Monitoring transcription by nascent RNA sequencing in crop plants

Plants can quickly adapt to changing environments and external stimuli by undergoing a series of transcriptional responses. The process of maturing nascent RNA (direct product of transcription) into mRNA, which is crucial for the plant’s response to external factors, involves co-transcriptional and post-transcriptional processing. Although RNA-seq has greatly facilitated the study of plant transcriptomes by providing snapshots of stable RNA molecules, detecting the transcriptional dynamic changes and unstable transcripts remains challenging. In recent years, various sequencing methods have been developed to identify nascent RNA in eukaryotes, shedding light on the dynamics of transcriptional processing and uncovering unstable transcripts. At the same time, analysis of nascent RNA has provided valuable insights into transcriptional regulation in crops, highlighting differences in their features compared to model plants and potentially influencing breeding strategies. This review aims to explore the applications of different nascent RNA sequencing technologies in plants, focusing on significant findings achieved in crops.