Fig. 5

A catalog of long non-coding (lnc) RNAs expression during early maize inflorescence development. a Expression profiles (plotted as normalized z-score) for 2679 lncRNAs across different stages of ear and tassel development. Euclidean distance was computed across rows (lncRNAs) and columns (tassel and ear developmental stages), and data were hierarchically clustered using the maximum linkage method. b The various classifications of lncRNAs used in this study, including their positions relative to PCGs. c MNase HS profiles across a composite genic and intergenic lncRNA model show highest densities around the TSS and TTS, similar to PCGs. d Expression profiles (plotted as normalized z-scores) during early ear and tassel development of lncRNAs that overlapped putative enhancer loci identified from maize leaf and husk tissue (enhancer-associated intergenic lncRNAs) [16]. e Context-specific methylation profiles plotted across a composite lncRNA model based on 45 enhancer-associated intergenic lncRNAs. CHH (red) methylation is plotted on the left, and CG (purple) and CHG (green) methylation on the right. e A representative co-expression module of lncRNA and PCG pairs located in a genomic window of < 2 kb. The diagonal axis indicates the co-expression value between each lncRNA and PCG pair expressed as the biweight midcorrelation. f Expression values of the seven lncRNA-PCG pairs within the module in (e). Dots represent the rlog values of lncRNAs (yellow) and PCGs (blue), and the line indicates the average expression level