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November 27, 2025
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Researchers have identified a new genetic mechanism that allows plants to keep acclimation genes ready for a rapid response to stress, which could enhance plant resilience under adverse climatic conditions.
- Researchers have identified a new genetic mechanism that allows plants to keep acclimation genes ready for a rapid response to stress.
- This process depends on a specific genetic architecture, a conserved feature that places stress-response genes in a stand-by state.
- This evolutionary strategy has been verified in major crops such as rice and maize, opening the door to developing crops with greater cold resistance.
Researchers from the Centre for Research in Agricultural Genomics (CRAG) and the Umeå Plant Science Centre (UPSC) have achieved a fundamental discovery to understand and enhance plant resilience under adverse climatic conditions.
This scientific research, published in the journal Molecular Plant and involving CRAG researcher Martí Quevedo and CSIC researcher at CRAG Elena Monte, has identified an unexplored genetic mechanism that allows plants to keep acclimation genes to environmental stress, such as cold, “ready” for a rapid response.
CASt and a special genetic architecture: the hidden stand-by mechanism
Transcription is the process that produces RNA from DNA inside the cell and subsequently gives rise to proteins through translation into amino acids. Although this is a general rule of molecular biology, it is not always the case. For example, Convergent Antisense Transcription (CASt) is a form of non-coding transcription, meaning a type of RNA that is not translated into proteins, which starts at the beginning of genes and in the opposite or antisense direction.
In this study, the researchers have shown that a group of stress-response genes retain a specific genetic architecture consisting of a first intron, or non-codifying DNA region, designed to host this CASt regulation. This combination of CASt and the intron allow genes to remain in a stand-by state at mild temperatures (22 °C), increasing their responsiveness when cold arrives (4 °C).
This rapid transcriptional response mechanism has been found mainly in genes encoding amino acid transporters, such as those of the AAP (Amino Acid Permease) family, which are crucial for moving cellular components quickly during stress response.
Left: illustration by Martí Quevedo, partially generated by AI. Middle: 7 days rice seedlings (Oryza sativa, japonica subspecies). Right: rice seedling in a sterile growth medium. Credit: CRAG.
Implications and future of the research
The research has also confirmed that this regulatory strategy is evolutionarily conserved in plants such as the model organism Arabidopsis thaliana, rice, and maize. Surprisingly, the researchers were able to predict in silico which genes will be stress-sensitive in rice based on their genetic structure and the presence of CASt and further, demonstrated it in in vitro cultures at CRAG.
“This study exemplifies the importance of consortia such as INUPRAG where CRAG cooperates with UPSC in Sweden and INRAE in France. The possibility of combining in silico bioinformatic analysis with in vitro rice cultures at CRAG has been essential to prove our theory”, says Martí Quevedo, co-author of the study.
This discovery reveals an evolutionary selected genomic feature linked to non-coding transcription that plants use to adapt to environmental fluctuations. Understanding how CASt primes genes open a field of study scarcely explored until now and offer enormous potential for the agri-food sector, with the possibility of designing plants with greater frost resistance and developing more robust crops to face future climate challenges.
Reference Article
Vasiliki Zacharaki, Marti Quevedo, Sarah Muniz Nardeli, Shiv Kumar Meena, Elena Monte and Peter Kindgren. Convergent antisense transcription primes hosting genes for stress responsiveness in plants. Molecular Plant (2025), https://doi.org/10.1016/j.molp.2025.10.001
About the authors and funding of the study
Research in P.K.’s laboratory was funded by the Swedish Research Council (2018-03926), Formas (2021-01065), the Carl Trygger Foundation (20:224), and by grants from the Knut and Alice Wallenberg Foundation and the Swedish Agency for Innovation Systems (KAW 2016.0355 and 2020.0240, VINNOVA 2016-00504). E.M. received grants and financial support from FEDER/Ministry of Science, Innovation and Universities – State Research Agency (PID2021-122288NB-I00); from the CERCA Programme/Generalitat de Catalunya (2021SGR-792), and from the Spanish Ministry of Economy and Competitiveness through the Severo Ochoa Programme for Centres of Excellence under CEX2019-000902-S funded by MCIN/AEI/10.13039/501100011033. M.Q. received postdoctoral funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 945043.
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