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3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]

ABSTRACT: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]

PROVIDER: PRJNA686959 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13281128_1.fastq.gz	Fastqsanger.gz
	SRR13281128_2.fastq.gz	Fastqsanger.gz
	SRR13281129_1.fastq.gz	Fastqsanger.gz
	SRR13281129_2.fastq.gz	Fastqsanger.gz
	SRR13281130_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [Hi-C]

Project description:We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

2021-04-26 | GSE163625 | GEO

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]

2021-04-26 | GSE163626 | GEO

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [RNA-Seq]

2021-04-26 | GSE163640 | GEO

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Project description:We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

2021-04-23 | GSE169088 | GEO

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Project description:3D genomics across the tree of life reveals condensin II as a determinant of architecture type

| PRJNA686983 | ENA

3D genomics across the tree of life reveals condensin II as a determinant of architecture type.

| S-EPMC8172041 | biostudies-literature

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [RNA-Seq]

Project description:3D genomics across the tree of life reveals condensin II as a determinant of architecture type [RNA-Seq]

| PRJNA686986 | ENA

3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]

Project description:3D genomics across the tree of life reveals condensin II as a determinant of architecture type [DamID-seq]

| PRJNA686962 | ENA

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

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

2021-04-26 | GSE163641 | GEO

The length and strength of compartmental interactions are modulated by condensin II activity [Hi-C]

Project description:Condensin II plays a crucial role in shaping chromosome structure throughout the cell cycle, but its specific functions during interphase have remained unclear. In this study, we utilized Oligopaints and Hi-C techniques to investigate how changes in condensin II levels affect chromosome organization across various length scales. Our findings reveal that condensin II has a significant impact on long-range interactions within chromosomes, which are essential for the organization of intrachromosomal compartments. Importantly, these effects occur independently of the chromatin state. Furthermore, overexpression of condensin II during interphase leads to the formation of "peri-centric super stripes" observed through Hi-C analysis, indicating a disruption of the boundary between heterochromatin and euchromatin on Drosophila chromosomes. Collectively, our results challenge the existing belief that compartments form without the involvement of a loop extruder and suggest that condensin II activity is a prerequisite for driving proximity between distal compartmental domains within chromosomes.

2023-09-03 | GSE242222 | GEO

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