Growth retardation under suboptimal low temperature is controlled through chromatin remodeling at the CBF cluster.

Temperature profoundly impacts plant growth and development. Response to temperature by plants is one of most crucial ecological factors determining the natural distribution of species, and the yield potential of crops. Among various temperature responses of plants, there remains a gap in understanding molecular mechanisms underlying growth retardation caused by low temperature. Here, we addressed genetic and epigenetic determinants that mediate growth retardation under low ambient temperature in plants. Transcriptome changes mediated by low ambient temperatures include upregulation of a series of regulatory genes, consequently resulting in growth retardation. Our study identified a regulatory network in which a Polycomb protein, VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), and a transcription factor, C-REPEAT BINDING FACTOR 1 (CBF1), operate to control growth under suboptimal low temperature. Under suboptimal low ambient temperature, VIL1 controls dynamic chromatin remodeling through transient chromatin loop formation and nucleosome rearrangement at the CBF cluster. Our study provides insights into how plants reprogram growth and development in response to suboptimal low ambient temperatures. Overall design: To investigate the molecular basis of suboptimal low ambient temperature-mediated growth retardation in WT and vil1 mutants, we performed RNA-sequencing (RNA-seq) analysis using whole rosettes at growth stages of 1.12 -1.13 (when 12 or 13 rosette leaves are greater than 1mm) of both WT and vil1 mutants grown at 12? or 22? in short day and compared the two transcriptomes.