Investigating SoxB mediated gene regulatory networks in embryogenesis and neurogenesis

Lead Research Organisation: University of Cambridge
Department Name: Genetics


PhD project strategic theme: Understanding the rules of life

In this PhD, I will investigate the role of Sox domain proteins in regulatory networks that drive early development and neurogenesis using Drosophila melanogaster as a model organism. Sox domain proteins are highly conserved across metazoans and mutant studies show that group B Sox proteins (Sox1, 2 and 3 in vertebrates; Dichaete and SoxNeuro in insects) act redundantly to regulate neural cell specification. In addition, Dichaete appears to have a unique role in early segmentation that appears to be conserved across invertebrates. However, we do not know how SoxB proteins regulate key aspects of development and why evolution has conserved proteins that can compensate for each other's function. These questions are of importance to the study of transcriptional regulation. Drosophila melanogaster is an attractive system to begin to address these questions as SoxB proteins are dynamically expressed during embryogenesis and the mammalian proteins are functionally related to both Dichaete and SoxNeuro. Therefore, the study of Dichaete and SoxN in Drosophila may provide useful insights into aspects of Sox B function in the more complex vertebrates.

SoxB domain proteins bind to DNA and change its structure to activate or repress genes in response to developmental cues. Although all SoxB TFs bind to a similar DNA motif, they regulate the expression of many different genes. Genetic and genomic studies suggest that their diverse functions may in part be due to their interactions with specific transcriptions factors. Of particular interest is the interaction of Dichaete with Odd-paired (Opa) during segmentation, and of both proteins with Ventral nervous system defective (Vnd) during neural specification. By binding to DNA with these distinct transcriptions factors Sox proteins change the structure of DNA and influence which genes can be transcribed at specific time points in development. To date, experiments have been conducted at low resolution and across most of embryonic development. To fully understand how Sox domain proteins are functioning we require a more detailed analysis of their interactions with these proteins and effect on chromatin structure and mRNA expression over the period spanning from zygotic genome activation to the end of embryogenesis.

Therefore, the aims of this PhD are

1) To define regulatory targets of Dichaete and SoxNeuro by performing ChIP-sequencing analysis using carefully staged embryos to map the binding of two TFs in the same chromatin preparations (i.e. Dichaete and Opa; Dichaete and Vnd; SoxN and Vnd).
2) To determine how chromatin accessibility impacts Sox-mediated gene regulatory networks by conducting ATAC-sequencing in both wildtype and mutant flies.

This work will be combined with hybridization chain reaction (HCR) in situ amplification to examine the expression and localization of target genes. Equipped with this data I hope to examine how the interactions of Sox proteins with DNA and transcription factors directs gene expression and in the process, advance our understanding of transcriptional regulation and chromatin architecture at a genome wide scale.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011194/1 01/10/2015 30/09/2023
2273135 Studentship BB/M011194/1 01/10/2019 30/09/2023 Sabila Chilaeva