Co-transcriptional gene regulation in plants

The essence of life lies in the precise regulation of genetic information flow, namely, the central dogma, with gene transcription playing a pivotal role as the starting point. For a living cell, it is not only essential via transcription to synthesize the RNA but also to ensure its timely processing, packaging, and sorting, thereby determining its distinct fate, such as nuclear retention, export, translation, or degradation. Initially observed in yeast and animals, and more recently in plants, a large amount of evidence indicates that RNA processing and protein-RNA packaging occur largely concomitantly with transcription, a phenomenon known as co-transcriptional gene regulation. Increasing evidence suggests that this mechanism provides extensive regulatory potential for gene expression. It not only ensures timely RNA processing, thus determining the fate of RNA, but may also influence the transcription dynamics of RNA polymerase II (Pol II) and the chromatin environment. In this review, we highlight recent advances in understanding co-transcriptional gene regulation in the model plant Arabidopsis thaliana, focusing on Pol II dynamics post-initiation and their interplay with RNA-processing events such as capping, splicing, 3' end processing, protein-RNA interactions, and RNA fate determination. By comparing these findings with progress in other model systems, we discuss the unique characteristics of co-transcriptional gene regulation in plants and its potential biological significance. Additionally, we introduce recent key discoveries at the FLOWERING LOCUS C (FLC) gene under warm conditions, which exemplify how co-transcriptional RNA processing influences the chromatin environment and leads to long-term regulatory impacts. Finally, we provide perspectives on yet-unanswered key questions related to co-transcriptional gene regulation in plants.