Identification of novel transcripts and peptides in developing murine lens

Shahid Y Khan,S Amer Riazuddin,Firoz Kabir,Nader Pourmand,Muhammad Ali,Chan Hyun Na,Ruiqiang Chen,Sean F Hackett,Mei-Chong W Lee

doi:10.1038/s41598-018-28727-w

Shahid Y Khan, S Amer Riazuddin + Show 7 more

Open Access

https://doi.org/10.1038/s41598-018-28727-w

Copy DOI

Abstract

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3′ splice site (A3SS), 1,900 alternative 5′ splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.

Highlights

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9)
We extend our analysis of the RNA sequencing (RNA-Seq) data using multiple bioinformatics tools to identify novel transcripts, fusion genes, and alternative splicing (AS) in developing mouse lens (Fig. 1)
We previously investigated mouse lens transcriptome at two embryonic (E15 and E18) and four postnatal (P0, P3, P6, and P9) time points using next-generation RNA sequencing, which identified a total of 14,465 genes along with 12 different classes of non-coding RNAs in mouse lens[22,23]

Summary

Introduction

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). We extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. We integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens. Next-generation RNA sequencing (RNA-Seq) has significantly enhanced our ability to decipher whole transcriptomes through the gene expression quantification, identification of novel transcripts, detection of fusion genes, and isoform diversity[1,2,3,4,5,6,7]. Srivastava and colleagues identified novel transcripts and splicing alterations in developing murine lens[21]

Methods

Results

Conclusion