Genome wide mapping of promoter-anchored interactions in the human retina

Abstract

Purpose : Variations in the human genome can cause or modify disease phenotypes. How non-coding variants affect retinal disease is poorly elucidated at this stage. Modification of the DNA and histones in the genome plays critical role in the gene regulation as they define the accessibility of regulatory sequence that is important for transcription and splicing. We hypothesize that genome wide analysis of promoters and enhancers in the human retina will assist in evaluating functional relevance of disease-associated non-coding variants.

Methods : Adult human retinas were collected from four healthy donors. Assay for Transposase-Accessible Chromatin using sequencing (ATAC seq) was performed on the peripheral retina. Genome wide mapping of the histone modification H3K4me3 associated with active promoters was performed by Cleavage Under Targets and Release Using Nuclease (CUT&RUN) on cryoprotected cells obtained from peripheral retina. HiC for other histone modifications and Hi-C chromatin immunoprecipitation (HiChIP) for H3K4me3 is being performed to identify chromatin interactions mediated by active promoters and other regulatory regions.

Results : H3K4me3 was present on promoters of genes that are expressed in adult retina and they seem to overlap with the open chromatin regions. Mapping of chromatin regions associated with H3K4me3 and other histone modifications is underway.

Conclusions : The histone modification H3K4me3 associates with active promoters in the human retina. Thus, mapping chromatin regions enriched for H3K4me3 and other histone modifications and their chromatin interactions will allow us to identify relevant regulatory regions important for retina homeostasis and disease.

This is a 2020 ARVO Annual Meeting abstract.