Figure 1.

Discovery of chimeric RNAs and their potential descendent genes.

(A) the pipeline for discovering potential genes derived from chimeric RNAs. The junction sequence of 778 chimeric RNAs with 50bp on each side was used to blast against reference RNA. Candidates were identified when over 90% similarity was found from the transcript of an intact gene. After filtering out false matches and repeat sequences, six candidates remained. (B,C) upper panels, RT-PCR of HNRNPA1L2-SUGT1 and MRPS31P5 in four different bladder cancer cell lines; middle panels, Sanger sequencing of chimeric RNA HNRNPA1L2-SUGT1 and MRPS31P5, with red arrows highlighting the nucleotide difference between HNRNPA1L2-SUGT1 and MRPS31P5; bottom panel, the sequence alignment in UCSC Genome Browser. (D) RT-PCR of MRPS31P5 and HNRNPA1L2-SUGT1 in normal human tissues.