High percentage of fusion RNAs involving neighboring genes, and strategy for identification novel cis-SAGe chimeric RNAs.

Abstract

<p><b>A,</b> fusion RNAs categorized into INTRACHR-SS-0GAP, INTRACHR-OTHER and INTERCHR. Percentages of each category in individual tumor (upper) and matched normal (lower) prostate samples were plotted. <b>B,</b> correlation of the percentage of INTRACHR-SS-0GAP fusions in matched tumor and normal cases. Peason R = 0.6. <b>C,</b> CTCF knockdown induced chimeric <i>SLC45A3-ELK4</i> RNA expression. LNCaP cells were transfected with either si—or siCTCF. <i>CTCF</i> and <i>SLC45A3-ELK4</i> expression were monitored by qRT-PCR. Transcript amount was normalized to internal control GAPDH. The level of these transcripts was set to 1 in si- transfected cells. <b>D</b>, experimental flow for identification and validation of cis-SAGe events. Quality of RAW sequencing data was checked using FastQC. Paired reads were mapped to both human genome and transcriptome to identify chimeric RNAs using SOAPfuse software. Three groups of chimeric RNAs, classified by genomic features between two parental parts, were validated by RT-PCR and Sanger sequencing. Five additional steps were then applied to remove potential non-neighboring fusions, or fusions resulting from interstitial deletion, and to identify cis-SAGe events.</p