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

Abstract

Background Polyploidy, 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. Results Here, 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. Conclusions We 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.

The Potential Role of RNA Structure in Crop Molecular Breeding

“…Two types of chemical probing methods have been successfully applied in crops (Deng et al, 2018 ; Su et al, 2018 ; Yang et al, 2021 ). One is the dimethyl sulfate (DMS)-based method whereby single-stranded A and C are methylated by DMS (Deng et al, 2018 ; Su et al, 2018 ), whilst the other method is the SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension)-based method, whereby the single-strandedness of all four nucleotides are acetylated (Yang et al, 2021 ). Both in vivo RNA structuromes in rice and wheat captured the RNA structures for over half of their transcriptomes, providing a comprehensive view of general RNA structure features (Deng et al, 2018 ; Yang et al, 2021 ).…”

“…The translation process is one of the key post-transcriptional regulations of gene expression (Zhang and Ding, 2021 ). The in vivo RNA structure landscapes in both rice and wheat revealed that the single-stranded region upstream of the start codon in the 5′UTR was significantly associated with high translation efficiency (Deng et al, 2018 ; Yang et al, 2021 ). This single-strandedness may promote ribosome binding and/or enhance ribosome initiation.…”

“… The gene functions of wheat homoeologous pairs preferring RNA structure-mediated translational subgenome asymmetry and the evolved riboSNitch during wheat domestication. (A) The detailed gene functions of wheat homoeologous pairs have significant correlation coefficients between subgenomic RNA structural and subgenomic translational differences (Yang et al, 2021 ). The green circles highlight the functions related to the responses to stimulus; the gray circles highlight the functions related to the intracellular anatomical structures; the red circles highlight the functions related to the binding functions; the rose fog circles highlight the functions related to the regulation of gene expression.…”

“…In addition to these individual examples of the importance of SNV-induced RNA structure alteration, a recent genome-wide study on the in vivo RNA structure landscape in the tetraploid durum wheat cultivar, Kronos, identified 3,564 SNVs which induced large structure disparities, known as riboSNitches between the A and B subgenomes (Yang et al, 2021 ). Among these riboSNitches, there were more transition (i.e., similar shape base interchanges) riboSNitches than transversion (i.e., dissimilar shape base interchanges) riboSNitches (Yang et al, 2021 ). These riboSNitches tend to be conserved across tetraploid T. turgidum spp.…”

“…This C41/A41 riboSNitch resulted in significant RNA structure differences between A and B subgenome homoeologs (Yang et al, 2021 ). The C41 formed into a C-G base pair with G22 in the A subgenome homoeolog while the A41 is single-stranded in the B subgenome homoeolog (Yang et al, 2021 ). Notably, this riboSNitch caused the translation efficiency of the A subgenome to be significantly lower than that of the B subgenome, suggesting that this riboSNitch was selected during domestication to diversify the translation efficiency between subgenomes (Yang et al, 2021 ).…”