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).