Identification and functional categorization of the most stably and most variably expressed genes and retained introns in Arabidopsis thaliana seedlings

We used a large, uniform, RNA-seq dataset to investigate the stability of gene expression and intron retention in Arabidopsis thaliana seedlings. Functional classification of the most stably and most variably expressed genes was determined by GO enrichment analyses, as well as for usually spliced and usually retained introns. Many variably expressed genes encoded proteins involved in photosynthesis and chloroplast structure, probably reflecting their sensitivity to changeable light intensities. After excluding these genes, the most variable expressors were enriched in stress response genes, which may facilitate adaptation to constantly shifting environmental conditions. By contrast, the most stably expressed genes encoded proteins involved in localization and intracellular transport of proteins, suggesting that wide fluctuations in the expression of these genes are not well tolerated by plants. GO analyses of usually retained introns revealed no clear enrichments in any specific functional categories. However, usually retained introns were often located in the first or last intron of pre-mRNAs. These terminal introns could contain 5' and 3' UTRs that influence gene expression through either transcriptional regulation or mRNA stability, respectively. Conversely, usually spliced introns were typically found in more central regions of pre-mRNAs, which may safeguard against missplicing and the formation of premature stop codons in coding regions. The large RNA-seq dataset we generated can be useful for investigating additional aspects of gene expression and pre-mRNA splicing in Arabidopsis seedlings.