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Evgenya Popova, Colin Barnstable; Chromatin and epigenetic changes in Rhodopsin promoter and gene during retina maturation. Invest. Ophthalmol. Vis. Sci. 2013;54(15):3732.
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© ARVO (1962-2015); The Authors (2016-present)
The change in chromatin structure at promoters and genes is an important contributor to tissue specification and regulation of large groups of genes during development, as well as normal tissue maintenance. Retinal development is accompanied by changes in epigenetic histone modifications and changes in nucleosome positions in the genome that correlate with changes in occupancy of transcription factors at gene promoters and with gene expression. We used Rhodopsin gene as example to follow the chromatin states during development. The goal of this study was to elucidate the precise sequence of events for chromatin structural and epigenetic changes for retinal specific genes during maturation.
Animal use was in accordance with ARVO/IACUC guidelines. Studies were conducted with eyes collected from C57BL/6j mice (Jackson Laboratory) at 4 developmental stages from P1 to PN30. ChIP-qPCR analysis of retinal chromatin was performed with antibodies against several histone acetylation and methylation modifications characteristic for active state of the gene.
We followed changes during retina maturation for H3K27ac, H3K9ac, H4K12ac and H3K4me2, H3K4me3; all are marks for active open chromatin. The chromatin state of Rhodopsin gene and its promoter were assessed with 10 genomic primer pairs in the area between - 3.5Kb to +6 Kb of TSS. In general, all histone modifications had less accumulation at CRX, NRL binding and DNase hypersensitive sites most likely due to the less nucleosomes at these areas. All acetylation marks appeared before PN7 and start to decrease after PN15. In contrast histone methylation marks started to appear at PN7 and increased up to PN30. Acetylation marks had two peaks of accumulation at -1.5Kb and +0.5Kb from TSS at PN15. H3K4me3 accumulated in a small peak at -1.5Kb and 2 big peaks at +0.5 and +3.5 at PN30, while H3K4me2 has unique patterns of distribution with broader accumulation on the area before TSS and the whole gene body after the second exon at PN30.
We propose that acetylation marks work to allow start of basal transcription, where is methylation works as maintenance mark to keep high level of transcription. The detection of active epigenetic sites outside the promoter region is intriguing and their function needs further investigation.
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