Association between lncRNAs and protein-coding genes based on correlation of expression across B-cell development. (A) WGCNA identifies clusters of protein-coding genes with comparable expression profiles across B-cell development: plots show a representative expression profile (eigengene) for each of 10 protein-coding gene clusters. (B) Stacked bar charts showing the number of lncRNAs whose expression is strongly correlated (|ρ| > 0.8) with the adjacent eigengene. Colors depict lncRNA classification on the basis of chromatin state. (Results are shown for WGCNA clusters with >10 associated lncRNAs.) (C) Heat map showing the normalized expression of cluster lightpink4 containing 31 protein-coding genes identified as upregulated or downregulated in marginal zone B cells. (D) The normalized expression profile of a single gene (Zc3h12c) from this cluster identified as upregulated in marginal zone B cells and a single eRNA (LNCGme02323) identified as strongly correlated with the respective WGCNA cluster. (E) Genome plots showing the location of Zc3h12c and LNCGme02323 as well as H3K4me1 and H3K4me3 chromatin signatures in marginal zone B cells and RNA-seq read coverage in all 8 B-cell populations considered in this study.