Figure 2

Examples of two stand-alone K562-specific vlincRNAs that are distal from annotations. VlincRNAs supported by EST evidence (A & B) and with no EST evidence (C & D) are shown. 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_500 and vlinc_21) refer to Supplementary Table S3 of Kapranov et al [12]. Vlinc_500 (A & B) represents an example of a novel region of ~350 kb whose left bound corresponds fairly well to a cluster of spliced ESTs that share the same 5' ends. Consistent with the K562-specific nature of this region, 9 out of 13 of these ESTs have been isolated from a chronic myelogenous leukemia (CML), the same cancer type as K562, with one of the 9 ESTs spanning almost the entire length of vlincRNA (A). The common 5' end of these ESTs falls within the annotated K562-specific promoter that has within its core an LTR sequence (B). Most of the RNAseq signal was in the intronic regions of these ESTs, consistent with the overall observation that majority of the "dark matter" RNA signal is intronic [12]. Unlike vlinc_500 which is supported by the EST evidence, Vlinc_21 (~121 kb; panels C & D) is located within a totally un-annotated region of chromosome 1 with no spliced EST, ~1.4 Mb from the closest UCSC gene annotation. It also has an LTR repeat at its core (D). 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.