The degree to which intergenic transcription is functional remains uncertain and controversial [9]–[12], [25]. In order to evaluate whether the lincRNAs identified in the present study are specifically regulated as opposed to transcriptional noise, we determined if the lincRNA genes harbor canonical epigenetic marks for activation and repression with the reasoning that noise transcripts should lack coherent epigenetic modification patterns. Consistent with observations based on earlier long noncoding RNA annotations [18], [19], [26], [27], analysis of ChIP-seq and RNA-seq data [28], [29] revealed that the catalog of lincRNAs shows patterns of epigenetic modification similar to protein coding genes (Figure 3A). Activating histone marks, H3K4me3 and H3K36me3, are both significantly enriched within highly expressed lincRNAs. Similarly, the repressive mark H3K27me3 is significantly enriched within lowly expressed lincRNAs. Thus, the expression of lincRNAs appears to be specifically regulated.
