Figure 3

Examples of two stand-alone K562-specific vlincRNAs that are adjacent (A & B) or overlap (C & D) annotations. Panels A & B show a vlincRNA potentially produced by bi-directional transcription from a promoter upstream of a known gene. Panels C & D show a vlincRNA antisense to known genes. Zoom-in on the corresponding promoter regions marked by arrows in A& C are shown in the panels B & D. The original 580 vlincRNAs[12] (black, non-strand specific) and the ENCODE vlincRNAs (green, strand-specific) are shown. The vlincRNA designations (vlinc_377 and vlinc_185) refer to Supplementary Table S3 of Kapranov et al[12]. Vlinc_377 (~122 kb, panels A & B) is adjacent to an annotated gene, ARL15. However, it does not appear to be connected to ARL15, but rather represent a stand-alone independently regulated unit. Expression of vlinc_377 was restricted to K562, while ARL15 was constitutively expressed and the direction of vlinc_377 transcription was opposite from ARL15 as shown by the vlincRNA from the ENCODE/CSHL long RNAseq dataset [56] produced with a protocol that reduced spurious second strand formation [57](Materials and Methods). Consistent with this, a K562-specific promoter element could be identified at the boundary of vlincRNA_377, upstream of the constitutive promoter controlling the ARL15 expression. Vlinc_185 (C & D) represents an interesting example of a very long antisense transcript. Due to the original constraint of annotating vlincRNAs as intergenic regions, the vlincRNA bounds did not extend over the KCNJ16 gene even though the RNAseq signal clearly extends into that gene (C). Furthermore, a spliced EST BE777672 connects vlinc_185 to an intron of KCNJ16 and the 5' end of this EST corresponds quite well with the end of the RNAseq signal and also with a K562-specific promoter (C & D). Consistent with this, BE777672 was also isolated from a CML source. The entire length of this vlincRNA would be ~130 kb. Finally, the ENCODE K562 vlincRNA shows the recapitulates the strand and the start site of the previously published vlincRNA. RNAseq data shows density of informative reads normalized by 10M informative reads. The Y-axis of the alignability track (Materials and Methods) is on the scale of 0 to 1. Coordinates: hg18.