Transcription and splicing variations of SR genes accompany with genome-wide accumulation of long-introns in pine

• Published in: Plant science (Limerick) 2024-05, Vol.342, p.112056-112056, Article 112056
• Main Authors: Chen, Shanlan, Zhang, Yingjie, Liu, Li, Mo, Yujian, Li, Junyi, Chen, Beibei, Zhou, Yi, Lin, Jinxing, Jiang, Xingyu, Wei, Long, Ling, Yu
• Format: Article
• Language: English
• Subjects: Alternative splicing; Alternative Splicing - genetics; Arabidopsis - genetics; DNA methylation; eukaryotic cells; Heat stress; introns; Introns - genetics; Long intron; Phylogeny; Pine; RNA Precursors - genetics; RNA Splicing; species; SR proteins; temperature; transposons
• ISSN: 0168-9452; 1873-2259
• DOI: 10.1016/j.plantsci.2024.112056

Most of mRNAs in Eukaryote were matured after the removal of introns in their pre-mRNA transcripts. Serine/arginine-rich (SR) proteins are a group of splicing regulators regulating the splicing processes globally. Expressions of SR proteins themselves were extensively regulated, at both transcription and splicing levels, under different environmental conditions, specially heat stress conditions. The pine genome is characterized by super-long and easily methylated introns in a large number of genes that derived from the extensive accumulation of transposons (TEs). Here, we identified and analyzed the phylogenetic characteristics of 24 SR proteins and their encoding genes from the pine genome. Then we explored transcription and pre-mRNA splicing expression patterns of SR genes in P. massoniana seedlings under normal and heat stress temperature conditions. Our results showed that the transcription patterns of SR genes in pine exhibited significant changes compared to other plant species, and these changes were not strictly correlated with the intron length and DNA methylation intensity of the SR genes. Interestingly, none of the long introns of SR genes underwent alternative splicing (AS) in our experiment. Furthermore, the intensity of AS regulation may be related to the potential DNA methylation intensity of SR genes. Taken together, this study explores for the first time the characteristics of significant variations in the transcription and splicing patterns of SR proteins in a plant species with an over-accumulation of super-long introns. •Compared to other plants, transcription patterns of SR genes in pine change significantly.•The influence of intron length and methylation on transcription and splicing regulation of pine SR gene is unclear.•Compared to other plants, alternative splicing regulation of SR genes in pine is less common.•None of the long introns of SR genes undergo alternative splicing under different temperature conditions.