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Characterisation of cis-regulatory modules controlling gene expression within sox17+ lineages during zebrafish embryonic development
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Elsayed, Randa (2021) Characterisation of cis-regulatory modules controlling gene expression within sox17+ lineages during zebrafish embryonic development. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b3853412~S15
Abstract
Precise spatial and temporal regulation of gene expression is critical for embryonic development. This is achieved in part via transcription factor binding to cis-regulatory modules (CRMs). However, in contrast to other germ layers, the gene regulatory network involved in endoderm formation is relatively understudied in vertebrates. In this study we use genomic approaches to study the chromatin landscape that governs endoderm specification and early endoderm organ formation in zebrafish embryos. Since the endoderm is a minor cell population, we employed two distinct methods to find to endoderm-specific CRMs: 1) to capture CRMs that regulate early endoderm-specific genes during early specification, we performed overexpression of the master regulator of endoderm formation, sox32, 2) to capture CRMs that function during early organogenesis, we have generated a three-colour transgenic line to specifically FACS isolate endoderm cells and study endoderm-specific CRMs at 28 hours post-fertilisation. Our results show that sox32 overexpression not only induces ectopic endoderm formation but also ectopic formation of progenitors of the zebrafish left/right organiser known as dorsal forerunner cells (DFCs), a phenomenon not previously discussed in literature. We also identified 16, 000 regions that exhibit enhanced accessibility by ATAC seq in embryos injected with sox32 mRNA compared to control and that a large number of these regions harboured motifs of transcription factors that play important roles during endoderm specification. Our findings also suggest that sorted GFP+ cells from the triple transgenic line comprise both endoderm and transdifferentiated Kupffer’s vesicle cells, which are implicated in left/right asymmetry in zebrafish. We also show by ATAC-seq analysis that a large number of accessible regions are likely shared by GFP+ cells and cells that are devoid of fluorescence. Finally, we show that changes in the chromatin landscape correlate with changes in gene expression at both stages of endoderm development through comparison of data from ATAC-seq and RNA-seq, but also that the chromatin landscape changes between endoderm specification and early organogenesis. Our results provide inside into how the chromatin landscape changes in the endoderm during development and also reveals a number of potentially important CRMs that may help shed light into how endoderm is formed during embryogenesis.
| Item Type: | Thesis (PhD) | ||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QL Zoology |
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| Library of Congress Subject Headings (LCSH): | Gene expression, Germinal layers, Chromatin, Zebra danio -- Embryos | ||||
| Official Date: | 31 May 2021 | ||||
| Dates: |
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| Institution: | University of Warwick | ||||
| Theses Department: | Warwick Medical School | ||||
| Thesis Type: | PhD | ||||
| Publication Status: | Unpublished | ||||
| Copyright Holders: | Nelson, Andrew (Lecturer in life sciences) ; Ott, Sascha | ||||
| Format of File: | |||||
| Extent: | xvii, 358 leaves : illustrations (chiefly colour) | ||||
| Language: | eng |
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