Fig. 5: GmLDL2 regulates target gene GmFER transcription via modulating H3K4 methylation.

a Normalized read density of H3K4me1, H3K4me2, and H3K4me3 signals at gene body regions, as well as upstream 1.5 kb and downstream 1.5 kb, lines show the average value of all genes in HX3 and ef1. b H3K4me1, H3K4me2, and H3K4me3 reads density among three groups of genes with different expression levels in HX3 and ef1. Gene body regions were divided into equal bins, upstream 1.5 kb of TSS and downstream of TES were calculated per 10 bp sliding window by read density. Metaplots represent the average of the normalized read density of genes in each group. Heatmaps show the distribution of read density of all genes. Genes in each group were sorted from high to low by gene expression levels (FPKM). TSS transcription start site, TES transcription end site. c Venn diagram showing the overlap among genes that are transcriptionally upregulated in ef1, H3K4me1 and H3K4me2 hypermethylated genes in ef1, and GmLDL2 binding genes. d Genome tracks of RNA-seq, anti-GmLDL2, anti-H3K4me1, and anti-H3K4me2 ChIP-seq data for GmFER locus in HX3 and ef1. Y-axis value means normalized read counts. Structure of GmFER. P1 to P4, specific regions used for ChIP-qPCR analysis. UTR untranslated region, CDS coding sequence. Gray block showing the higher H3K4me1 and H3K4me2 modification levels in ef1 than HX3. e qRT-PCR analysis of GmFER expression level. GmActin was used as an internal control. f, g ChIP-qPCR analysis of H3K4me1 and H3K4me2 methylation status at the GmFER locus. h ChIP-qPCR analysis of GmLDL2 associated with GmFER locus. Data represent means ± SD (n = 3 biological replicates) in (e–h). The P value was generated from a two-sided Student’s t-test. Source data are provided as a Source Data file.