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Martial Kamdem Mbefo, Mathieu Quinodoz, Carlo Rivolta, Yvan Arsenijevic; H3K27me3-based Chip-Seq reveals distinct occupancy of specific genes during retinal degeneration. Invest. Ophthalmol. Vis. Sci. 2018;59(9):2326.
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© ARVO (1962-2015); The Authors (2016-present)
The molecular mechanisms that orchestrate the degenerative process in retinitis pigmentosa involved many genes. In view of our previous study demonstrating that the Polycomb Group (PcG) protein BMI1 plays a crucial role during the photoreceptor death (Zencak et al., 2013), we thus sought to investigate whether gene expression changes may be due to other PcG proteins inducing epigenetic modifications.
We used cross sections from FVB Rd1 and FVB WT mouse retinas at different postnatal ages to screen for the changes of histones marks H3K27me3, H3K4me3 and H3K9me2 by immunohistochemistry and confirm our data with samples from Human donors. We next performed chromatin immunoprecipitation followed by Illumina sequencing (Chip-Seq) on whole retinal extracts to isolate and identify the genes enriched with histones marks at their transcription start site (TSS). Finally, we applied bioinformatic tools including gene ontology (GO) and RStudio for data analysis and statistical meanings
In Rd1 mice as well as in two Rhodopsin mutant rodents (P23H and S334 ter) of retinal degeneration, cell death was preceded by abnormal accumulation of the H3K27me3 mark within the nucleus of certain photoreceptors. Similar results were also obtained with samples obtained from two Human RP patients. Our Chip-Seq data has revealed only mild overall changes of H3K27me3 and H3K4me3 TSS chip-Seq density profiles (r = 0,94 and r=0,99 respectively; Pearson correlation, 95% confidence), suggesting that H3K27me3 hyper-trimethylation may appears only in cells programmed for death. Topping the genes according to their H3K27me3 enrichment, GO analysis has revealed that the genes with the highest H3K27me3 in WT and Rd1 were enriched (p value (FDR) < 0.001) in the biological processes controlling the cell cycle, morphogenesis, and cell differentiation. However, genes enriched of H3K27me3 only in Rd1 mice (Fold enrichment > 3) were found in cellular processes regulating the defense mechanism, cell cycle, cellular trafficking and cell death. The candidate genes are currently being investigated in vivo.
Together, our preliminary data shed light on epigenetic H3K27me3 modifications as an important biological mechanism that may participate to photoreceptor degeneration mechanisms in Rd1 mice.
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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