSNitches;    Xiaofei Yang and Haopeng Yu contributed equally to this study.;   

DOI  :  10.1186/s13059-021-02549-y

来源: Springer

【 摘 要 】

BackgroundPolyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene content and expression. Polyploid wheats are allopolyploids with most genes present in two (tetraploid) or three (hexaploid) functional copies, which commonly show subgenome expression asymmetry. It is unknown whether a similar subgenome asymmetry exists during translation. We aim to address this key biological question and explore the major contributing factors to subgenome translation asymmetry.ResultsHere, we obtain the first tetraploid wheat translatome and reveal that subgenome expression asymmetry exists at the translational level. We further perform in vivo RNA structure profiling to obtain the wheat RNA structure landscape and find that mRNA structure has a strong impact on translation, independent of GC content. We discover a previously uncharacterized contribution of RNA structure in subgenome translation asymmetry. We identify 3564 single-nucleotide variations (SNVs) across the transcriptomes between the two tetraploid wheat subgenomes, which induce large RNA structure disparities. These SNVs are highly conserved within durum wheat cultivars but are divergent in both domesticated and wild emmer wheat.ConclusionsWe successfully determine both the translatome and in vivo RNA structurome in tetraploid wheat. We reveal that RNA structure serves as an important modulator of translational subgenome expression asymmetry in polyploids. Our work provides a new perspective for molecular breeding of major polyploid crops.

【 授权许可】

CC BY