Figure 3.

Example of a transcription-induced chimera between C21orf59 and TCP10L. The results of a 5′ RACE/tiling array analysis of the HSA21 TCP10L gene are presented. The GENCODE-annotated transcripts of this section of the ENCODE region ENm005 are shown (green, at the bottom). The index exon where the primer used for the 5′ RACE maps is indicated. RACEfrags-positive regions obtained upon hybridization of the tiling array by the RACE reactions performed in 12 human tissues and three cell lines are shown (black boxes, upper part). Red boxes joined by thin red lines depict connectivity between index exons and RACEfrags selected to be independently verified by RT-PCR. The corresponding RACEfrags are highlighted in the upper part of the panel. The hybridization of these RT-PCR reactions to the same tiling arrays allowed us to identify RT-PCRfrags (blue boxes, see text for details). Note that some of the RT-PCRfrags do not intersect RACEfrags, denoting that not all transcripts were detected by the RACE reactions. The cloning and sequencing of the RT-PCR reactions amplimers’ revealed the exon composition and chimeric nature of transcripts containing the targeted RACEfrags (purple transcripts).