Computational Analysis of the 3D Genomic Architecture in Atlantic salmon
The advent of Chromosome Conformation Capture (3C) assays, particularly Hi-C, have revolutionized our understanding of three-dimensional (3D) genome organization. 3D genomic structures play crucial roles in gene regulation, cellular division, and embryonic development, and show evolutionary conserva...
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Norwegian University of Life Sciences
2024
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ftunivmob:oai:nmbu.brage.unit.no:11250/3148387 2024-09-15T17:55:58+00:00 Computational Analysis of the 3D Genomic Architecture in Atlantic salmon Furseth, Eline Simen Rød Sandve Torgeir Rhoden Hvidsten 2024 application/pdf https://hdl.handle.net/11250/3148387 eng eng Norwegian University of Life Sciences no.nmbu:wiseflow:7098065:59125654 https://hdl.handle.net/11250/3148387 Master thesis 2024 ftunivmob 2024-08-26T14:07:54Z The advent of Chromosome Conformation Capture (3C) assays, particularly Hi-C, have revolutionized our understanding of three-dimensional (3D) genome organization. 3D genomic structures play crucial roles in gene regulation, cellular division, and embryonic development, and show evolutionary conservation across species. Although the 3D genome has primarily been studied in humans and select model species of mammals, 3D organization can vary between species. Consequently, our understanding of 3D genome organization in other species remains limited. This thesis aims to perform the first general characterization of 3D chromatin structures in the non-model species Atlantic salmon (Salmo salar), focusing on compartments and topologically associating domains (TADs). Atlantic salmon has also undergone a relatively recent whole genome duplication (WGD). The sub aim is therefore to assess the impact of WGD on 3D genome organization and regulatory evolution. By combining Hi-C data with RNA-seq and ATAC-seq, we characterized the 3D genome landscape in Atlantic salmon liver, and the connection to gene regulation. Our analyses revealed similarities with established 3D structures and their gene regulatory roles, albeit with a notably lower presence of CTCF at TAD boundaries compared to many studies in mammals, challenging the causal link between TAD formation and CTCF proteins. Additionally, we established associations between compartmentalization and gene expression patterns in duplicated regions post-WGD, suggesting the involvement of 3D chromatin structures in the expression divergence of duplicated genes. While selection on transcript dosage merge as a possible driver for this, understanding selective pressures on genomic 3D organization remains an ongoing topic of investigation. Furthermore, our findings challenge the expected correlations between TAD metrics (gene content similarity and TAD strength) and gene expression levels in duplicated regions. In conclusion, this study advances our general understanding of 3D ... Master Thesis Atlantic salmon Salmo salar Open archive Norwegian University of Life Sciences: Brage NMBU |
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Open archive Norwegian University of Life Sciences: Brage NMBU |
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English |
description |
The advent of Chromosome Conformation Capture (3C) assays, particularly Hi-C, have revolutionized our understanding of three-dimensional (3D) genome organization. 3D genomic structures play crucial roles in gene regulation, cellular division, and embryonic development, and show evolutionary conservation across species. Although the 3D genome has primarily been studied in humans and select model species of mammals, 3D organization can vary between species. Consequently, our understanding of 3D genome organization in other species remains limited. This thesis aims to perform the first general characterization of 3D chromatin structures in the non-model species Atlantic salmon (Salmo salar), focusing on compartments and topologically associating domains (TADs). Atlantic salmon has also undergone a relatively recent whole genome duplication (WGD). The sub aim is therefore to assess the impact of WGD on 3D genome organization and regulatory evolution. By combining Hi-C data with RNA-seq and ATAC-seq, we characterized the 3D genome landscape in Atlantic salmon liver, and the connection to gene regulation. Our analyses revealed similarities with established 3D structures and their gene regulatory roles, albeit with a notably lower presence of CTCF at TAD boundaries compared to many studies in mammals, challenging the causal link between TAD formation and CTCF proteins. Additionally, we established associations between compartmentalization and gene expression patterns in duplicated regions post-WGD, suggesting the involvement of 3D chromatin structures in the expression divergence of duplicated genes. While selection on transcript dosage merge as a possible driver for this, understanding selective pressures on genomic 3D organization remains an ongoing topic of investigation. Furthermore, our findings challenge the expected correlations between TAD metrics (gene content similarity and TAD strength) and gene expression levels in duplicated regions. In conclusion, this study advances our general understanding of 3D ... |
author2 |
Simen Rød Sandve Torgeir Rhoden Hvidsten |
format |
Master Thesis |
author |
Furseth, Eline |
spellingShingle |
Furseth, Eline Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
author_facet |
Furseth, Eline |
author_sort |
Furseth, Eline |
title |
Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
title_short |
Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
title_full |
Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
title_fullStr |
Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
title_full_unstemmed |
Computational Analysis of the 3D Genomic Architecture in Atlantic salmon |
title_sort |
computational analysis of the 3d genomic architecture in atlantic salmon |
publisher |
Norwegian University of Life Sciences |
publishDate |
2024 |
url |
https://hdl.handle.net/11250/3148387 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
no.nmbu:wiseflow:7098065:59125654 https://hdl.handle.net/11250/3148387 |
_version_ |
1810432185439617024 |