Universal features of Alternative splicing in response to diverse environmental stimuli in rice and the vital roles of TFs in AS regulation

BackgroundPre-mRNA alternative splicing (AS) plays essential roles in response to environmental stimuli in plants. However, the universal and specific features of splicing in response to diverse environmental conditions remain not fully understood. Recent studies have shown the co-transcriptional characteristics of splicing, which lead to the reasonable speculation that the elements or factors regulating transcription can also affect splicing. Among of which, the effects of transcription factors on alternative splicing in plants under environmental stimuli are still confusing. A large amount 0f public available RNA sequencing data are valuable resources to be re-analyzed for answering questions beyond the aims of their original studies. ResultsWe explored the universal features of AS using a standard RNA-seq dataset TENOR, which stems from rice samples under controlled diverse conditions to provide comprehensive and comparable AS analysis under various conditions. We found that AS widely occurs in rice under stimuli, with significant tissue specificity, temporal dynamics, commonality among different stresses or treatments as well as significant difference between differential alternative splicing and expressed genes (DASGs and DEGs) in rice under environmental stimuli. The majority of DASGs under various stresses are splicing factors and transcription factors. The correlation analysis shows that the expression level of transcription factors is significantly correlated with the PSI of AS events. The predominant transcription factors correlating with alternative splicing events come from bHLH, bzip and hsfa families. We validated the effects of transcription factors on AS by analyzing RNA-seq data from transcription factor mutants and found substantial differential AS events between mutants and wild type. Furthermore, the significant correlation was discovered between the transcription levels of transcription factors and splicing factors. ConclusionWe found universal features of AS and the predominant AS events of SFs and TFs in plants under diverse environments. We propose that TFs might regulated AS of download genes partly by changing the patterns of their own transcription and splicing to further regulate the transcription of SFs. This work illuminate the studies on the possible mechanisms by which TFs modulate AS in plant, especially under environmental stimuli.