Heat stress is one of the most critical environmental factors limiting plant growth and productivity, as it disrupts essential molecular processes that maintain cellular homeostasis. Among these, gene transcription is particularly vulnerable. During transcription, RNA Polymerase II (RNAPII) synthesizes RNA from DNA templates, but this process can be interrupted by several obstacles, such as compact chromatin structures, bound regulatory proteins, DNA lesions, or misincorporated nucleotides. These interruptions can cause RNAPII to pause or stall, resulting in incomplete or faulty RNA transcripts that compromise gene expression and stress tolerance.

In this study, we investigated how Arabidopsis thaliana and barley (Hordeum vulgare) respond to heat-induced transcriptional stress. Using a combination of genetic, molecular, and biochemical approaches, we analysed the roles of transcription elongation factors and RNA surveillance pathways that assist RNAPII in maintaining efficient transcription under elevated temperatures. Our findings indicate that plants deficient in key elongation or transcription recovery components show reduced thermotolerance, increased transcriptional arrest, and an accumulation of aberrant RNA species.

Furthermore, comparative analysis between Arabidopsis and barley revealed both conserved and species-specific mechanisms that support transcriptional integrity under heat stress. This highlights an evolutionarily adaptable network that safeguards transcriptome stability in diverse plant species. Overall, our results suggest that plants depend on a coordinated system of transcriptional support proteins and post-transcriptional quality control mechanisms to sustain accurate gene expression during thermal stress. By maintaining transcriptome integrity, these processes contribute to cellular resilience and enhance the plant’s overall adaptability to changing environmental conditions.