Fig. 1

Characterization of OCRs and epigenome marks in maize ear and tassel. a Developing ears and tassels (2–4 mm) were dissected for all experiments. Bar = 0.3 mm. b A large proportion (80–85%) of OCRs overlapped between ear and tassel, but there were also some tissue-specific OCRs. c Distribution of local and distal OCRs and 3 types of histone modification (H3K4me3, H3K9ac, and H3K27me3) in ear and tassel. d Gene expression (RNA-seq), chromatin accessibility (ATAC-seq), H3K4me3, H3K9ac, H3K27me3, and DNA methylation (CG) profiles on a selected region of chromosome 10 (75.75–76.1 Mb). LoOCRs and dOCRs in ear and tassel are indicated by red and yellow bars at the bottom, respectively. Gray shading shows an example of dynamic chromatin accessibility and histone modifications with the altered transcription of a nearby gene between ear and tassel. e Epigenome profiles at LoOCRs and dOCRs centered on OCR summits in ear. Shown are regions ± 3 kb from OCR summits. f The correlation between gene expression levels and different clusters of chromatin accessibility and histone modifications in ear. g The percentages of dOCRs that overlap intergenic transcripts in the same tissue in ear and tassel showing that ~ 12% of dOCRs are transcribed. Control: the same number of distal regions as dOCRs generated by randomly shifting dOCRs. h Comparison of transcription levels showing that coding genes have a higher expression level than transcribed dOCRs. The Wilcoxon test was used to test significance. i, j DNA motifs enriched in LoOCRs (i) and dOCRs (j) of ear. The corresponding candidate motif-binding TFs are shown