Alternative transcription initiation and termination and its control through epigenetic marks in rice revealed by nanopore RNA sequencing

Gene transcription is a complex process. The alternative transcription-initiation (ATI) and termination (ATT) contribute to the complexity of transcriptomes and subsequently cause structural and functional diversity of proteomes. Investigations on ATI and ATT were mainly explored in animal, while it was rarely investigated in plants. Here, with the assay of full-length RNA sequencing by nanopore, we identified new- and tissue specific transcripts, ATI and ATT events during rice floret developmental stages, revealing the rice transcriptome diversity. Differentially expressed ATI among the three floret developmental stages highlighted the importance of TI sites selection during developmental switches. By integrating DNA methylation data, we found that the selection of alternative transcription initiation (ATI) and termination (ATT) sites was significantly correlated with low DNA methylation levels. In addition, genes exhibiting ATI/ATT events were significantly associated with a highly open chromatin state. Taken together, nanopore sequencing offers advantages in obtaining the full-length new transcripts, which improve the annotation and accuracy of the rice genome. The integrative analysis sheds light on those epigenetic marks regulates the selection of TI and TT sites, which resulted in transcriptome complexity in rice.