Date of Award

Spring 6-15-2024

Document Type

Undergraduate Honors Thesis

Degree Name

B.S in Molecular Biology

Organizational Unit

Biological Sciences, College of Natural Science and Mathematics

First Advisor

Stanley Kanai

Second Advisor

David Clouthier

Third Advisor

Nancy Lorenzon


Single-cell RNA sequencing, Cranial neural crest cells (CNCC), Early B-cell factor 3 (ebf3a), Pharyngeal arches, Sanger sequencing, Gel electrophoresis, Colorimetric in situ hybridization (ISH), Fluorescence, Sense probe, Antisense probe, Plasmid, Restriction digest, Embryonic development, Expression pattern, Cell cycle regulator, Pluripotent stem cells (PSCs)


Proper craniofacial development requires many genes. Single-cell RNA sequencing (scRNA-seq) allows us to identify genes expressed in precursor cells for craniofacial structures, but the function of many of these genes in craniofacial development has yet to be characterized. In our scRNA-seq of cranial neural crest cells (NCCs), which are precursor cells for the craniofacial skeleton, we found a gene called early B-cell factor 3 (ebf3a) that may be involved in craniofacial development. In our scRNA-seq data, ebf3a expression is restricted to cranial NCCs of the dorsal and ventral domains of pharyngeal arches 1 and 2. In humans, damaging variants in EBF3 are associated with facial dysmorphism. Based on these observations, we hypothesize that ebf3a is an important gene in craniofacial development. In this study, we begin to test this hypothesis by characterizing the expression pattern of ebf3a in cranial NCCs in zebrafish. Through fluorescence in situ hybridization, we confirmed that ebf3a is expressed in the cranial NCCs of the dorsal and ventral patterning domains of pharyngeal arches 1 and 2. This result will be a starting point for future experiments that will investigate the function of ebf3a in craniofacial development.

Copyright Date


Copyright Statement / License for Reuse

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Publication Statement

Copyright is held by the author. User is responsible for all copyright compliance.

Rights Holder

Shujan A. Sharafeldeen


Received from author

File Format



English (eng)


19 pgs

File Size

546 KB