# Deciphering how 3D genome organization orchestrates cardiac cellular identity

> **NIH NIH R35** · UNIVERSITY OF PENNSYLVANIA · 2024 · $866,689

## Abstract

Project Summary
During cardiac development, coordinate gene expression changes facilitate the progressive lineage restriction
of multipotent progenitors into a terminal identity that is maintained over their lifespan. Compromised
differentiation and/or cell state have been linked to multiple diseases, including aspects of congenital heart
disease and heart failure. Thus, the mechanisms underlying cellular identity are of intense interest. Models
underlying fate determination and the identity often focus on transcription factors and/or niche signals. Current
paradigms fail to reconcile how the interplay between a finite number of morphogens and lineage specific
transcription factors result in 200+ cell types with distinct and stable identities. I hypothesize that nuclear
architecture represents a critical mechanism for achieving coordinated regulation of hundreds of genes
underlying cellular identity by governing their accessibility or availability. Supporting our hypothesis, we have
built a strong body of work demonstrating that nuclear architecture regulates cardiac cellular identity in
development and disease. First, we discovered mechanisms by which critical transcription factors not only
govern transcription, but also choreograph genome folding to regulate cardiac neural crest fate determination.
Second, our work shows that spatial positioning of chromatin safeguards cardiac cellular identity and likely
contributes to human cardiac disease (i.e. laminopathies). Decades of work have shown that gene expression
programs are regulated by the recruitment and activity of activator and opposing repressor proteins. In addition
to revolutionizing our understanding of transcription, this work has led to therapies directly targeting transcription
factors. The mechanisms that similarly balance formation, maintenance and dissolution of nuclear architecture
are poorly understood. In the EIA application I outline an interdisciplinary vision to uncover how these
mechanisms control cardiac cellular identity. In Theme 1, I propose strategies to identify and decipher how
molecular players guiding establishment, maintenance and disassembly of genome folding impact cardiac cell
state. In Theme 2, I propose strategies to uncover how epigenetic, transcriptional, and mechanical inputs
regulate spatial positioning of the genome in relation to the nuclear lamina in physiologic and pathologic
conditions. We have established a multipronged program that will use high throughput 3D imaging, genetic
manipulations with precise spatiotemporal resolution, tunable cardiac microtissues, epigenome engineering,
super-resolution imaging and state-of-the-art genomics to tackle the propose studies, with a focus grounded in
physiological relevance. The orthogonal approaches promote rigor, but require flexibility. My strong track record
of building an impactful body of work support our pursuit of this paradigm shifting work. The proposed studies
have the potential to reshape our under...

## Key facts

- **NIH application ID:** 10829874
- **Project number:** 5R35HL166663-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Rajan Jain
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $866,689
- **Award type:** 5
- **Project period:** 2023-05-01 → 2030-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10829874

## Citation

> US National Institutes of Health, RePORTER application 10829874, Deciphering how 3D genome organization orchestrates cardiac cellular identity (5R35HL166663-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10829874. Licensed CC0.

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