NAD+-capped RNAs are widespread in rice (Oryza sativa) and spatiotemporally modulated during development

In this study, we report the identification of NAD-RNAs in rice (Oryza sativa) by NAD-capQ and NAD captureSeq for the first time. NAD-RNAs in rice are predominantly mRNAs from nuclear and mitochondrial genes, and the NAD-RNAs from nuclear genes are spliced and polyadenylated. We also find that NAD-RNAs are spatiotemporally produced and dynamically regulated during rice growth and development, as some NAD-RNAs are commonly shared in both shoot and root or among the three stages in spikelets, and others display tissue- or stage-enrichment. In addition, GO enrichment analysis reveals that genes producing NAD-RNAs participate in environmental responses, growth and development and redox homeostasis in rice. Moreover, besides the orthologous genes producing NAD-RNAs in both rice and Arabidopsis, several monocot-specific transcripts including noncoding RNAs are selected for NAD+-capping, indicating the species-specificity of RNA NAD+ modification. Taken together, our study will shed light on the functional study of NAD-RNAs.