# Defining the dynamic 3D genome during hearing regeneration in the adult zebrafish inner ear

> **NIH NIH FI2** · NATIONAL HUMAN GENOME RESEARCH INST · 2021 · —

## Abstract

Project Summary
Humans cannot renew the mechanoreceptors (hair cells, HCs) in the inner ear after damage-induced cell death leading
to hearing loss. Unlike mammals, zebrafish can regenerate HCs. We aim to reveal key genetic switches that will
eventually lead us to approaches that could trigger HC regeneration programs in humans. To avoid developmental
variations, we assess the zebrafish adult inner ear to truly understand the genomic elements during homeostasis and
regeneration. HC regeneration is a balancing act of supporting cells (SCs) and HC progenitors (HCPs), that oscillate
between self-renewal, proliferation, and terminal differentiation required to replace lost HCs. I believe HC renewal
would be better understood as a combinatorial regulation of gene networks during homeostasis, injury, and
regeneration, and that it can be linked to the spatial organization of the genome. Super-resolution microscopy and
sequencing-based genomic technologies, such as Hi-C, have revealed that the genome is hierarchically organized in
the nucleus of eukaryotic cells. This 3D organization is denoted by multilevel chromatin architectural features such as
chromosome territories, A/B compartments, topologically associated domains (TADs), and long-range chromatin
loops. The underlying genome architecture of HCPs that initiate regeneration and instruct HC differentiation remains
unexplored. Stable TADs are thought to be mediated and regulated through CTCF, a DNA binding transcription and
boundary factor along with the cohesin complex. Interestingly, these play a role in development and differentiation.
Our unpublished data revealed dynamic changes in transcription and chromatin accessibility during HC regeneration.
Results from bulk ATAC-seq on zebrafish inner ears obtained during homeostasis detected CTCF as a top motif.
Moreover, scATAC-seq data showed that CTCF is enriched in HCPs emerging peaks as consequence of HC
regeneration. Based on our findings, I hypothesize that de novo formation of TADs and chromatin loops during HC
regeneration will reveal a 3D “homeostasis vs. regeneration” profile and any rearrangement will modify the HCP
regenerative plasticity. The objective of the proposed research is to take a multi-dimensional genomics approach to
construct a comprehensive picture of the regulatory program of HC development and regeneration in the adult inner
ear. The hypothesis will be addressed in two specific aims. In Aim 1, we will identify the inner ear 3D nuclear
architecture in homeostasis and during HC regeneration. We will employ scATAC-seq, scRNA-seq, and scHi-C assays
to map the 3D genome of HCPs, SCs, and HCs in the adult inner ear comparing wild-type and Tg(myo6b:hDTR), a
unique transgenic zebrafish with the capacity for conditional HC-ablation in vivo. In Aim 2, we will test the in vivo
functionality between TADs and regulatory elements using CRISPR/Cas9 and super-resolution microscopy.
Completion of the aims will provide training in modern appro...

## Key facts

- **NIH application ID:** 10272356
- **Project number:** 1FI2GM142471-01
- **Recipient organization:** NATIONAL HUMAN GENOME RESEARCH INST
- **Principal Investigator:** Luis Colon-Cruz
- **Activity code:** FI2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** —
- **Award type:** 1
- **Project period:** 2021-09-01 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10272356

## Citation

> US National Institutes of Health, RePORTER application 10272356, Defining the dynamic 3D genome during hearing regeneration in the adult zebrafish inner ear (1FI2GM142471-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10272356. Licensed CC0.

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