Single-molecule nascent RNA profiling reveals multiple layers of co-transcriptional splicing and their reprogramming by cold in Arabidopsis

Prolonged cold exposure in Arabidopsis thaliana globally enhances co-transcriptional splicing across all Pol II position classes, promotes coordinated first-and-last intron splicing, and reduces consecutive unspliced introns.

• Why it matters: Coupling between Pol II progression and multiple RNA processing events in single nascent transcripts, especially under environmental change, is still unclear.
• What they did: The study developed plant polymerase intact nascent transcript sequencing (pPOINT-seq) to profile Ser5-phosphorylated Pol II-associated nascent transcripts, resolving Pol II position alongside co-transcriptional splicing states.
• The result: Transcripts extending beyond transcription end sites showed reduced upstream intron splicing, linking splicing with 3'-end processing and termination; cold remodelling indicates dynamic multiscale coordination during temperature adaptation.

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