Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus

• RNA-Seq analysis of horn cancer and normal sample through 454 sequencing.
• Transcript assembly and expression analysis by Cufflinks and Cuffdiff, respectively.
• Identification of novel exon and transcripts and verification by UCSC and IGV genome browsers.
• Validation of selected 28 novel transcripts by RT-PCR.
• qRT-PCR validation of 12 novel transcripts on 4 samples each of cancer and normal.

Horn cancer (HC) is a widely prevalent cancer amongst Bos indicus cattle and frequently associated with economic losses due to reduction in draught and milk production capacity. To identify novel transcripts and characterize HC transcriptome, we employed high throughput RNA-Seq analysis of HC and horn normal (HN) tissue. Total of 584,450 and 920,450 high quality reads were analyzed for HN and HC tissue, respectively, resulting in the identification of 16,803 unique genes comprising of 14,754 annotated genes and 2049 novel transcripts. We found 251 significant differentially expressed genes in HC transcriptome, which includes 52 putative novel transcripts. We validated presence of 23 out of 28 novel transcripts by RT-PCR and confirmed differential expression of 12 novel transcripts through RT-qPCR on 4 samples each of HC and HN. Functional analysis revealed that HC is characterized by deregulation of genes involved in epithelial cell differentiation and complement cascade. Our study will serve as a step further in detailed characterization of HC transcriptome and provide firm base to explore and mitigate HC at finer resolution.