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An exploration of the mouse epigenome at metaphase and interphase during embryonic differentiation

Bowker, Richard Michael (2015)
Ph.D. thesis, University of Birmingham.

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Histone modifications form an important part of the epigenetic landscape that controls many aspects of cellular function, including regulation of gene expression and cell differentiation. The persistence and inheritance of many of these modifications through the cell cycle and differentiation are still unknown. Here, I show global epigenetic karyotypes of metaphase chromosomes labelled to highlight specific marks. Metaphase is transcriptionally inactive and so epigenetic marks here are not simply reflective of gene transcription. I found that histone marks such as H3K27me3 are inherited through differentiation, whereas others such as H4K20me3 have re-organised distributions. FISH analysis allowed the alignment of genetic features with H3K4me3 and H3K27me3 distributions, showing that these marks are correlated with increased gene density, revealing a deeply intertwined distribution in ES cells, indicating bivalency.

Focusing on the Hoxa cluster using N-ChIP in ES cells allowed the analysis of histone modification prevalence at the single gene level in ES cells. Most histone modifications remain stable between G1/S phase and G2/M phase, although H3K9ac decreases in ES cells at G2/M. Results for bivalent modifications show permissive chromatin environments denoted by high H3K4me3 and low H3K27me3 methylation at gene promoters that are expressed soon after the onset of differentiation, denoting a predictive chromatin signature. This signature was altered after five days of differentiation, where H3K4me3 increases and H3K27me3 decreases at most Hoxa promoters, concomitant with the rise in expression of some Hoxa genes, displaying the dynamic properties necessary to represent a mechanism for control of transcription during differentiation.

Type of Work:Ph.D. thesis.
Supervisor(s):O'Neill, Laura
School/Faculty:Colleges (2008 onwards) > College of Medical & Dental Sciences
Department:School of Immunity and Infection
Subjects:QH426 Genetics
QR Microbiology
Institution:University of Birmingham
ID Code:6073
This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder.
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