title: The precise regulation of different COR genes by individual CBF transcription factors in Arabidopsis thaliana.
abstract: The transcription factors CBF1/2/3 are reported to play a dominant role in the cold responsive network of Arabidopsis by directly regulating the expression levels of cold responsive (COR) genes. In this study, we obtained CRISPR/Cas9-mediated loss-of-function mutants of cbf1∼3. Over 3,000 COR genes identified by RNA-seq analysis showed a slight but significant change in their expression levels in the mutants compared to the wild-type plants after being treated at 4 °C for 12 h. The C-repeat (CRT) motif (5'-CCGAC-3') was enriched in promoters of genes that were up-regulated by CBF2 and CBF3 but not in promoters of genes up-regulated by CBF1. These data suggest that CBF2 and CBF3 play a more important role in directing the cold response by regulating different sets of downstream COR genes. More than 2/3 of COR genes were co-regulated by two or three CBFs and were involved mainly in cellular signal transduction and metabolic processes; less than 1/3 of the genes were regulated by one CBF, and those genes up-regulated were enriched in cold-related abiotic stress responses. Our results indicate that CBFs play an important role in the trade-off between cold tolerance and plant growth through the precise regulation of COR genes in the complicated transcriptional network.
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Yihao
authors.initials: Y
authors.lastname: Shi
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Jiaying
authors.initials: J
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Tianshu
authors.initials: T
authors.lastname: Sun
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Xuefei
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Chenqi
authors.initials: C
authors.lastname: Zhu
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Yuxi
authors.initials: Y
authors.lastname: Ai
authors.affiliation: State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Hongya
authors.initials: H
authors.lastname: Gu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D064113:CRISPR-Cas Systems / Q000235:genetics; D016000:Cluster Analysis; D015536:Down-Regulation / Q000235:genetics; D005615:Freezing; D000072669:Gene Editing; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D009154:Mutation / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors
keywords: CBF; COR; CRISPR/Cas9; cold tolerance; single CBF-regulated genes