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. 2021 Jan 27;12:626. doi: 10.1038/s41467-020-20883-w

Fig. 5. LFY binding in the context of nucleosome-enriched chromatin activates flower related genes.

Fig. 5

a Browser view of LFY occupancy (this study) and presence of H3K27me3/H3 or H3K4me3/H3 based on analysis of a public ChIPseq dataset69 in root explants at AP1, RAX1, and ACT7. Significant ChIP peaks (q value ≤ 10−10 MACS2 for LFY and q value ≤ 10−100 for histone modifications) are marked by horizontal bars, with the color saturation proportional to the negative log 10 q value (as for the narrowPeak file format in ENCODE). b Volcano plot of genes differentially expressed 24 h after dexamethasone relative to mock treatment (n = 2042, adjusted DESeq2 p value ≤ 0.01). Red color denotes log 2 FC ≥ 2, arrows point to AP1 and RAX1. c Significantly enriched development related Gene Ontology terms for LFY regulated genes whose LFY binding site was nucleosome occupied (Nucleosomal n = 202, FDR < 0.005; top) or nucleosome free (Free n = 101, FDR < 0.05; bottom). All significant GO terms identified are listed in Supplementary Data 2. See also Supplementary Fig. 7.