Transcription fidelity and control of alternative splicing contribute to heat stress survival in Arabidopsis

Transcriptional quality control is essential to maintain the integrity of genetic information. Although well characterized in yeast and metazoans, the regulation of transcriptional fidelity in plants remains elusive. We explored transcriptional fidelity and alternative splicing control in Arabidopsis thaliana using genetic, molecular biology, and deep sequencing tools. Using circle-sequencing assays, we analyzed the error landscape of the transcriptome at single-nucleotide depth under ambient and heat-stress conditions in wild-type and different quality control mutant plants. We found that the frequency of nucleotide misincorporations and insertions is significantly elevated under heat stress, and that nucleotide imbalance also leads to error-prone transcription. We demonstrate that the RNA polymerase II-associated elongation cofactor TFIIS is a fidelity factor for both transcription and alternative splicing, as its absence reduces the accuracy of both processes. Moreover, we found that the nonsense-mediated mRNA decay (NMD) cytoplasmic surveillance system is also required for heat-stress tolerance: NMD degrades transcripts containing premature termination codons, generated by 1 to 2 nucleotide indels of erroneous transcription and by alternative splicing during heat stress. In conclusion, the interplay between these RNA surveillance systems safeguards the correct genetic information flow and is critical for developmental regulation and heat-stress adaptation in plants.