Understanding the chromatin architectural landscape of retinal development at the single-cell level
Ended Project Grant Awarded Last action
- Award ID
- F31EY036274
- Recipient
-
The Johns Hopkins University UEI FTMTDMBR29C7
- Awarding agency
-
National Eye Institute
National Institutes of Health, Department of Health and Human Services
- Obligated
- $118,398
Award facts
- Assistance listing
- 93.867 Vision Research
- Completion date
- Place of performance
- Maryland, USA
Award details come from USAspending.gov.
Description
- 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-cell multi-omic dataset of retinal development will allow improved construction of retinal gene regulatory networks and novel targets for treating retinal disorders.
Transactions
| Action | Obligated | Date |
|---|---|---|
| Amendment | -$28,524 | |
| Amendment | $0 | |
| Amendment | $48,974 | |
| Amendment | $0 | |
| Amendment | $48,974 | |
| Amendment | $0 | |
| Original award | $48,974 |
Quick answers
Who received award F31EY036274?
F31EY036274 was awarded to The Johns Hopkins University by National Eye Institute (National Institutes of Health) on January 30, 2025.
How much is award F31EY036274 worth?
$118,398 has been obligated on F31EY036274.
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