Rice reproductive development

Transcription is a complex process. Alternative transcription initiation (ATI) and alternative transcription termination (ATT) contribute to the complexity of transcriptomes, and subsequently cause structural and functional diversity of proteomes. Previous investigations of ATI and ATT in the genome were mainly conducted in animal system, those in plants are limited.Here, by nanopore full-length transcriptome sequencing, we identified new- and tissue specific transcripts, ATI and ATT events in rice, revealing the rice transcriptome complexity. The identification of different transcription initiation (TI) and transcription termination (TT) sites across three floret developmental stages highlighted the significant roles of ATI and ATT during developmental switches. Sites selection of TI and TT were found to be tightly correlated with the DNA methylation and chromatin accessibility. Specifically, for ATI, the CG and CHG methylation levels of the flanking region of the alternative transcription start site (TSS) were often low, while increased CHH methylation level was observed in the upstream region of the alternative TSS. In contrast, ATT always occurred at the alternative transcription end site (TES) with flanking region having low CHG and CHH methylation level, while increased CG methylation level in upstream region of alternative TES promoted ATT. Moreover, enhanced chromatin accessibility was identified in ATI, while decreased chromatin accessibility was associated with ATT.Taken together, Nanopore sequencing offers advantages in detecting novel full-length transcripts, which improve the transcript annotation of the rice genome. The integrative analysis brings about new insight that epigenetic marks affected the selection of TI and TT sites, which resulted in transcriptome complexity in rice.