Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chip-chip of condensin subunits Brn1 and Smc4 and Scc2/4 and cohesin and Tfc3 (TFIIIC) on budding yeast chromosomes

ABSTRACT: Eukaryotic chromosomes reach their stable rod-shaped appearance in mitosis in a reaction dependent on the evolutionarily conserved condensin complex. Little is known about how and where condensin associates with chromosomes. Here, we analyse condensin binding to budding yeast chromosomes using high resolution oligonucleotide tiling arrays. Condensin binding sites coincide with those of the loading factor Scc2/4 of the related cohesin complex. The sites map to tRNA genes, ribosomal protein genes, and other places characterised by the RNA polymerase III transcription factor TFIIIC. An ectopic B-Box element, recognised by TFIIIC, constitutes a minimal condensin binding site, and TFIIIC and the Scc2/4 complex promote productive condensin association with chromosomes. A similar pattern of condensin binding is conserved along fission yeast chromosomes. This reveals that TFIIIC binding sites, including tRNA genes, constitute a hitherto unknown chromosomal feature with important implications for chromosome architecture during both interphase and mitosis. Keywords: Chip-chip, cell type comparison

ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae

PROVIDER: GSE12149 | GEO | 2008/07/21

SECONDARY ACCESSION(S): PRJNA113761

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide analysis of condensin binding sites in vertebrate genome

Project description:The condensin complex is well known to be essential for correct packaging and segregation of chromosomes during mitosis and meiosis in all eukaryotes. To date, the genome wide location and the nature of condensin binding sites has remained elusive in vertebrate systems. A detailed knowledge of condensin binding sites is essential to understand the as-yet enigmatic function of this complex and to define its greater role in chromosome architecture. To address this, we have used next generation sequencing to map condensin I in chicken DT40 cells. Unexpectedly, we found condensin I binds predominately to promoter sequences in mitotic cells. We also found a striking enrichment at both centromeres and telomeres, highlighting the importance of the complex in chromosome segregation. Taken together, the results show condensin I is largely absent from heterochromatic regions. These results reveal for the first time the condensin I binding sites in the vertebrate genome, and demonstrate the importance of the complex in genome segregation and suggest a novel function in gene regulation. Condensin associated DNA from chicken DT40 cells were affinity purified using streptavidin and deep sequenced by Illumina Hiseq2000

2013-10-03 | E-GEOD-45552 | biostudies-arrayexpress

Genome-wide analysis of condensin binding sites in vertebrate genome

2013-10-03 | GSE45552 | GEO

Molecular basis for condensin enrichment at pericentromeres [Brn1 ChIP-seq Lrs4-Ycg1]

Project description:Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the oriented attachment of kinetochores to microtubules at mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direct interaction between its Ycg1 subunit and the pericentromeric adaptor protein, shugoshin (Sgo1). We identify a Short Linear Motif (SLiM), termed CR1, within the C-terminal region of Sgo1 which inserts into a conserved pocket on Ycg1. Disruption of this interface abolishes the Sgo1-condensin interaction, prevents condensin recruitment to pericentromeres and results in defective sister kinetochore biorientation in mitosis. Similar motifs to CR1 are found in known and potential condensin binding partners and the Ycg1 binding pocket is broadly conserved, including in mammalian CAP-G proteins. Overall, we uncover the molecular mechanism that targets condensin to define a specialized chromosomal domain.

2025-02-12 | GSE284788 | GEO

Molecular basis for condensin enrichment at pericentromeres [Brn1 ChIP-seq Lrs4-Ycg1 2]

2025-02-12 | GSE284791 | GEO

Genome-wide binding of condensin II and TFIIIC upon respective knockdown of a TFIIIC and condensin II subunit

Project description:Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. However, little is known about the role of condensin complexes in interphase. Condensins exists in two complexes, condensins I and II, in higher eukayotic cells. During interphase, condensin II is predominantly localized in the nucleus throughout the cell cycle, whereas condensin I is localized at the cytoplasm in interphase. The distinct localization patterns suggest that condensin II, but not condensin I, may contribute to genome organization in interphase. Our results suggest that condensin II is associated with TFIIIC complex in vivo. The aim of these experiments is to unravel the dependency of each other on binding to chromatin.

2017-06-01 | GSE80034 | GEO

Ortholog replacement reveals stable TFIIIC complexes are required for proper mitotic chromosome segregation

Project description:Transcription factors are speculated to play crucial roles in adaptive evolution. Here we investigated how essential transcription factors (eTFs) change using ortholog replacement assays. Several orthologous eTFs from other yeast species could not fully complement the mutants in Saccharomyces cerevisiae, suggesting that these eTFs have changed their functions or interactions to become incompatible. We further characterized TFIIIC, a protein complex assisting RNA polymerase III transcription, that exhibits complete or partial incompatibility in several subunits. In the orthologous Tfc7-replacement line, the binding of TFIIIC to tRNA genes is reduced, but the abundance of tRNAs is not severely affected. However, Tfc7-replacement cells often mis-segregate chromosomes during mitosis and their fitness is further reduced in the spindle checkpoint mutant. Chromatin immunoprecipitation experiments showed that unstable TFIIIC binding results in defective cohesion loading, leading to chromosome mis-segregation. Swapping the highly divergent C-terminal domain of Tfc7 orthologs rescues its interaction with Tfc1 and cell fitness, suggesting that incompatibility is caused by altered interactions between complex subunits. Our results reveal separatable essential functions of a well-studied protein complex.

2025-01-17 | GSE287186 | GEO

TBP ChIP-chip on Jurkat cells

Project description:During mitosis, TATA-binding protein(TBP), which remains bound to DNA during mitosis, recruits PP2A and also interacts with a subunit of the condensin complex to allow efficient dephosphorylation and inactivation of condensin near these promoters to inhibit their compaction. These result suggest that TBP function is not only important for expression of genes transcribed bDuring mitosis, TATA-binding protein(TBP), which remains bound to DNA during mitosis, recruits PP2A and also interacts with a subunit of the condensin complex to allow efficient dephosphorylation and inactivation of condensin near these promoters to inhibit their compaction. These result suggest that TBP function is not only important for expression of genes transcribed by all three RNA polymerase during interphase, but also for transmitting the memory of gene activity through mitosis to daughter cellsy all three RNA polymerase during interphase, but also for transmitting the memory of gene activity through mitosis to daughter cells We use ChIP-chip approach to identify TBP-bindind sites in mitotic Jurkat cells at genome-wide level. Input DNA fragments and DNA fragments immunoprecipitated by TBP antibodies by ChIP assay on mitotic Jurkat cells were used to probe the Affymetrix Genechip human tiling 2.0c to identift TBP-binding sites in mitotic Jurkat cells. Input and ChIP sample were replicated three times as following: Input rep1, TBP ChIP1, Input rep2, TBP ChIP2, Input rep3, TBP ChIP3.

2010-04-03 | E-GEOD-12256 | biostudies-arrayexpress

Genome-wide binding of condensin II and TFIIIC in human HEK293 cells

2018-09-05 | GSE119418 | GEO

Chip-chip of condensin subunits Brn1 and Smc4 and Scc2/4 and cohesin and Tfc3 (TFIIIC) on budding yeast chromosomes

Project description:Chip-chip of condensin subunits Brn1 and Smc4 and Scc2/4 and cohesin and Tfc3 (TFIIIC) on budding yeast chromosomes

| PRJNA113761 | ENA

Scc2 Is a Potent Activator of Cohesin's ATPase that Promotes Loading by Binding Scc1 without Pds5

Project description:In addition to sharing with condensin an ability to organize DNA into chromatids, cohesin regulates enhancer-promoter interactions and confers sister chromatid cohesion. Association with chromosomes is regulated by hook-shaped HEAT repeat proteins that Associate With its Kleisin (Scc1) subunit (HAWKs), namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently displaces Pds5 during loading. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin’s ATPase activity, loading, and translocation while Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin’s initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2’s association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states, one with Pds5 bound to Scc1 that is not able to hydrolyse ATP efficiently but is capable of release from chromosomes and another in which Scc2, transiently replacing Pds5, stimulates the ATP hydrolysis necessary for loading and translocation away from loading sites.

2018-07-17 | GSE106182 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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