# Understanding the chromatin architectural landscape of retinal development at the single-cell level

> **NIH NIH F31** · JOHNS HOPKINS UNIVERSITY · 2024 · $48,974

## Abstract

Project Abstract:
 The 3D organization of the genome is important in controlling neuronal cell lineage commitment. As an
extension of the CNS, the retina is an excellent model for studying neuronal development. One issue in
studying the mouse retina is that it is dominated by rod photoreceptors, leading to bulk studies that overlook
less abundant cell types. The Blackshaw Lab and others have used single cell technologies to develop
transcriptomic (scRNA-seq) and epigenomic (scATAC-seq) atlases of mouse retinogenesis. These studies
have revealed cell-type-specific patterns of transcription factor (TF) mediated remodeling of chromatin that
occurs during developmental cell state transcriptions and are predicted to influence the 3D chromatin
architecture; however, the direct link has not been established. Previous studies on genome-wide chromatin
interactions using Hi-C have been conducted at the bulk level, are sparse, or focused only on rod
photoreceptors. A higher-resolution single-cell Hi-C (scHi-C) study is needed to understand changes in
chromatin organization associated with the specification of different retinal cell types.
 Through the integration of multi-omic data at single cell resolution, I aim to identify how transcription
factors manipulate genomic structure to control cell fate specification. During retinal development, expression
of the NFI family of TFs (NFIA/B/X) controls the competence of late-stage RPCs and drives specification of
late-born retinal cell types (late-born rods, bipolar cells, and Muller glia). The Blackshaw lab’s previous scRNA-
seq and scATAC-seq studies have found many thousands of genes and cis-regulatory-elements that are
differentially regulated upon Nfia/b/x loss-of-function, which suggests that the NFI family TFs affect chromatin
state. Other studies have also found that the NFI family TFs affect chromatin compartmentalization and
promote the formation of super-enhancers. However, little is known about whether the NFI family TFs directly
regulate chromatin structure to activate downstream genes.
 In this proposed research, I will capture the 3D chromatin interactions of mouse retinal cells at the
single-cell level and at key developmental stages, using droplet microfluidic scHi-C (Aim 1). ScHi-C will be
adapted for the 10x Genomics droplet single-cell system and applied to the mouse retina at key developmental
stages. I will then use scHi-C to capture changes in chromatin organization associated with retinal progenitor-
specific loss-of-function of Nfia/b/x (Aim 2). To do this, I will first combine scHi-C with the Blackshaw Lab’s
previously obtained scATAC-seq, scRNA-seq, and Nfia/b/x ChIP-seq datasets to form a multiomic dataset of
retinal cells. I will then use the dataset to identify chromatin interactions associated with NFIA/B/X that drive
specification of late-stage RPCs. The droplet microfluidic scHi-C protocol will provide a generalizable method
that can be used for other genomic studies. The single-...

## Key facts

- **NIH application ID:** 10901167
- **Project number:** 1F31EY036274-01
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Vickie Trinh
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $48,974
- **Award type:** 1
- **Project period:** 2024-08-15 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10901167

## Citation

> US National Institutes of Health, RePORTER application 10901167, Understanding the chromatin architectural landscape of retinal development at the single-cell level (1F31EY036274-01). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10901167. Licensed CC0.

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