J Integr Plant Biol. ›› 2021, Vol. 63 ›› Issue (11): 1874-1887.DOI: 10.1111/jipb.13161

Special Issue: Abiotic stress Temperature signaling

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The direct targets of CBFs: In cold stress response and beyond

Yue Song, Xiaoyan Zhang, Minze Li, Hao Yang, Diyi Fu, Jian Lv, Yanglin Ding, Zhizhong Gong, Yiting Shi* and Shuhua Yang   

  1. State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China

    These authors contributed equally to this work.
    *Correspondence: Yiting Shi (shiyiting@cau.edu.cn)
  • Received:2021-06-20 Accepted:2021-08-10 Online:2021-08-11 Published:2021-11-01

Abstract: Cold acclimation in Arabidopsis thaliana triggers a significant transcriptional reprogramming altering the expression patterns of thousands of cold-responsive (COR) genes. Essential to this process is the C-repeat binding factor (CBF)-dependent pathway, involving the activity of AP2/ERF (APETALA2/ethylene-responsive factor)-type CBF transcription factors required for plant cold acclimation. In this study, we performed chromatin immunoprecipitation assays followed by deep sequencing (ChIP-seq) to determine the genome-wide binding sites of the CBF transcription factors. Cold-induced CBF proteins specifically bind to the conserved C-repeat (CRT)/dehydration-responsive elements (CRT/DRE; G/ACCGAC) of their target genes. A Gene Ontology enrichment analysis showed that 1,012 genes are targeted by all three CBFs. Combined with a transcriptional analysis of the cbf1,2,3 triple mutant, we define 146 CBF regulons as direct CBF targets. In addition, the CBF-target genes are significantly enriched in functions associated with hormone, light, and circadian rhythm signaling, suggesting that the CBFs act as key integrators of endogenous and external environmental cues. Our findings not only define the genome-wide binding patterns of the CBFs during the early cold response, but also provide insights into the role of the CBFs in regulating multiple biological processes of plants.

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