Figure 1

Detection of ZC3HAV1L - CHMP1A chimeric RNA in human cells. (A) Schematic representation of the ZC3HAV1L-CHMP1A chimeric RNA. Blue and yellow boxes indicate exons from ZC3HAV1L and CHMP1A, respectively. Above the predicted fusion, colored bars indicate paired reads from the ENCODE HMEC RNA-seq data. The same color indicates a read pair supporting the fusion. Arrows below the predicted fusion indicate primer pairs used in PCR analyses (primer pair a for PCR in panel B, and primer pairs b and c for nested PCR in panel E). (B) RT-PCR detection of the ZC3HAV1L-CHMP1A chimeric RNA in human cells and tissues. Filled arrowhead indicates the major predicted fusion; open arrowheads indicate minor alternative chimeric transcripts (i-iv). “RT -” indicates no reverse transcriptase negative controls. “NTC” indicates no template control for PCR analysis. (C) Junction sequence of the ZC3HAV1L-CHMP1A chimeric RNA. Blue and yellow shading highlights sequences from the end of ZC3HAV1L exon 4 and start of CHMP1A exon 5, respectively. Lower case letters indicate intron sequences. The chromatogram shows Sanger sequencing results at the junction from RT-PCR analysis of HMLE cells. (D) Schematic representation of minor alternative ZC3HAV1L-CHMP1A chimeric RNAs detected from PCR shown in (B). Partial exon and introns (“i”) are indicated by different shades of color. Sequence alignment for the major and minor chimeric RNAs is provided in an additional file. (E) ZC3HAV1L-CHMP1A fusion may encode a novel protein. Shown is nested RT-PCR amplification of the predicted fusion coding sequence from HMLE and CAPAN1 cells. The larger band indicates the expected PCR product, whereas the smaller band in HMLE lane indicates the ZC3HAV1L exon3^- variant. (F) ZC3HAV1L-CHMP1A chimeric RNA levels differ in different human cell and tissue types. The copy number of the RNA fusion between ZC3HAV1L exon 4 and CHMP1A exon 5 is normalized against beta-actin mRNA.