Fig. 1.

Intergenic K4-K36 domains in the human genome produce multiexonic noncoding RNAs. (A) Representative example of an intergenic K4-K36 domain for lincFOXF1. For each histone modification (K4me3, green; K36me3, blue), the results of ChIP-sequence experiments are plotted as the number of DNA fragments obtained by ChIP-sequence at each position divided by the average number across the genome. Intergenic K4-K36 domains were interrogated for presence of transcription by hybridizing RNA to DNA tiling arrays. The resulting RNA hybridization intensity (red) within each K4-K36 domain is plotted with respect to its genomic location. The start and stop of each exon, as determined by our RNA peak calling algorithm (SI Methods), is indicated by a black bar. Arrowheads indicate the orientation of transcription. (B) Sequence conservation scores (SI Methods) across 21 mammalian species indicates lincRNAs (blue) are much more conserved than neutrally evolving intronic sequences (red), although less so than protein-coding genes (green). For each lincRNA exon, protein-coding gene exon, and protein-coding gene intron, a conservation score was calculated and plotted along the x axis as a log-odd enrichment score (compared with random genomic regions of equivalent size). The cumulative number of exons with a given score or lower is represented on the y axis.