# Functional characterization of craniofacial enhancers at single cell and single base pair resolution

> **NIH NIH R01** · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · 2020 · $389,500

## Abstract

Abstract
Craniofacial abnormalities are some of the most commonly occurring human birth defects worldwide,
with up to 200,000 children born every year with some type of craniofacial defect. These defects can
occur as part of complex syndromes that involve multiple tissues and organs. The syndromic forms of
these disorders have been successfully linked to nearly 500 genes including TWIST1 for
craniosynostosis and IRF6 for orofacial clefting. However more frequently no other part of the body is
directly involved (50% of craniosynostoses, 70% of orofacial clefts). Genome wide association studies
indicate heritability for such defects, however the vast majority of associations fall outside of genes
suggesting defective gene regulation is a major contributor to incidence of such defects. Gene
regulatory elements can be located throughout the genome and typically have tissue-specific activity,
making them difficult to identify and predict what gene they control. The overall objective of this
application is to identify the cell types present in the developing human face and functionally
characterize important regulatory elements that specify them as single base pair resolution. In Aim 1
we propose to systematically identify populations of cell types using single-cell based methods for
measuring the transcriptome and active regulatory sites across the genome in human craniofacial
tissue from 4 to 5 weeks of gestation and mouse from embryonic days 10.5 and 11.5. In Aim 2 we
propose to identify physical interactions between regulatory sequences and target genes in these
same tissue types. Finally, in Aim 3 we will identify regulatory elements from these tissues that can
be tested in a cell culture model of cranial neural crest cells. These enhancers will be assessed for
effects on gene expression when repressed or removed from the genome. Those with significant
effects on gene expression will be tested for every variant to identify important locations within them.
Our proposed studies will generate the most comprehensive view of the cell types active in the
developing human face and reveal the contributions individual noncoding variants make on gene
expression.

## Key facts

- **NIH application ID:** 9971495
- **Project number:** 5R01DE028945-02
- **Recipient organization:** UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
- **Principal Investigator:** Justin Lee Cotney
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $389,500
- **Award type:** 5
- **Project period:** 2019-07-03 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9971495

## Citation

> US National Institutes of Health, RePORTER application 9971495, Functional characterization of craniofacial enhancers at single cell and single base pair resolution (5R01DE028945-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9971495. Licensed CC0.

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