elncRNA and plncRNA loci have similar sequence features. (A) The lengths of elncRNA (enh-TIR, median = 293 nucleotide, green) and plncRNA (prom-TIR, median = 342 nucleotide, blue) TIRs are similar (two-tailed Mann–Whitney test, P = 0.52), (B) as are the lengths of elncRNA (median = 1006 nucleotide) and plncRNA (median = 903 nucleotide) transcripts (two-tailed Mann–Whitney test, P = 0.24). (C) The percentage of elncRNAs that are mono-exonic (47%, dark green) is similar to that for plncRNAs (54%, dark blue, two-tailed Fisher’s exact test, P = 0.37). Light green and blue represent the percentage of multiexonic elncRNAs and plncRNAs, respectively. (D) Relative transcriptional orientation for lncRNAs (black) and their closest protein-coding gene (grey). For simplicity lncRNAs are represented here as transcribed from 5′ to 3′. Arrow represents the direction of transcription. (E) Percentages of lncRNA-protein-coding gene pairs with relative orientation head-to-head (white; elncRNAs = 31%, plncRNAs = 41%); tail-to-tail (light-grey, elncRNAs = 45%, plncRNAs = 35%); tail-to-head (dark-grey; elncRNAs = 19%, plncRNAs = 14%) and head-to-tail (black; elncRNAs = 5%, plncRNAs = 10%). (F) Total number of polyA selected RNA sequencing reads (y-axis) associated with the transcriptional start sites of protein-coding gene (black), elncRNA (green) and plncRNA (blue) meta-genes’ transcriptional start sites (±50 bp, x-axis). Arrow indicates the location of the transcriptional start site and the direction of the meta-gene transcription. NS, not significant.
Marques et al. Genome Biology 2013 14:R131 doi:10.1186/gb-2013-14-11-r131