Identification of intergenic lncRNAs with enhancerlike and promoterlike characteristics. Examples of intergenic lncRNA loci with chromatin signatures in marginal zone B cells that are characteristic of (A) eRNA loci (LNCGme01103) and (B) pRNA loci (LNCGme01293). The former are distinguished by high H3K4me1 read coverage across the TSS and the absence of a corresponding H3K4me3 peak. The latter are distinguished by high H3K4me3 coverage, the presence of which excludes H3K4me1 from the TSS. (B) Also shown is a second lncRNA (LNCGme01244) that arises as a result of bidirectional transcription from the Scyl1 promoter, but this is not classified as an eRNA or pRNA because its proximity to a coding gene. CHR, chromosome. (C) The proportion of the 2349 intergenic lncRNAs identified in this study that could be classified as either eRNAs or pRNAs on the basis of their chromatin state. Remaining lncRNAs are either classified as unassigned (insufficient read coverage/fold-change to determine chromatin state) or conflicted (classified as eRNA in 1 B-cell stage and pRNA in another). (D) The proportion of eRNA and pRNA loci that are classified as multiexon or single exon. (E) Pairwise comparisons showing the consistency of chromatin signatures across B-cell populations. Within each B-cell population, intergenic lncRNAs are ranked on the ratio of H3K4me1:H3K4me3 coverage across their TSS. Individual plots show the local regression (loess) of rank order between 2 B-cell populations. (F) Distribution of the Pearson’s correlation coefficient between the expression of an eRNA or pRNA and expression of the more highly correlated of either its nearest upstream or downstream protein-coding gene. (G) Distribution of median expression values (rlog-transformed read counts) calculated across all cell stages. (H) Distribution of cell stage specificity of expression of eRNAs and pRNAs. ***Mann-Whitney U test: p < .0001.