The central discovery is that plant cold adaptation is not one continuous program but two. As temperatures fell, the researchers could distinguish two separate sets of genes switching on at different points along the thermal gradient. One set, which they named COOLING genes, responds to moderate cold as the mercury begins to slide. A second, distinct set, dubbed CHILLING genes, activates only once temperatures drop below 10 degrees Celsius. This partitioning means that a plant does not simply turn up the same molecular dial as it gets colder; instead, it crosses a threshold into an entirely different regulatory regime. The finding reframes how scientists should think about winter hardiness, suggesting that moderate autumn coolness and true chilling conditions engage largely non-overlapping transcriptional machinery.

Sitting right at the boundary between these two programs, the study found, is a family of transcription factors that cold biologists know well: the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTORS, or CBFs. These regulators have long been celebrated as master switches of cold tolerance, but in this gradual-cooling experiment their induction turned out to be transient, flaring briefly at the interface between the COOLING and CHILLING responses rather than staying elevated throughout the season. That transient behavior hints that the CBFs may act less like a sustained winter thermostat and more like a one-time signal that helps the plant transition between two states, handing over control to other regulators once the deeper chilling program is underway.

Perhaps the most surprising player to emerge from the study is the circadian clock. The researchers found that CIRCADIAN CLOCK-ASSOCIATED 1, or CCA1, a core component of the plant’s internal 24-hour timekeeper, is essential for transcriptional responses at both moderate cold and chilling temperatures. When the team examined mutant plants lacking functional CCA1, the normal activation of cold-responsive genes was disrupted across both temperature ranges. In other words, the internal clock is not merely a bystander that modulates cold responses at the margins; it is a load-bearing component of the entire low-temperature transcriptional architecture. This makes ecological sense: a plant descending into winter needs to know not only how cold it is, but what time of day it is, because nighttime and daytime cold impose very different physiological challenges.

To understand how these transcriptional changes are physically enabled, the team turned to ATAC-seq, a genome-wide assay that maps chromatin accessibility, revealing which stretches of DNA are physically open and available for transcription factor binding. The results revealed a striking asymmetry. Genes that were induced by cold showed a measurable increase in the accessibility of their promoter regions, as if the chromatin were being pried open to admit the transcriptional machinery. Genes that were switched off by cold, however, did not lose promoter accessibility. Their promoters remained open even as their transcripts faded away, a configuration that keeps them poised for rapid reactivation.

That asymmetry has profound implications for how plants survive the erratic swings of late autumn and early winter. A warm spell can arrive at any moment, and a plant that had to rebuild chromatin accessibility from scratch every time temperatures rebounded would lag dangerously behind the weather. By keeping the promoters of down-regulated genes open, the plant effectively bookmarks them, allowing transcription to resume almost immediately when conditions improve. The study thus provides a mechanistic explanation for the remarkable speed with which plants can reverse their cold acclimation, a flexibility that laboratory experiments with abrupt, sustained cold treatments had largely failed to capture.

The experimental design deserves attention in its own right. Rather than exposing seedlings to a single cold shock, the researchers programmed growth chambers to follow temperature profiles that tracked the average trajectory of autumn-to-winter cooling over several weeks, and in parallel ran a fluctuating regime that layered daily variability on top of that seasonal decline. Comparing transcriptomes across these conditions allowed them to ask which genes respond to the seasonal trend itself and which respond to the noise of daily fluctuation. Supplementary analyses, including phenotypic characterization of wild-type and mutant plants under freezing treatment, connected the molecular programs to tangible differences in how plants cope with the ultimate test of winter: ice formation in their tissues.

Why does this matter beyond the Arabidopsis plot? Temperate crops, from cereals to brassicas, share much of the cold-response machinery that thale cress deploys, and winter survival is a major determinant of yield in agriculture. If moderate cooling and true chilling engage distinct genetic programs, then breeding or engineering strategies that target only the classic CBF pathway may be strengthening one arm of cold adaptation while leaving the other untouched. The identification of CCA1 as a required regulator across both temperature ranges, and the demonstration that promoter accessibility dynamics govern how quickly plants can respond to warming, offer new molecular entry points for improving the resilience of crops in a climate whose winters are becoming both warmer on average and more volatile in their swings.

The study also adds a cautionary note about how cold biology has been measured. Most of what the field knows about plant cold responses comes from experiments in which plants are moved from warmth into steady chilling for hours or days. The new work shows that under realistic, gradually cooling conditions, the identity of the responding genes, the timing of their activation, and the role of regulators such as CBFs and CCA1 can look quite different. Daily oscillations of circadian clock and light signaling persisted throughout the long-term autumn-winter treatment, indicating that the clock continues to run and to shape transcriptional output even as the seasonal program unfolds around it. Dissecting responses under naturalistic regimes, the authors argue, is essential for understanding genuine acclimation.

Published open access in Genome Biology, the study was supported by the Spanish Ministry of Science and Innovation, the Severo Ochoa Excellence Program, the Generalitat de Catalunya, the European Union through a Marie Skłodowska-Curie postdoctoral fellowship, and the Netherlands Organization for Scientific Research, among other funders. Its contribution is a comprehensive map of how an entire genome reorganizes itself, in both transcript abundance and chromatin architecture, across a season rather than a shock. Two programs, one boundary, a clock at the center, and promoters that remember the warmth: that is the emerging picture of how a small weed prepares for winter, and it is a picture that crop scientists will now want to paint for the plants we eat.

Subject of Research: Transcriptional and chromatin dynamics of cold acclimation in Arabidopsis thaliana under naturalistic autumn-winter temperature regimes

Article Title: Autumn–winter progression triggers distinct transcriptional programs in Arabidopsis thaliana

Article References: Ormancey, M., Tremblay, B. J. M., Cheng, Y., Praat, M., Antoniou-Kourounioti, R. L., Krumbach, J., van Zanten, M., & Qüesta, J. I. (2026). Autumn–winter progression triggers distinct transcriptional programs in Arabidopsis thaliana. Genome Biology. https://doi.org/10.1186/s13059-026-04289-3

Image Credits: AI Generated

DOI: 10.1186/s13059-026-04289-3

Keywords: Arabidopsis thaliana, cold acclimation, transcriptional regulation, CBF transcription factors, CCA1 circadian clock, chromatin accessibility, ATAC-seq, RNA-seq, chilling stress, plant molecular biology, temperature fluctuation, Genome Biology