Abstract
Lens development involves a complex and highly orchestrated regulatory program. Here, 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 show that the extent of novelty 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.
Highlights
Lens development involves a complex and highly orchestrated regulatory program
We investigated the transcriptomic alterations and splicing events during lens formation, and constructed a molecular portrait of known and novel transcript isoforms in the mouse lens
Increasing number of studies using RNA-sequencing protocols are able to generate a wild type control as part of their research projects leading to stage-specific developmental transcriptomes[56,57,58], several issues need to be considered before employing them in large-scale meta-analysis studies, which can significantly improve the quality and number of high confidence predictions
Summary
We investigate the transcriptomic alterations and splicing events during mouse lens formation using RNAseq data from multiple developmental stages, and construct a molecular portrait of known and novel transcripts. The past decade has seen a surge in transcriptome-level studies for specific developmental stages of the eye and its tissue sub-types[1, 2]. The development of the eye involves a complex and highly orchestrated regulatory program with several specification and differentiation processes[3, 4]. Employing RNA-Seq datasets for genome-scale elucidation of the splicing alterations across developmental[11] and disease states[12] or to study inter-individual differences in humans is still in its early stages[13]. High quality raw sequence reads were processed and aligned to mouse reference genome mm[10] using HISAT and output collected as SAM files
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
