Fig. 4

Identification of vernalization-related ACRs. a Strategies for identifying cis-regulatory elements (distal ACRs and promoters). A represents activated (H3K4me3 and H3K27ac); R represents repressed (H3K27me3); M represents mixed (both A and R); U represents unmodified. b Counts of vernalization-related K4-dACRs and nK4-dACRs identified based on chromatin accessibilities and histone modifications. c Genome coverage images showing the epigenomic modifications around VRN1 and the 30Kb upstream distal ACRs of VRN3. P1~P4 are the fragments selected for the following experiments. d-e GC contents and SNP densities of identified regulatory elements. nK4-dACRs represents distal ACRs without H3K4me3; K4-dACRs represents distal ACRs neighboring to H3K4me3; P represents promoter. f-g Percentages of identified regulatory elements overlapping with eQTL. Shuffle represents the average percentage of randomly selected genomic regions (1000 times). SPC represents spike compactness; RCL represents red coleoptile; AWN represents awnedness; GWLR represents grain width to length ratio; SPN represents spikelet number per spike; SPL represents spike length; HT represents height; HDT represents heading date; GW represents grain weight; GAR represents grain area; GL represents grain length; TGW represents thousand grain weight. h Counts of DEGs with changed chromatin accessibilities during vernalization. Induced represents increased chromatin accessibility after vernalization; Repressed represents decreased chromatin accessibility after vernalization; Up represents up regulated gene; Down represents down regulated gene. nK4-dACRs represents distal ACRs without H3K4me3; K4-dACRs represents distal ACRs neighboring to H3K4me3. i Transcriptional regulatory activities of vernalization responsive distal ACRs through luciferase (LUC) activity assays in wheat protoplasts. The results depicted in the Fig 4i. represent the ratio of the regulatory activity of the fragment in the vernalized state compared to its activity in the non-vernalized state. Wheat protoplasts were extracted from leaf with/without vernalization (4℃ for 4 weeks). P1~P4 are the ACRs marked in Fig. 4c, and P5 is the ACR marked in Fig. S6a. j Chromatin state shift of nK4-dACRs during cold vernalization. k Expression changes of genes with chromatin state shift. A-U represents genes whose chromatin states are A before vernalization and U after vernalization, similarly for R-U, U-A and U-R