July 2018
Volume 59, Issue 9
Open Access
ARVO Annual Meeting Abstract  |   July 2018
RNA-seq, ATAC-seq, and proteomic analysis of mammalian lens differentiation
Author Affiliations & Notes
  • Ales Cvekl
    Ophthalmology & Vis Sci & Genetics, Albert Einstein Coll of Medicine, Bronx, New York, United States
  • Footnotes
    Commercial Relationships   Ales Cvekl, None
  • Footnotes
    Support  NIH R01 EY014237
Investigative Ophthalmology & Visual Science July 2018, Vol.59, 2607. doi:https://doi.org/
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      Ales Cvekl; RNA-seq, ATAC-seq, and proteomic analysis of mammalian lens differentiation. Invest. Ophthalmol. Vis. Sci. 2018;59(9):2607. doi: https://doi.org/.

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

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Abstract

Presentation Description : Purpose. Cellular differentiation is driven by an orchestrated expression of hundreds to thousands of genes required to establish terminally differentiated phenotypes. At the chromatin level, activation and repression of individual genes is mediated through the generation of “open” chromatin domains, including the promoters and enhancers. Gene expression, chromatin organization, and regulatory regions of transcription can be probed at a genome-wide scale using a combination of RNA-seq, ATAC-seq, ChIP-seq, and Hi-C.
Methods. RNA-seq analysis of E14.5, E16.5, E18.5, and P1 stages of mouse lens development were conducted using microdissected lens epithelia and lens fibers (n=3). To study chromatin structure dynamics, ATAC-seq experiments were conducted using epithelia and fibers from E14.5 and P1 lenses. Unbiased analysis of potential cis-regulatory motifs within +/- 2kb promoter regions was conducted using The MEME Suite (Motif-based sequence analysis tools). Micro-scale proteomic studies provide the information regarding the quantities of proteins in relation to their mRNAs.
Results. The current analysis revealed 4,358 and 2,925 genes differentially expressed throughout the lens epithelium and lens fiber cell compartments. The data analysis unravels novel waves of coordinated gene expression in both lens epithelium and lens fiber cell compartments. In lens fibers, notable upregulation of genes within the GO categories translational initiation, lipid metabolism process, vesicle-mediated transport, autophagy, protein ubiquitination pathway, and cholesterol biosynthesis are found. Over 30 novel candidate DNA-binding transcription factors for lens differentiation have been identified. Promoters of lens epithelial and fiber genes are enriched for E2F, Ets, Smad, Sox, and Tead, and E-box (N-Myc), Ets, Hif1a, Maf, NF-kb, Prox1, RARE, and Smad cis-sites, respectively. ATAC-seq data demonstrate dynamics of “open” chromatin between different lens cell types.
Conclusions. Collectively, our data lay down a comprehensive foundation to understand the complex process of gene regulation during lens development.

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.

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