# Cell lineage and transcriptional analysis of the vertebrate neural plate border

> **NIH NIH R01** · CALIFORNIA INSTITUTE OF TECHNOLOGY · 2024 · $529,579

## Abstract

Both neural crest progenitors and ectodermal placode cells arise from the neural plate border (NPB).
While the neural crest gives rise to the craniofacial skeleton, the placodes form the lens, ear and olfactory system;
both contribute to cranial sensory ganglia. However, rather than being fixed to a neural crest or placodal fate,
our results show that cells in the neural plate border appear to coexpress transcription factors characteristic of
multiple lineages, ranging from neural crest to neural to placodal. Moreover, we find there is a stem cell niche
within the dorsal neural tube that expresses pluripotency factors including Sall4, Nanog, Oct4, Klf4, and cMyc
as confirmed in our single cell RNA-seq data. Thus, the question of what maintains stem cells with the potential
to form neural crest, placode and neural tube derivatives at the neural plate border remains open. Our preliminary
data suggest that Sall4 may form a feed-back loop with other multipotency genes, including Pou5f3/Oct4 and
Sall1. Moreover, overexpression of Sall4 prevents neural crest specification and upregulates Oct4. To test the
hypothesis that these pluripotency factors maintain multipotency of the neural plate border and that
their downregulation is necessary for neural crest and/or placode specification, we will explore the effects
of their gain and loss of function, identify enhancers that mediate their expression and examine dynamic changes
in their gene expression during neural plate border maturation. To this end, the following aims will be performed.
Aim 1: Effects of ectopic maintenance or loss of pluripotency factors on neural crest and placode
development. We will test the role of pluripotency factors Sall4, Oct4, Nanog and Klf4 in vivo in neural plate
border development using gain and loss of function approaches coupled with single cell RNA-seq. In particular,
we will test the hypothesis that these pluripotency factors maintain the multipotency of the neural plate border
and their downregulation is necessary for completion of neural crest specification. We will also examine other
transcription factors to test their role in driving lineage specification at the neural plate border.
Aim 2: Identification and cis-regulatory analysis of putative enhancers mediating expression of
pluripotency factors and neural plate border transcriptional regulators. Detailed cis-regulatory analysis
allows identification of active enhancers and their direct inputs, both positive and negative, thus informing upon
gene regulatory network connections. We propose to use single cell ATAC-seq to identify putative regulatory
elements active at the forming neural plate border, particularly those mediating expression of pluripotency factors
and transcriptional regulators. Putative enhancers will be tested for inputs and their ability to drive expression.
Aim 3: Dynamic analysis of enhancer-mediated expression during maturation of the neural plate border.
By coupling live imaging with enhancer d...

## Key facts

- **NIH application ID:** 10757050
- **Project number:** 5R01DE027538-07
- **Recipient organization:** CALIFORNIA INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Marianne Bronner
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $529,579
- **Award type:** 5
- **Project period:** 2018-02-01 → 2028-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10757050

## Citation

> US National Institutes of Health, RePORTER application 10757050, Cell lineage and transcriptional analysis of the vertebrate neural plate border (5R01DE027538-07). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10757050. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*