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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE163641 | GEO | 2021/04/26

REPOSITORIES: GEO

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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 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.

| S-EPMC8172041 | biostudies-literature

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 [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 [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: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 [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

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization.

Project description:Interaction domains in Drosophila chromosomes form by segregation of active and inactive chromatin in the absence of CTCF loops, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here, we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, causes increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.

| S-EPMC6424357 | biostudies-literature

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