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

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

PROVIDER: PRJNA686983 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13282025.fastq.gz	Fastqsanger.gz
	SRR13282026.fastq.gz	Fastqsanger.gz
	SRR13282027.fastq.gz	Fastqsanger.gz
	SRR13281128_1.fastq.gz	Fastqsanger.gz
	SRR13281128_2.fastq.gz	Fastqsanger.gz

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

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 | 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 [Hi-C]

2021-04-26 | GSE163625 | 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 [Hi-C]

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

| PRJNA686959 | 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 [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.

| S-EPMC8172041 | biostudies-literature

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

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism

Project description:This data is from BS3 crosslinked condensin tetramer How protein complexes of the SMC family fold DNA into the large loops that are fundamental for the 3D organization of genomes is a central unresolved question of chromosome biology. We used electron cryomicroscopy to investigate the reaction cycle of the SMC complex condensin, which is a key determinant of chromosome morphology and behavior during mitosis. Our structures of the Saccharomyces cerevisiae condensin holo complex at different functional stages suggest that ATP binding induces the transition from a folded-rod SMC conformation into an open architecture and triggers the exchange of the two HEAT-repeat subunits at the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA binding sites in the catalytic core that form the basis of the DNA translocation and loop-extrusion activities of condensin.

2020-07-28 | PXD019275 | Pride

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