Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq

被引：0
作者：
Subhash J. Jakhesara
Prakash G. Koringa
Neelam M. Nathani
Chaitanya G. Joshi
机构：
[1] Anand Agricultural University,Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry
来源：
3 Biotech | 2016年 / 6卷
关键词：
Horn cancer; Alternative splicing; GS-FLX Titanium; Transcriptome profiling; Splice isoform;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions. Based on pathway clustering and in silico verification, 102 novel splice isoforms were selected and further analysed with respect to change in protein sequence using Blastp. Finally, fourteen novel splicing events supported both by Cufflinks and UCSC genome browser were selected and confirmed expression by RT-qPCR. Future studies targeted at in-depth characterization of these potential candidate splice isoforms might be helpful in the development of relevant biomarkers for early diagnosis of HC. The results reported in this study refine the available information on transcriptome repertoire of bovine species and boost the research in the line of development of relevant biomarkers for early diagnosis of HC.
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