About the Project
Due to mutations in enhancers and promoters, leads to multifactorial and congenital disorders. Due to the lack of understanding of the underlying transcriptional codes and their roles in developmental gene regulation, however, we still are unable to predict the developmental consequences of changes in transcriptional regulatory elements at various stages of development, from the onset of transcription to completion of morphogenesis. The primary aim of this studentship is to understand the fundamental roles of different classes of cis-regulatory elements in vertebrate development and the mechanisms by which they respond to developmental cues under different modes of regulation. By measuring promoter and enhancer activity dynamics at key developmental transitions in early embryo this project will aim to understand how dynamic transcription regulation of individual genes and whole functional classes of genes in single cells contribute to morphogenesis of a complex organism. This project will build on our previous work which combined computational genome-wide analysis with the recording of transcriptional initiation events at nascent transcripts2, 3 and extend that to high-resolution in vivo imaging of transcription and genome editing at key individual genes loci under different modes of gene regulation in an early model vertebrate embryo (zebrafish). We shall ask the question: what is the transcription initiation dynamics at the level of a single gene in a single cell in the developing organism? We shall exploit the transparency of zebrafish embryos and utilize a novel 4D visualization technology we recently developed (BioRxiv http://doi.org/cr3h) to detect transcription initiation on individual genes belonging to different functional classes in individual cells of the embryo during key developmental transitions. One of the models applied in the programme will be zebrafish larval brain in which we shall visualise both the global transcriptional activity of neurons during stimulus mediated neural activity in vivo and in situ and that of individual selected genes. We shall monitor individual genes by using antisense oligomeric probes and various aptamers5 which we will generate in collaboration with School of Chemistry (Fossey). We shall integrate computational genomic high resolution data (e.g. CAGE- sequencing) with single-cell based transcription data visualized in vivo to achieve new models of transcription regulation during morphogenesis.
Skills training will include: 4D Imaging with light sheet microscopy and image analysis of large scale (hundreds of gigabytes) light sheet image data (Mueller), CrispR/Ca9 targeting to generate lesions in genomes (Mueller), Synthetic chemistry of Morpholino oligonucleotides and aptamers (Fossey), Image processing and large data analysis (Mueller). The student will train in tools of developmental transcription regulation, in vivo imaging and various aspects of molecular biology, thus offering the candidate a highly desirable set of skills attractive to prospective academic and non-academic employers.
References
Wragg, J. & Müller, F. Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos. Adv Genet 95, 161-194 (2016).
2. Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., et al.,… O., Ferg, M., Strähle, U., Carninci, P., Müller F.* Lenhard B. (2014) Two independent transcription initiation codes overlap on vertebrate core promoters. Nature, 507(7492):381-5, *co-corresponding author.
3. Nepal, C. et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res 23, 1938-1950 (2013).
4. Hadzhiev, Y., Qureshi, H., Wheatley, L., Cooper, L., et al.,… Sik, A., Hutvagner, G., Tora, L., Gambus, A., Fossey, JS., and Müller F. (2018 ) A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation bioRxiv 366468.
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