Cold Responsive Transcription Factor Binding Overlaps Open Chromatin at Gene Promoters

Rice originated in subtropical environments, yet its cultivation has expanded into regions where low temperatures threaten growth, development, and yield. Japonica rice generally tolerates cold better than indica rice, and researchers have linked this adaptation to changes in stress-responsive gene expression. Much attention has focused on C-repeat binding factors, a group of transcription factors that help coordinate plant cold responses.

However, these proteins may directly regulate only 10%–20% of cold-regulated genes, suggesting that many other regulators operate alongside them. For numerous rice genes, the identities of those regulators and the locations of the DNA sequences they recognize remain unclear. A wider map of these interactions is therefore needed to understand cold adaptation and identify potential targets for crop improvement.

A study (DOI: 10.48130/tp-0026-0034) published in Tropical Plants on 24 September 2026 by Zhuo Chen's & Peitao Lü's team, Fujian Agriculture and Forestry University, identifies potential connections between cold-responsive transcription factors and their target genes by integrating gene expression, DNA accessibility, and genome-wide binding data.

The researchers compared three rice cultivars: cold-sensitive indica Yangdao 6 and cold-tolerant japonica Koshihikari and Lijiangxintuanheigu. Seedlings at the three-leaf stage were exposed to 4 °C or maintained at 28 °C, with leaf samples collected after 12 and 24 hours. RNA sequencing measured changes in gene expression, while DNase sequencing identified accessible chromatin regions where regulatory proteins could potentially interact with DNA.

The team then used DNA affinity purification sequencing to map binding sites for 20 selected cold-induced transcription factors and incorporated published datasets for three additional factors, producing profiles for 23 proteins from 11 families. This approach linked changes in gene activity with both the availability of regulatory DNA and the capacity of individual proteins to recognize particular genomic DNA sequences. Gene expression analysis identified 12,346 cold-responsive genes, including 6,778 activated by cold in at least one cultivar.

After 24 hours, 561 cold-induced genes showed significantly higher expression in both japonica cultivars than in Yangdao 6. These genes were enriched in pathways involving the production and signaling of stress-related hormones, including abscisic acid, jasmonic acid, and salicylic acid. Chromatin analysis found accessible regions concentrated around gene start sites and promoters. Binding footprints and sequence patterns implicated several transcription factor families, including MYB, NAC, WRKY, and bZIP, suggesting a regulatory system extending beyond the familiar C-repeat binding factors.

Across the binding datasets, 10,312 cold-responsive genes contained at least one transcription factor binding signal in their promoters; 6,142 also showed overlap between a binding signal and accessible chromatin. Specific examples connected multiple factors to the promoter of OsNCED4, a gene involved in abscisic acid production, while DREB1G and EIL2 bound promoters of genes associated with jasmonic acid production. Together, these complementary analyses pinpointed candidate regulatory relationships and their DNA locations for follow-up experiments.

The study offers a detailed starting point for exploring how multiple regulators shape rice cold responses. Its online database allows researchers to visualize regulatory signals and download datasets, supporting further investigation and potential breeding applications. Because the binding experiments were performed outside living plants, the proposed connections require molecular and genetic validation. Establishing which regulatory sequences influence cold tolerance could ultimately help breeders adjust stress responses through targeted genome editing.