An exploration of non-coding sequence variation across human erythroid differentiation
<p>The ability to precisely regulate genes has been pivotal in the evolution of complex life and humanity. A cell’s ability to dynamically control the 3D structure of the genome to physically bring together regulatory elements allows for the precise spatiotemporal expression of genes. Variatio...
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| Format: | Thesis |
| Language: | English |
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2024
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| _version_ | 1811139899638677504 |
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| author | Gosden, ME |
| author2 | Hughes, J |
| author_facet | Hughes, J Gosden, ME |
| author_sort | Gosden, ME |
| collection | OXFORD |
| description | <p>The ability to precisely regulate genes has been pivotal in the evolution of complex life and humanity. A cell’s ability to dynamically control the 3D structure of the genome to physically bring together regulatory elements allows for the precise spatiotemporal expression of genes. Variation within the human genome is widespread and well documented, and accounts for the vast differences in phenotypes seen within a population. However, this variation can also lead to disease as the disruption of coding regions or a regulatory network can alter protein levels beyond a tolerable range leading to detrimental downstream effects. </p>
<p>In this thesis I have explored the genome wide variation present in a local population of 50 individuals by using a well-established erythroid differentiation system. By assessing open chromatin data and histone modifications, regions that are active in some individuals but not others have been found and defined. Many of these differential regions can be defined as a ‘loss of function’ variant, whereby a previously identified active region is shown to have its activity reduced. Additionally, with the use of allelic skew methods and haplotype analysis, we also demonstrate examples of the more elusive ‘gain of function’ variant, whereby a new element unique to a single haplotype is created.</p>
<p>To fully decipher the effects imparted by these variants, chromatin interaction data can be generated to uncover the regulatory networks of a specific cell type and stage. I have used MCC to generate high resolution interaction profiles that can unambiguously link regulatory elements whilst simultaneously generating transcription factor binding footprints. Moreover, technical advances of this assay have allowed the generation of allele specific interaction profiles from heterozygous variants, which has enabled the deciphering of variants and GWAS SNP mechanisms. </p>
<p>Due to the nature of cell differentiation, the precise genome regulation at each cell stage affects subsequent downstream cell stages. It is therefore important to consider the effects of these variants throughout a cell’s lineage, as early disruption to processes in differentiation can impact terminally differentiated cells. By using the scMultiome system, I have been able to assess the changing genomic landscape across erythropoiesis to uncover variants that affect gene regulation early in differentiation. From these data it is clear that there is high enrichment for variant effects across all stages of erythropoiesis, but particularly at the later stages. </p> |
| first_indexed | 2024-09-25T04:13:25Z |
| format | Thesis |
| id | oxford-uuid:239f02fc-1be6-4d02-9b5f-67845b30e615 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:13:25Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | oxford-uuid:239f02fc-1be6-4d02-9b5f-67845b30e6152024-07-10T11:02:18ZAn exploration of non-coding sequence variation across human erythroid differentiationThesishttp://purl.org/coar/resource_type/c_db06uuid:239f02fc-1be6-4d02-9b5f-67845b30e615Functional genomicsEnglishHyrax Deposit2024Gosden, MEHughes, JDavies, J<p>The ability to precisely regulate genes has been pivotal in the evolution of complex life and humanity. A cell’s ability to dynamically control the 3D structure of the genome to physically bring together regulatory elements allows for the precise spatiotemporal expression of genes. Variation within the human genome is widespread and well documented, and accounts for the vast differences in phenotypes seen within a population. However, this variation can also lead to disease as the disruption of coding regions or a regulatory network can alter protein levels beyond a tolerable range leading to detrimental downstream effects. </p> <p>In this thesis I have explored the genome wide variation present in a local population of 50 individuals by using a well-established erythroid differentiation system. By assessing open chromatin data and histone modifications, regions that are active in some individuals but not others have been found and defined. Many of these differential regions can be defined as a ‘loss of function’ variant, whereby a previously identified active region is shown to have its activity reduced. Additionally, with the use of allelic skew methods and haplotype analysis, we also demonstrate examples of the more elusive ‘gain of function’ variant, whereby a new element unique to a single haplotype is created.</p> <p>To fully decipher the effects imparted by these variants, chromatin interaction data can be generated to uncover the regulatory networks of a specific cell type and stage. I have used MCC to generate high resolution interaction profiles that can unambiguously link regulatory elements whilst simultaneously generating transcription factor binding footprints. Moreover, technical advances of this assay have allowed the generation of allele specific interaction profiles from heterozygous variants, which has enabled the deciphering of variants and GWAS SNP mechanisms. </p> <p>Due to the nature of cell differentiation, the precise genome regulation at each cell stage affects subsequent downstream cell stages. It is therefore important to consider the effects of these variants throughout a cell’s lineage, as early disruption to processes in differentiation can impact terminally differentiated cells. By using the scMultiome system, I have been able to assess the changing genomic landscape across erythropoiesis to uncover variants that affect gene regulation early in differentiation. From these data it is clear that there is high enrichment for variant effects across all stages of erythropoiesis, but particularly at the later stages. </p> |
| spellingShingle | Functional genomics Gosden, ME An exploration of non-coding sequence variation across human erythroid differentiation |
| title | An exploration of non-coding sequence variation across human erythroid differentiation |
| title_full | An exploration of non-coding sequence variation across human erythroid differentiation |
| title_fullStr | An exploration of non-coding sequence variation across human erythroid differentiation |
| title_full_unstemmed | An exploration of non-coding sequence variation across human erythroid differentiation |
| title_short | An exploration of non-coding sequence variation across human erythroid differentiation |
| title_sort | exploration of non coding sequence variation across human erythroid differentiation |
| topic | Functional genomics |
| work_keys_str_mv | AT gosdenme anexplorationofnoncodingsequencevariationacrosshumanerythroiddifferentiation AT gosdenme explorationofnoncodingsequencevariationacrosshumanerythroiddifferentiation |