Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations

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...

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Bibliographic Details
Published in:Scientific reports 2017-09, Vol.7 (1), p.11572-17, Article 11572
Main Authors: Srivastava, Rajneesh, Budak, Gungor, Dash, Soma, Lachke, Salil A, Janga, Sarath Chandra
Format: Article
Language:English
Subjects:
Alternative Splicing
Animals
Bioinformatics
Computational Biology - methods
Cyclin-dependent kinase 4
Datasets
Developmental stages
Embryos
Exons
Eye
Eye lens
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Developmental
Genomes
High-Throughput Nucleotide Sequencing
Isoforms
Lens, Crystalline - embryology
Lens, Crystalline - metabolism
Mice
Molecular Sequence Annotation
Pax6 protein
Phylogeny
Polymerase chain reaction
Post-transcription
Ribonucleic acid
RNA
RNA Isoforms
Transcription
Transcriptome
Zebrafish
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-10615-4