Transposable element (TE) has long been a dark side of genetic studies, whose biological function is hampered by the long distance of TEs to genes and no typical functional sequence features. This study combines nascent RNA sequencing technology with genetic evidence to reveal that polyploid wheat subgenome-specific transposons mediate spike specificity, providing new ideas and clues for studying the function of transposons, and demonstrating the close relationship between transposon expansion and polyploid developmental plasticity.

Transposons largely contribute divergent sequences in wheat

Wheat is a highly successful crop cultivated worldwide. The majority of wheat we plant today is hexaploid through two successive polyploidization events, resulting in the presence of three similar, yet distinct subgenomes. Notably, the sequence variances among subgenomes were primarily generated by specific transposable element (TE) expansions in diploid progenitors, predominantly in the intergenic regions. On the one hand, these variations are potentially key factors enabling the formation and stable inheritance of allohexaploid wheat. On the other hand, these diverse sequences themselves also harbor regulatory capabilities that co-opt with the host genome.

The hidden force beneath the TE sequences

TEs, once considered "junk" DNA, have recently been demonstrated to play diverse roles after prolonged interaction with the host genome. In our previous research, we explored the multifaceted functions of TEs in wheat from various perspectives. In the work of 3D-genomic organization, we demonstrated subgenome-dominant TE families associated with maintaining subgenome-specific chromatin territories1. In the work of building the wheat regulatory network by DAP-seq, we observed that despite that TE transposition is largely suppressed by hyper DNA methylation, some specific TE families contributes to a large amount of transcription factor binding site (TFBS)2. These findings highlight the versatility of TEs in influencing not only the stability of the wheat genome but also its regulatory potential. 
     To deduce their cellular functions, we employed epigenomic signatures to distinguish active and repressive chromatin architecture surrounding these TE-derived regulatory elements 3. We further validated the activity of enhancer-like elements in wheat by using nascent RNA sequencing4, a technology detecting nascent transcription from genes and regulatory elements. We demonstrated that enhancer nascent RNA (eRNA) serves as a reliable marker of enhancer activity in mammalian analysis. These findings lay a solid foundation for investigating the expansion of TEs in relation to regulatory specificity and the developmental plasticity of polyploids.

Subgenome-biased TE-derived enhancer-like elements regulating subgenome-biased spike specificity

In order to decipher the biological function of TEs, we probed tissue-specific nascent RNA expression across typical developmental stages via CAGE (cap-analysis gene expression) sequencing, a technology detecting the transcription start site of nascent transcripts. By employing a hidden Markov model integrating CAGE-seq, epigenomic and transcriptomic profiles, we detected  11,452 enhancer-like elements (ELEs) produce nascent ncRNAs. Approximately 20% of the ELE-RNA TSSs are embedded in TEs, which is much higher than the proportion of gene TSS that overlapped with TEs (5%). 
     Among the TE families highly abundant in the wheat genome, the top enriched TE subfamily that contributed to ELE-RNA is RLG_famc7.3, whose expansion occurred specifically in the diploid progenitor of subgenome A after the divergence from the A-B-D common ancestor. RLG_famc7.3-ELE also exhibited the most significant tissue specificity, biased transcript in spike. Both RLG_famc7.3 knocked down and overexpression resulted in increased distance between spikelets, which is a domesticated phenotype of wheat.  Evolutionary comparison indicate that this TE subfamily were gradually fixed in polyploid wheat, possibly by domestication. 
     These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.
     The strategy and findings help to elucidate the causal effects of TEs on agronomic traits, providing insight into the direct regulatory function of numerous TEs in common wheat, and their contribution to developmental specificity and polyploid plasticity.

For details, please refer to our paper at https://www.nature.com/articles/s41467-023-42771-9. 

Photo and article writing: Yilin Xie, Yijing Zhang

References:

1    Jia, J. et al. Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression. Genome Biol 22, 26, doi:10.1186/s13059-020-02225-7 (2021).
2    Zhang, Y. et al. Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat. Nat Commun 13, 6940, doi:10.1038/s41467-022-34290-w (2022).
3    Li, Z. et al. The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements. Genome Biol 20, 139, doi:10.1186/s13059-019-1746-8 (2019).
4    Xie, Y. et al. Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat. Genome Biology 23, 109, doi:10.1186/s13059-022-02675-1 (2022).