June 2017
Volume 58, Issue 8
Open Access
ARVO Annual Meeting Abstract  |   June 2017
RNA-seq based identification of long non-coding RNAs (lncRNAs) in early lens development
Author Affiliations & Notes
  • Deepti Anand
    Biological Sciences, University of Delaware, Newark, Delaware, United States
  • Atul Kakrana
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States
  • Archana D Siddam
    Biological Sciences, University of Delaware, Newark, Delaware, United States
  • Irfan Saadi
    University of Kansas Medical Center, Department of Anatomy and Cell Biology, Kansas City, Kansas, United States
  • Salil Lachke
    Biological Sciences, University of Delaware, Newark, Delaware, United States
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States
  • Footnotes
    Commercial Relationships   Deepti Anand, None; Atul Kakrana, None; Archana Siddam, None; Irfan Saadi, None; Salil Lachke, None
  • Footnotes
    Support  NIH/NEI R01 EY021505
Investigative Ophthalmology & Visual Science June 2017, Vol.58, 1717. doi:
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      Deepti Anand, Atul Kakrana, Archana D Siddam, Irfan Saadi, Salil Lachke; RNA-seq based identification of long non-coding RNAs (lncRNAs) in early lens development. Invest. Ophthalmol. Vis. Sci. 2017;58(8):1717.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : One of the unanticipated findings of the post-genome era is the widespread transcription of non-coding genomic DNA that leads to thousands of diverse long non-coding RNAs (lncRNAs). Despite the numerous insights into their involvement in regulating diverse cellular events, a comprehensive atlas of lncRNA expression in the lens is unavailable. We report the identification of lncRNAs from the early stages of mouse lens development, beginning at the lens vesicle stage, by RNA-sequencing (RNA-seq)

Methods : Mouse lenses were micro-dissected at the lens vesicle stage (Embryonic day (E) 10.5), initiation of primary fiber differentiation stage (E12.5), and beyond (14.5, E16.5) and analyzed by deep paired-end RNA-seq. Further, to include in this analysis late embryonic and early postnatal (P) lens stages, we obtained mouse lens RNA-seq data for E15.5, E18.5, P0, P3, P6 and P9 from NCBI GEO

Results : This comprehensive data from ten distinct lens embryonic and early postnatal development stages together provided >1,145 million genome mapped read pairs. The ab-initio assembly from this data reconstructed a total of 36,453 high-confidence transcripts generated from 11,848 distinct transcriptional loci. Preliminary analysis of this high-quality lens transcriptome identified 4,996 long non-coding transcripts that are expressed in at-least two different developmental stages in lens at expression level >1 FPKM. These include 3,421 previously annotated non-coding RNAs, 1,118 lncRNAs with sense overlap with coding genes, 68 cis-natural antisense (cis-NAT) lncRNAs and 105 novel lincRNAs transcripts. As expected, lncRNAs expressed in lens shows a stark difference with protein-coding transcripts in number of exons and length of transcripts, lncRNA transcripts were 905-nt long on average with 3.2 exons, compared to 3175-nt long coding transcripts that have 11.5 exons on average. Interestingly, 457 and 496 lncRNA candidates were specifically expressed in embryonic and post-natal lens stages, respectively

Conclusions : As an important step toward understanding lncRNA function in the lens, these RNA-seq efforts provide a comprehensive atlas of the temporal expression of lncRNAs in the developing mouse lens. Integration of these lncRNA data –along with other transcript expression data obtained from these RNA-seq efforts– in the eye gene discovery tool iSyTE will impact future studies on the molecular control of lens development

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.

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