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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Structural evidence for Scc4-dependent localization of cohesin loading

ABSTRACT: Purpose: The Goal of this study is to look at 1) Differences in genome wide localization of Scc2 between wild type and scc4-m35 cells in S-phase 2) Differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: 1) Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains. 2) Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: 1) This experiment did not yield meaningful data. 2) All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms 1) ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant (samples VM1-VM4). 2) ChIP-seq for Scc1-6HA in metaphase-arrested cells in Wild type and in scc4-m35 mutant (samples VM5-VM10) Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis https://github.com/AlastairKerr/Hinshaw2015

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Alastair Kerr

PROVIDER: E-GEOD-68573 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Structural evidence for Scc4-dependent localization of cohesin loading

Project description:Purpose: The goal of this study is to look at differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms

2015-06-05 | GSE68573 | GEO

localization of Scc2 between wild type and scc4-m35 cells in S-phase

Project description:Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains. ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis

2016-07-21 | E-GEOD-70316 | biostudies-arrayexpress

localization of Scc2 between wild type and scc4-m35 cells in S-phase

2016-07-21 | GSE70316 | GEO

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

Calibrated Scc1 ChIP-seq for wild type and rad61Δ strains arrested in metaphase with and without tension

Project description:Calibrated Scc1 ChIP-seq for wild type and rad61Δ strains arrested in metaphase with and without tension

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Calibrated Scc1 ChIP-seq for wild type and chl4Δ strains arrested in metaphase with and without tension

Project description:Calibrated Scc1 ChIP-seq for wild type and chl4Δ strains arrested in metaphase with and without tension

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The Scc2NIPBL/Scc4MAU2 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions [ChIP-seq]

Project description:The Scc2/Scc4 complex binds to broad nucleosome-free regions in the promoters of highly expressed genes. The cohesin loader is recruited to these sites by the RSC chromatin remodeling complex ChIp- Sequencing analysis of the distribution of Scc2 and Scc4 on budding yeast chromosomes.An input sample was analysed as a control.

2014-08-01 | E-GEOD-56993 | biostudies-arrayexpress

Structure of the Cohesin Loader Scc2-Scc4 and its Binding to a Folded Cohesin

Project description:The functions of cohesin are central to genome integrity, chromosome organization, and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex, however, little is known about how it stimulates the cohesin loading activity. Here we determine the large “hook” structure of Scc2 responsible for catalyzing cohesin loading. We identify key Scc2 surfaces that are crucial for DNA binding and for cohesin loading in vivo. Using previously determined structures and modeling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, our crosslinking and electron microscopy analyses reveal that Scc2-Scc4 utilizes its modular structure to make multiple contacts with a folded cohesin at an interface created by the cohesin head-hinge interaction.

2017-01-11 | PXD004692 | Pride

Genome-wide binding of the cohesin protector Sgo1 in the presence and absence of the meiosis I-specific Spo13 protein

Project description:ChIP-seq profile of Sgo1 binding sites arrested in metaphase I by deletion of the APC/C activator CDC20. The aim of this experiment is to identify whether Sgo1 binding differs in wild type cells and cells deficient of the meiosis I-specific protein Spo13, which is required for retention of pericentromeric cohesin after metaphase I.

2019-04-25 | GSE112167 | GEO

Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break [ChIP-seq]

Project description:Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2, but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding. We investigated Scc1 FLAG tagged binding in WT ans Scc2-4 mutant in absence and presence of a single DNA DSB on Chr. VI

2014-10-21 | E-GEOD-62493 | biostudies-arrayexpress

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