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Xiuqian Mu, Fuguo Wu, Darshan Sapkota, Tao Liu, zihua hu; Transcriptomic and epigenomic analysis of retinal ganglion cell development. Invest. Ophthalmol. Vis. Sci. 2017;58(8):568.
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© ARVO (1962-2015); The Authors (2016-present)
In the gene regulatory network controlling the formation of retinal ganglion cells (RGCs), how individual regulators (transcription factors) carry out their functions is largely unknown. Likely these factors fulfill their roles through influencing and interacting with the epigenetic landscape to achieve the transcriptional outcome specific to and essential for RGC development. Our purpose is to understand how key transcription factors contribute to the RGC-specific epigenome and transcriptome during RGC development.
We used RNA-seq to identify genes that are dependent on three key transcription factors, Atoh7, Pou4f2 and Isl1. We also used ChIP-seq to identify RGC-specific enhancers. In addition, we made new mouse lines in which retinal cells at the different stages of RGC development are labeled by fluorescent proteins, which allows us to use purify cells at different stages of RGC development.
Previous work have identified some downstream genes of Atoh7, Pou4f2 and Isl1 using custom microarrays, but those results are far from complete. Taking advantage of the mouse lines we have, we performed RNA-seq for Pou4f2-null, Isl1-null, and Atoh7-null retinas at E14.5 and identified differentially expressed genes in these mutants, as compared with the wild-type retinas. These results revealed new pathways and players in RGC development. Meanwhile, we have also performed ChIP-seq for H3K4me1 and H3K27ac, two active enhancer makers, with E14.5 wild-type and Atoh7-null retinas, and are in the process of identifying enhancers that are specifically active in RGCs at a global level. In addtition, by gene targeting, we have created new mouse lines in which RGC-competent retinal progenitor cells and fate-determined RGCs are labeled by different fluorescent proteins. We will use these lines to purify cells at different stages of RGC development by FACS and further study their properties by transcriptomic and epigenomic analysis.
Using a combined approach of RNA-seq, ChIP-seq and mouse genetics, we will be able to understand how the epigenetic landscape shifts during RGC development and how the shift is regulated. The results will further reveal the genetic mechanisms underlying RGC formation during development. The new mouse lines we have created will significantly facilitate our effort by allowing us to study this process with purified cell populations.
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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