Brassinosteroid receptors reveal conserved features of exon-embedded gene regulation

Background

In multicellular organisms, precise spatial regulation of gene expression is essential for proper development. Traditionally, this regulation is attributed to cis-regulatory elements located in promoters, intergenic regions, or introns. However, recent studies in diverse eukaryotic systems suggest that coding sequences carry regulatory sequences that influence spatial gene expression (Mouren et al., 2026). This was supported by the prediction of thousands of candidate exonic enhancers (EEs) in the plant model Arabidopsis thaliana (hereafter Arabidopsis).

Consistent with this idea, a previous study suggested that the gene body of BRI1, which encodes a receptor of the phytohormones brassinosteroids, contains regulatory information that contributes to its spatial expression pattern in roots (Blanco-Touriñán et al., 2024). However, the molecular mechanism(s) through which the BRI1 coding region controls spatial gene expression remained unknown (Blanco-Touriñán & Hardtke, 2025). To investigate how BRI1 regulates its own expression, Denia-Mondéjar and colleagues dissected its coding sequence in their latest preprint.

Key findings of the preprint

After ruling out alternative transcription start sites and DNA methylation as potential mechanisms, the author team identified an exonic enhancer within the BRI1 coding sequence containing several transcription factor binding sites (Fig. 1). Using different constructs and confocal microscopy, they demonstrated that this exonic enhancer contributes to the spatial expression pattern of BRI1, which is essential for optimal root growth (Fig. 1).

Using available datasets, the authors then investigated the prevalence and genomic distribution of exonic enhancers across the Arabidopsis genome. Remarkably, more than 20% of protein-coding genes carry exonic enhancers, which are preferentially located in the 3′ regions of genes involved in environmental responses and developmental processes. The authors further extended their analysis to other plant species, including tomato and the non-vascular plant Marchantia polymorpha (Fig. 1). Excitingly, they identified exonic enhancers with similar genomic features in both species, suggesting that this regulatory mechanism may be conserved across land plants.

Finally, their analyses suggested that the regulatory effects of exonic enhancers may extend beyond the host gene, potentially influencing neighboring and even distant genes through chromatin interactions.

What I like about the preprint

This preprint reveals an additional layer of transcriptional regulation and provides a new perspective on how we decipher the genome. The findings are exciting and paradigm-shifting as they challenge the conventional view of exons as simple carriers of protein coding information. Also, this work perfectly highlights the importance of considering the genome as a 3D structure.

Future directions

Functional characterisation of exonic enhancers will be essential to determine the extent to which they contribute to different aspects of gene regulation, as the results of this study indicate that their function is not universally restricted to the control of spatial gene expression.
Also, single-cell transcriptomic could reveal whether exonic enhancers not only determine spatial expression patterns but also modulate levels of gene expression within each cell type.

From an evolutionary perspective, future studies with Marchantia could provide valuable insights into how exonic enhancers evolved and contribute to gene regulation across land plants. Expanding these comparisons to a broader range of plant species may provide insight into the evolutionary pressures that shaped the recruitment and distribution of these regulatory elements.

Questions for the authors

Are genes carrying multiple EEs associated with specific biological processes? Have you examined whether their TFBS enrichment is complementary or rather redundant?

If EEs can influence neighboring and distal genes, have you checked whether these genes have been previously described as forming a GRN?

Based on the GO term enrichment, I would expect many genes with EEs to belong to the Arabidopsis accessory or super-accessory genome. Have you considered investigating this?

What is your hypothesis about how this regulatory layer has been recruited and maintained alongside promoters and other cis-regulatory elements? Especially, given that BRI1 EE acts in concert with its promoter.

Have you considered comparing your results with the Monroe et al. datasets to check whether genes containing EEs display higher mutation rates or frequencies? One hypothesis for the presence of regulatory elements within exons would be that it provides better protection from mutations. Interestingly, they showed that genes with higher mutation probabilities are also associated with environmental responses and development.

References

Mouren, J., Torres, M., Van Ouwerkerk, A., Manosalva, I., Gallardo, F., Spicuglia, S., & Ballester, B. (2026). Exonic enhancers are a widespread class of dual-function regulatory elements. Nature Communications, 17(1). https://doi.org/10.1038/s41467-026-71220-6

Blanco-Touriñán, N., Rana, S., Nolan, T. M., Li, K., Vukašinović, N., Hsu, C., Russinova, E., & Hardtke, C. S. (2024). The brassinosteroid receptor gene BRI1 safeguards cell-autonomous brassinosteroid signaling across tissues. Science Advances, 10(39), eadq3352. https://doi.org/10.1126/sciadv.adq3352

Blanco‐Touriñán, N., & Hardtke, C. S. (2025). Specificity of brassinosteroid perception and its integration at signaling crossroads in vascular development. The Plant Journal, 124(3), e70570. https://doi.org/10.1111/tpj.70570

Tags: brassinosteroid receptors, chromatin interactions, gene expression regulation, plant biology, regulatory genomics