Fusion transcript loci share many genomic features with non-fusion loci

Abstract

BackgroundFusion transcripts are found in many tissues and have the potential to create novel functional products. Here, we investigate the genomic sequences around fusion junctions to better understand the transcriptional mechanisms mediating fusion transcription/splicing. We analyzed data from prostate (cancer) cells as previous studies have shown extensively that these cells readily undergo fusion transcription.ResultsWe used the FusionMap program to identify high-confidence fusion transcripts from RNAseq data. The RNAseq datasets were from our (N = 8) and other (N = 14) clinical prostate tumors with adjacent non-cancer cells, and from the LNCaP prostate cancer cell line that were mock-, androgen- (DHT), and anti-androgen- (bicalutamide, enzalutamide) treated. In total, 185 fusion transcripts were identified from all RNAseq datasets. The majority (76 %) of these fusion transcripts were ‘read-through chimeras’ derived from adjacent genes in the genome. Characterization of sequences at fusion loci were carried out using a combination of the FusionMap program, custom Perl scripts, and the RNAfold program. Our computational analysis indicated that most fusion junctions (76 %) use the consensus GT-AG intron donor-acceptor splice site, and most fusion transcripts (85 %) maintained the open reading frame. We assessed whether parental genes of fusion transcripts have the potential to form complementary base pairing between parental genes which might bring them into physical proximity. Our computational analysis of sequences flanking fusion junctions at parental loci indicate that these loci have a similar propensity as non-fusion loci to hybridize. The abundance of repetitive sequences at fusion and non-fusion loci was also investigated given that SINE repeats are involved in aberrant gene transcription. We found few instances of repetitive sequences at both fusion and non-fusion junctions. Finally, RT-qPCR was performed on RNA from both clinical prostate tumors and adjacent non-cancer cells (N = 7), and LNCaP cells treated as above to validate the expression of seven fusion transcripts and their respective parental genes. We reveal that fusion transcript expression is similar to the expression of parental genes.ConclusionsFusion transcripts maintain the open reading frame, and likely use the same transcriptional machinery as non-fusion transcripts as they share many genomic features at splice/fusion junctions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2235-4) contains supplementary material, which is available to authorized users.

Discovering and understanding oncogenic gene fusions through data intensive computational approaches

“…Furthermore, the expression and tissue specificity of the fusion transcript correlated with expression patterns of the upstream parent gene ( 1 ). In accord, a more recent study of transcription read-through fusions in prostate cancer demonstrated that fusion transcript expression is similar to parental expression, and that fusion transcript levels respond similarly to androgen and anti-androgen treatment ( 114 ). By contrast, a study of cis -spliced fusions in prostate cancer found that only half of the fusions were significantly expressed relative to the parent genes ( 8 ).…”

Clinker: visualising fusion genes detected in RNA-seq data

“…In addition, each of the six samples also expressed an isoform of P2RY8-CRLF2 which joined the first exon of P2RY8 to the 5' UTR of CRLF2, and resulted in an inframe transcript. This alternate fusion also featured the typical GT/AG donor/acceptor motif which exists at the majority of fusion junctions (Lai et al, 2015). The presence of the alternate breakpoints in the samples was confirmed using PCR and Sanger sequencing.…”

Clinker: visualizing fusion genes detected in RNA-seq data

“…In addition, each of the six samples also expressed an isoform of P2RY8-CRLF2 that joined the first exon of P2RY8 to the 5′ UTR of CRLF2 and resulted in an in-frame transcript. This alternate fusion also featured the typical GT/AG donor/acceptor motif that exists at the majority of splice junctions [ 21 ]. The presence of the alternate fusion isoforms in the samples was confirmed using Reverse Transcription PCR and Sanger sequencing.…”