Poster abstracts
Poster number 110 submitted by Rajneesh Srivastava
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations
Rajneesh Srivastava (Biohealth Informatics, IU School of Informatics and Computing, IUPUI), Gungor Budak (Biohealth Informatics, IU School of Informatics and Computing, IUPUI), Soma Dash (Biological Sciences, University of Delaware), Salil A. Lachke (Biological Sciences, University of Delaware), Sarath Chandra Janga (Biohealth Informatics, IU School of Informatics and Computing, IUPUI)
Abstract:
Lens development involves a complex and highly orchestrated regulatory program. In this study, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. We present a database “Express” (http://www.iupui.edu/~sysbio/express/) that unifies the processed mouse lens transcriptome across multiple developmental stages. Express provides heatmap and browser view allowing easy navigation of the genomic organization and expression of transcripts or gene loci. It enables the export of both the visualizations and the embedded data to facilitate downstream analysis. We also demonstrate that the extent of novelty (compared to annotated isoforms from reference databases) of expressed transcripts decreases significantly in post-natal lens compared to embryonic stages. Characterization of novel transcripts into partially novel transcripts (PNTs) and completely novel transcripts (CNTs) (novelty score ≥ 70%) revealed that the PNTs are both highly conserved across vertebrates and highly expressed across multiple stages. Functional analysis of PNTs revealed their widespread role in lens developmental processes while hundreds of CNTs were found to be widely expressed and predicted to encode for proteins. We verified the expression of four CNTs across stages. Examination of splice isoforms revealed skipped exon and retained intron to be the most abundant alternative splicing events during lens development. We validated by RT-PCR and Sanger sequencing, the predicted splice isoforms of several genes Banf1, Cdk4, Cryaa, Eif4g2, Pax6, and Rbm5. Finally, we present a splicing browser Eye Splicer (http://www.iupui.edu/~sysbio/eye-splicer/), to facilitate exploration of developmentally altered splicing events and to improve understanding of post-transcriptional regulatory networks during mouse lens development.
References:
Khan SY, Hackett SF, Lee MC, Pourmand N, Talbot CC Jr & Riazuddin SA. Invest Ophthalmol Vis Sci. 2015 Jul;56(8):4919-26.
Dash, S., Siddam, A.D., Barnum, C.E., Janga, S.C. & Lachke, S.A. Wiley Interdiscip Rev RNA. 2016 Jul;7(4):527-57.
Lachke, S.A. & Maas, R.L. Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):305-23.
Srivastava, R., Budak, G., Dash, S., Lachke, S.A. & Janga, S.C. Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. Scientific Reports. 2017 (In press).
Budak G., Dash, S., Srivastava, R., Lachke, S.A. & Janga, S.C. Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. Exp Eye Res. (Accepted)
Keywords: Mouse development, Eye tissue, Alternative splicing