The 3D map reveals the DNA tissue within human retinal cells

NIH researchers have revealed new insights into
how gene structure determines gene expression, tissue-specific function, and disease phenotypes for blinding diseases.

Scientists at the National Institute of Ophthalmology (NEI) have mapped the tissue
of chromatin in human retinal cells.
These fibers pack 3 billion nucleotide-long DNA molecules into tight structures and match
the chromosomes within each nucleus.
The resulting comprehensive gene regulatory network provides insights into the general regulation of gene expression and the regulation of retinal function, including rare and common eye diseases
.
The study was published today (October 7, 2022) in the journal Nature Communications
.

Dr Anand Swaroop, lead investigator of the study, said: "This is the first detailed integration of the retina-regulated genomic topology with genetic variants associated with senile macular degeneration (AMD) and glaucoma, which are the two main causes
of vision loss and blindness.
"

Adult retinal cells are highly specialized sensory neurons that do not divide and are therefore relatively stable
.
This makes them helpful in exploring how the three-dimensional structure of chromatin contributes to the expression
of genetic information.

Chromatin fibers are wrapped in long strands of DNA that are wrapped around histone proteins and then repeatedly circulate to form highly compact structures
.
All of these cycles create multiple contact points, where the gene sequences that code for proteins interact with gene regulatory sequences, such as superenhancers, promoters, and transcription factors
.

For a long time, this non-coding sequence was considered "junk DNA
.
" However, more advanced studies have shown that these sequences can control which genes are transcribed
and when.
This reveals specific mechanisms by which noncoding regulatory elements exert a controlling role on the DNA strand, even if their position on the DNA strand is far from the genes
they regulate.

Using deep Hi-C sequencing, a tool used to study 3D genomic tissue, the scientists created a high-resolution map that included 704 million touchpoints
in chromatin in retinal cells.
The map was drawn using posthumous retinal samples from
four donors.
"To elucidate genomic regulation in the human retina, we mapped chromatin exposure at high resolution and integrated super-enhancers (SEs), histone markers, CTCF binding and selected transcription factors
," they commented.

This is a moving image of the interaction within chromatin over time, including hot spots of gene activity and areas that are insulated to varying degrees from other regions of DNA
.
"Further integration of chromatin-hibitor contact with histone markers, chromatin accessibility, selected TF [transcription factor] binding and gene expression datasets revealed the target of CREs and revealed the three-dimensional chromatin tissue properties
of SEs in the human retina.
"

The team integrated chromatin topology maps with datasets of retinal genes and regulatory elements
.
This is a moving image of the interaction within chromatin over time, including hot spots of gene activity and areas that are insulated to varying degrees from other regions of DNA
.

They found different interaction patterns on the retinal gene, which shows how 3D tissue of chromatin plays an important role
in tissue-specific gene regulation.

"Having such a high-resolution image of genomic structure will continue to provide insights
into gene control of tissue-specific functions," Swaroop said.

In addition, similarities between mouse and human chromatin tissue indicate conservation across species, emphasizing the correlation between chromatin tissue patterns and retinal gene regulation
.
More than one-third (35.
7 percent) of gene pairs interacted through chromatin rings in mice, as well as
in the human retina.

The scientists combined chromatin topology maps with data from genetic variants linked to age-related macular degeneration (AMD) and glaucoma, two of the leading causes
of vision loss and blindness.
The findings point to specific candidate pathogenic genes
associated with these diseases.

An integrated genomic regulatory map will also help to evaluate genes associated with other common retina-related diseases such as diabetic retinopathy, identify missing heritability, and understand genotype-phenotypic correlations
for hereditary retinal and macular diseases.

High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci" by Marchal C, Singh N, Batz Z, Advani J , Jaeger C, Corso-Diaz X, and Swaroop A, 7 October 2022, Nature Communications