Wheat in vivo RNA structure landscape reveals a prevalent role of RNA structure in modulating translational subgenome expression asymmetry
| Autor: | Ricardo H. Ramirez-Gonzalez, Bao Liu, Wenqing Sun, Ling Ding, Xiaofei Yang, Fei Lu, Ji Li, Cristobal Uauy, Xuebo Zhao, Jitender Cheema, Haopeng Yu, Azahara C. Martín, Yiliang Ding, Huakun Zhang |
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| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
QH301-705.5 Arabidopsis Biology QH426-470 riboSNitches 01 natural sciences Genome Transcriptome Domestication Evolution Molecular Polyploidy 03 medical and health sciences Polyploid Gene Expression Regulation Plant Xiaofei Yang and Haopeng Yu contributed equally to this study Translational regulation Gene duplication Genetics Nucleic acid structure Biology (General) RNA structure Gene Triticum 030304 developmental biology 2. Zero hunger 0303 health sciences Gene Expression Profiling Research RNA food and beverages Homoeologous asymmetry Tetraploidy Evolutionary biology RNA Plant Wheat Hybridization Genetic Genome Plant 010606 plant biology & botany |
| Zdroj: | Genome Biology Genome Biology, Vol 22, Iss 1, Pp 1-26 (2021) |
| ISSN: | 1474-760X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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