# Modeling Gene Regulatory Networks for Early Cardiopharyngeal Development

> **NIH NIH R01** · NEW YORK UNIVERSITY · 2020 · $603,920

## Abstract

Congenital heart defects affect ~1% of newborn infants and are often associated with craniofacial
defects as is the case in the DiGeorge/CardioVeloFacial syndrome (DGS/CVFS). The latter is
often caused by spontaneous de novo 22q11.2 deletions, which result in TBX1
haploinsufficiency, a major cause of the disease. TBX1 is thought to function in multipotent
progenitors for the second heart field and branchiomeric/pharyngeal head muscles in early
embryos, and thus combined cardiac and craniofacial malformations emerge from early defects
in the cardiopharyngeal mesoderm. The existence of multiple interacting genetic modifiers of
DGS penetrance hints at the complex gene regulatory network (GRN) controlling early
cardiopharyngeal development. Despite progress in identifying key genetic determinants, the
relative complexity of vertebrate embryos has hindered progress in modeling cardiopharyngeal
networks. The tunicate Ciona is a tractable model where early cardiopharyngeal development
can be studied with unprecedented spatial and temporal resolution in chordates, using
functional genomics methods. In previous studies, comprehensive gene expression and
chromatin accessibility profiles were obtained by lineage-specific whole genome assays,
including single cell RNA-seq (scRNA-seq) and ATAC-seq. A method combining sample
barcoding, CRISPR/Cas9-mediated mutagenesis, and scRNA-seq was developed to
systematically interrogate the function of coding and non-coding genetic elements using
high-content scRNA-seq assays. First, this approach will be used to profile loss-of-function
perturbations for candidate transcription regulators expressed in the cardiopharyngeal lineage.
Ciona and available mouse datasets will be integrated into cross-species models to jointly learn
conserved and divergent features of cardiopharyngeal GRNs. Next, perturbations of accessible
non-coding elements for selected transcription regulators (plus high-content scRNA-seq assays
and new computational methods) will permit the explicit integration of non-coding elements in
the context of our GRN models. Finally, perturbing regulators of cardiopharyngeal-specific
chromatin accessibility followed by lineage-specific ATAC-seq will further disentangle the
impact of transcription regulators on accessibility vs. activity. Integrating these datasets into
lasting and evolving GRN models will support comprehensive understanding of early
cardiopharyngeal development and the etiology of congenital cardio-craniofacial syndromes.

## Key facts

- **NIH application ID:** 9989883
- **Project number:** 5R01HD096770-03
- **Recipient organization:** NEW YORK UNIVERSITY
- **Principal Investigator:** RICHARD A BONNEAU
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $603,920
- **Award type:** 5
- **Project period:** 2018-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9989883

## Citation

> US National Institutes of Health, RePORTER application 9989883, Modeling Gene Regulatory Networks for Early Cardiopharyngeal Development (5R01HD096770-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9989883. Licensed CC0.

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