Editing the message: 3′UTR cis-regulatory elements at the nexus of post-transcriptional regulation and crop improvement

Abstract

Climate change and soil degradation pose increasingly serious threats to global food security, highlighting the need for continued innovation and diversification in plant breeding strategies. Plant growth and development rely on precise and dynamic regulation of gene expression that enables rapid responses to environmental cues. Increasing evidence highlights the central roles of cis-regulatory elements (CREs), including RNA sequence motifs, RNA modifications, and secondary or tertiary RNA structures, in post-transcriptional control. These CREs are enriched within the untranslated regions (UTRs) of plant mRNAs. In this review, we summarize the diverse CREs characterized to date, particularly those located within the 3′UTR, and describe how they function together with trans-acting factors like RNA-binding proteins to regulate mRNA stability, translation efficiency, subcellular localization, and non-cell-autonomous mobility. These processes constitute key mechanisms for the spatiotemporal regulation of gene expression that underlies plant environmental responses and resilience. We further discuss emerging opportunities and challenges in harnessing 3′UTR CREs as targets and tools for next-generation crop improvement. By integrating recent advances in post-transcriptional biology with molecular breeding frameworks, 3′UTR CREs offer a promising framework for achieving precise, tunable, and robust regulation of agronomically important traits.

Keywords

3′ untranslated region (3′UTR) / Cis-regulatory elements / Post-transcriptional regulation / N⁶-methyladenosine (m⁶A) / RNA structure / Crop breeding

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Funding

National Natural Science Foundation of China(32370366)

Hubei Hongshan Laboratory(105-11020113)

Huazhong Agricultural University(start-up funding)

Young Scientist Fostering Funds for the National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops (52010020108)

Japan Society for the Promotion of Science(25H01341)

RIGHTS & PERMISSIONS

The Author(s)