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Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

ABSTRACT: Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

PROVIDER: PRJNA704985 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13786472_1.fastq.gz	Fastqsanger.gz
	SRR13786472_2.fastq.gz	Fastqsanger.gz
	SRR13786473_1.fastq.gz	Fastqsanger.gz
	SRR13786473_2.fastq.gz	Fastqsanger.gz
	SRR13786474_1.fastq.gz	Fastqsanger.gz

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Comparative 3D Genome Architecture in Vertebrates

Project description:Comparative 3D Genome Architecture in Vertebrates

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Comparative 3D Genome Architecture in Vertebrates (Hi-C)

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Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Project description:Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

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Comparative 3D Genome Architecture in Vertebrates (Hi-C)

2022-04-12 | GSE167579 | GEO

Comparative 3D genome architecture in vertebrates.

Project description:BackgroundThe three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species.ResultsThis analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture.ConclusionsOur analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

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Comparative 3D Genome Architecture in Vertebrates

Project description:This SuperSeries is composed of the SubSeries listed below.

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Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States.

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