3.4 CRIR1 regulates the expression of genes involved in the stress response
In order to elucidate the molecular mechanism of CRIR1 -mediated cold resistance, we performed RNA-sequencing (RNA-seq) on WT and two OE lines grown under normal (N) and cold-treated (C) conditions. Among 33 975 detected genes, 6 129, 5 108, and 6 440 differentially expressed genes (DEGs) were identified after cold treatment in wild-type, OE #1 and OE #5 plants, respectively, indicating that low temperature induced global changes of gene expressions (Figure 4a, Table S2). To identify DEGs specifically regulated by CRIR1 , we compared the transcriptomes between OE lines and WT plants under normal and cold-treated conditions. As shown in the venn diagram (Figure 4b), a total of 285 CRIR1 -responsive DEGs were identified both in the OE#1 and OE#5 plants under normal conditions. Among them, 30% of DEGs were cold-regulated genes. After cold treatment, there were 316 genes differentially regulated by CRIR1 , and a strong overlap between the cold-related genes and CRIR1 -responsive DEGs were observed. Subsequently, GO enrichment analysis indicated that these DEGs encode proteins were significantly enriched in biological processes associated with stimulus responses, abiotic stimulus responses, and hormone responses under normal conditions. In cold conditions, a high proportion of DEGs can be classified as monocarboxylic acid metabolic, single-organism metabolic, and secondary metabolite biosynthetic process GO categories (Figure 4c). Furthermore, KEGG pathway analysis showed their functions were significantly enriched in the carotenoid biosynthesis pathway, the starch and sucrose metabolism pathway, and the biosynthesis of secondary metabolites pathway under both normal and cold-treated conditions (Figure S1a).