Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [RNA-seq]

ABSTRACT: Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. Here we used an X chromosome specific condensin that represses transcription for dosage compensation in C.elegans, to determine how DNA topology affects SMC translocation in vivo. We applied auxin-inducible degradation of topoisomerases I and II to determine their effect on condensin DC binding and function. We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC spreading over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within gene bodies, specially of highly expressed and long genes. Both TOP-1 and TOP-2 depletion resulted in X chromosome upregulation indicating that condensin DC translocation at both scales is required for its function in transcriptional repression. Together our work reveals distinct DNA topological requirements for two modes of condensin DC association with chromatin: long-range linear translocation that requires decatenation and unknotting of DNA and short-range binding to genes that requires resolution of transcription-induced supercoiling.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE188850 | GEO | 2021/11/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [ChIP-Seq II]

Project description:Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. Here we used an X chromosome specific condensin that represses transcription for dosage compensation in C.elegans, to determine how DNA topology affects SMC translocation in vivo. We applied auxin-inducible degradation of topoisomerases I and II to determine their effect on condensin DC binding and function. We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC spreading over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within gene bodies, specially of highly expressed and long genes. Both TOP-1 and TOP-2 depletion resulted in X chromosome upregulation indicating that condensin DC translocation at both scales is required for its function in transcriptional repression. Together our work reveals distinct DNA topological requirements for two modes of condensin DC association with chromatin: long-range linear translocation that requires decatenation and unknotting of DNA and short-range binding to genes that requires resolution of transcription-induced supercoiling.

2022-05-23 | GSE203534 | GEO

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [Hi-C]

2022-05-23 | GSE203533 | GEO

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [RNA-Seq II]

2022-05-23 | GSE203532 | GEO

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [ChIP-seq]

2021-11-14 | GSE188612 | GEO

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [HiC]

2021-11-16 | GSE188849 | 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

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

Project description:This data is from sulfo-SDA crosslinked condensin pentamer. Two datsets, one without atp aand one with ATP. 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 | PXD019274 | Pride

Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage

Project description:Background: Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood. Results: Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2 arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite its low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response. Conclusions: In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.

2020-09-14 | GSE143338 | GEO

Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans

Project description:Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans

| PRJNA780508 | ENA

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

Project description:Structural maintenance of chromosomes (SMC) complexes play critical roles in chromosome dynamics in virtually all organisms but how they function remains poorly understood. In Bacillus subtilis, SMC condensin complexes are topologically loaded at centromeric sites adjacent to the replication origin. Here we provide evidence that these ring-shaped assemblies tether the left and right chromosome arms together while traveling from the origin to the terminus (>2 Mb) at rates >50kb/min. Condensin movement scales linearly with time arguing for an active transport mechanism. These data support a model in which SMC complexes function by processively enlarging DNA loops. Loop formation followed by processive enlargement provides a mechanism for how condensin complexes compact and resolve sister chromatids in mitosis and how cohesin generates topologically associating domains (TADs) during interphase.

2017-02-03 | GSE85612 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data