Universal features of alternative splicing and the regulatory roles of transcription factors in this process under diverse environmental stimuli in rice.

key messageThe universal features of AS in rice under diverse environments have been discovered. These features involve tissue variations, temporal fluctuations, commonalities among distinct stresses or treatments, as well as notable differences between differentially alternative splicing and expressed genes. Many differentially AS genes were found to be splicing factors and transcription factors (TFs), and there was a significant correlation between the expression levels of TFs and the PSIs of AS events. The impact of TFs on AS was confirmed through analyzing the transcriptome data of TF mutants and identifying a large number of differential AS events between mutants and wild type. The transcription levels of transcription factors showed a significant correlation with those of splicing factors under abiotic stresses. It was concluded that transcription factors can influence the splicing patterns of stress-responsive genes by regulating the expression of splicing factors. This provides a survey of the existing public resources and approaches that support the roles of AS in plant adaptation to changing environments and the studies on AS regulation. Pre-mRNA alternative splicing (AS) plays an essential role in response to environmental stimuli in plants. Recent studies have revealed the co-transcriptional nature of splicing, leading to the reasonable speculation that elements or factors regulating transcription can influence splicing. However, the impact of transcription factors (TFs) on AS in plants under environmental stimuli is still elusive. Herein, we investigated the universal characteristics and the regulatory roles of TFs in AS under various controlled conditions using a standard RNA-seq dataset, TENOR in rice. Accordingly, we found AS widely occurred in rice under stimuli, showing significant differences between shoots and roots, temporal dynamics, commonalities among different stresses or treatments as well as significant differences between differentially alternatively spliced genes (DASGs) and differentially expressed genes (DEGs). Moreover, a large number of DASGs under various stresses encode for splicing factors (SFs) or TFs. A significant correlation was shown between the expression levels of TFs and the percent spliced in values (PSIs) of AS events. The predominant TFs came from the bHLH, bZIP and HsfA families, and the mutants of OsbHLH148, OsbZIP62 and OsHsfA2e showed obviously different AS events compared with the wild types under abiotic stresses. Furthermore, a significant correlation was discovered between the transcription levels of TFs and SFs. These results suggest that TFs might regulate AS of downstream genes partly by altering their own transcriptional and splicing patterns, thereby further regulating the transcription of SFs. This work provides insights into the general characteristics of AS and the potential mechanisms by which TFs regulate AS in plants.