Shock, Betsy

Research Activities

In the Schock lab, we are interested in understanding the development of an embryonic stem cell population called the neural crest. This cell population gives rise to much of the craniofacial skeleton and also contributes significantly to other cell types in the face (pigment, neurons/glia, Schwann cells, smooth muscle, connective tissue). We are particularly interested in understanding how neural crest cells make cell fate decisions to give rise to this plethora of cell types. To study this, we deploy the developmental model system, Xenopus tropicalis. This model system has many advantages including: external fertilization of a large number of eggs from a single female, large egg size, ease of microinjections into the embryo. Additionally, these embryos are kept in a simple salt solution, helping to make them a very cost effective model system. Importantly, these is a high degree of conservation in genes between frogs and humans. Developmentally, these genes are deployed for the same processes that are observed in amniotes, allowing our findings to be relevant to human health.

SoxE transcription factors (Sox8/9/10) are required for the formation of the neural crest in the embryo and are known to play important roles in the differentiation of those cells. Interestingly, while SoxE factors are functionally redundant during neural crest formation, they take on distinct roles are neural crest cells differentiate. Sox9 is a master regulator from chondrogenesis (cartilage) while Sox10 promotes the formation of pigment cells and peripheral glia. In my lab, we are interested in understanding the apparent subfunctionalization of these factors. To do so, we will assess global occupancy of these transcription factors in neural crest cells using ChIP-seq. We aim to determine if there is a temporal, lineage-specific, shift in genomic occupancy of these factors, or if there are differences as they are initially expressed in the neural crest. Next, we want to understand this difference in protein function at the level of functional domains. SoxE factors have four main functional domains: a dimerization domain, a DNA-binding (HMG) domain, and two transactivation domains. We have developed a series of Sox9-Sox10 chimeras that we will use to dissect how sequence differences in these domains lead to functional differences between these proteins. Once we have identified domains that contribute to divergent functions, we will perform ChIP- and RNA-seq in neural crest cells to determine how these domains affect genomic occupancy and subsequent gene activation.

Finally, mutations in Sox9 and Sox10 are associated with two syndromes, Campomelic dysplasia and Waardenburg syndrome, respectively. We aim to understand how mutations in those genes lead to the craniofacial phenotypes observed in patients. Both of these syndromes are typically associated with haploinsufficiency; however, instances of dominant negatives variants have been reported. A major unanswered question is if/how disease etiology differs for haploinsufficient vs dominant negative variants. For each syndrome, we have selected a patient variant with putative dominant negative activity, as determine by in vitro assays. We will express these variants in Xenopus embryos and assay neural crest cell formation, migration, and differentiation. These findings will be compared to results for haploinsufficient models for the syndromes. We will also perform ChIP- and RNA-seq in neural crest cells expressing these variant proteins to determine how these domains affect genomic occupancy and subsequent gene activation.

Overall, these genomics approaches will help us to gain a comprehensive understanding of SoxE transcription factors activity in the neural crest.

List of Projects

Project 1- Sox9 and Sox10 temporal occupancy
We will use ChIP-seq to assess how occupancy of these factors changes over time in the neural crest.
Project team: Betsy Schock (PI) and Paul Huber (Staff scientist)

Project 2- SoxE functional domains
We will use Sox9-Sox10 chimeras to determine how sequence differences in functional domains contribute to changes in genomic occupancy (ChIP-seq) and subsequent gene activation (RNA-seq).
Project team: Betsy Schock (PI) and future graduate student

Project 3: Disease etiology for SOXopathies
We will investigate how patient-specific variants lead to craniofacial phenotypes in Campomelic dysplasia/waardenburg syndrome
Project team: Betsy Schock (PI) and future graduate/undergraduate students

Computational Methods

command line; RStudio

List of Software

fastqc; fastp; bowtie2; STAR; rsem; picard; MACS2; genrich; HOMER; bedtools; deepTools; alphafold; samtools; R/RStudio; DiffBind; DESeq2; htseq-count; ggplot2;

Collaborators

UK students and employees (postdoc/technician/staff scientist), all of whom are members of the Schock lab, will be involved in the project. Data may be shared with other members of the Biochem department to aid in data analysis/interpretation.