Impact of ageing on 3D genome architecture in adIRD model in killifish, an aquatic animal model
Age is a critical factor for the onset of visual defects in most common IRD, including autosomal dominant IRD (adIRD). Although it is increasingly acknowledged that complex structural variants and non-coding defects play a role in the progression of IRD, the impact of aging on the regulatory landscape of IRD-associated genes has not been studied yet. The PhD student (DC1) will take advantage of unique features of the short-lived (<6 months) turquoise killifish (Nothobranchius furzeri) to investigate chromatin architecture and cis-regulatory maps in aging retinas. To this end, DC1 will use a combination of conformation capture methods: Hi-C (for global chromatin architecture) and HiChIP for H3K4me3 (that mark active promoters’ interactions); in combination with chromium single-cell multi-omics (scRNA-seq + scATAC-seq) to interrogate the transcriptome and epigenome simultaneously in retinas from aged animals. In parallel, DC1 will develop animal models for adIRD in killifish, either by targeting disease genes [e.g. by establishing a transgenic line] or by mimicking structural or non-coding human variants in killifish [i.e. by CRISPR-Cas9 targeting of specific cis-regulatory elements or CTCF loops]. Chromatin architecture and cis-regulatory maps will be then examined in the disease models generated to identify regulatory modules potentially involved in aging and disease progression. The 3D topology in killifish will be compared with the 3D topology generated in human retina (by DC5).