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Genowide-wide analysis of scc2-4 binding.

ABSTRACT: The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients. One hypothesis is that, reduced binding of Scc2 causes gene misregulation. To further explore this idea ChIP-seq was performed using an scc2-4 mutant. We observed from the analysis, we observe reduce binding of Scc2 to Pol II transcribed genes (snoRNAs, ribosomal protein genes) and pol II transcribed genes (tRNAs). Studies are currently underway to examine the biological implications of this observation. Examining genome-wide binding of scc2-4 mutant

ORGANISM(S): Saccharomyces cerevisiae BY4741

SUBMITTER: Musinu Zakari

PROVIDER: E-GEOD-55357 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The cohesin loader Scc2 regulates key regulatory genes critical for development

Project description:The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients.This has led to the hypothesis that developmental disorders in CdLS patients are a result of dysregulated gene expression. To examine the transcriptional program of Scc2 mutants called scc2-4, RNA sequencing was performed. Analysis of gene expression program shows upregulation of genes involved in ribosome biogenesis and downregulation of genes needed for oxidative phosphorylation. Studies are currently underway to investigate how scc2-4 mutation causes gene misregulation. The answer(s) could provide insight into the molecular etiology of CdLS. Examining gene expression in 3 biological replicates of scc2-4 relative to wt by Ilumina sequencing

2015-06-16 | E-GEOD-55316 | biostudies-arrayexpress

The cohesin loader Scc2 regulates key regulatory genes critical for development

2015-06-16 | GSE55316 | GEO

Genowide-wide analysis of scc2-4 binding.

Project description:The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients. One hypothesis is that, reduced binding of Scc2 causes gene misregulation. To further explore this idea ChIP-seq was performed using an scc2-4 mutant. We observed from the analysis, we observe reduce binding of Scc2 to Pol II transcribed genes (snoRNAs, ribosomal protein genes) and pol II transcribed genes (tRNAs). Studies are currently underway to examine the biological implications of this observation.

2015-06-16 | GSE55357 | GEO

Releasing activity disengages cohesinâs Smc3/Scc1 interface in a process blocked by acetylation

Project description:Sister chromatid cohesion conferred by entrapment of sister DNAs within a tripartite ring formed between cohesinâs Scc1, Smc1, and Smc3 subunits is generated during S and eventually destroyed at anaphase through cleavage of Scc1 by separase. Throughout the cell cycle, cohesinâs association with chromosomes is controlled by opposing activities: loading by the Scc2/4 complex and release by a separase independent releasing activity. Co-entrapment of sister DNAs during replication is accompanied by acetylation of Smc3 by Eco1, which blocks releasing activity and ensures that sisters remain stably connected. Because fusion of Smc3 to Scc1 prevents release and bypasses the requirement for Eco1, we suggested that release is mediated by disengagement of the Smc3/Scc1 interface. We now show that all mutations capable of bypassing Eco1, be they in cohesinâs Smc1, Smc3, Scc1,Wapl, Pds5, or Scc3 subunits, greatly reduce dissociation of N-terminal cleavage fragments of Scc1 (NScc1) from Smc3. We show that this process involves interaction between Smc ATPase heads and is inhibited by Smc3 acetylation Effect of mutations QQ and EQ in Smc3 on cohesin loading onto chromosomes

2016-02-18 | E-GEOD-76890 | biostudies-arrayexpress

Disruption of Nipbl/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome

Project description:Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, Nipbl/Scc2 were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanism driving the CdLS phenotypes are not understood. Apart from its canonical role in sister chromatid cohesion, cohesin has also been involved in the regulation of the spatial organization of the genome. Here, we investigated the transcriptome of CdLS-derived primary fibroblasts (gene expression microarray data included in the manuscript as an excel file) and observed the downregulation of genes involved in development and system skeletal organization providing a link to the developmental alterations and limb abnormalities characteristics of the CdLS patients. Genome-wide distribution studies demonstrated a global reduction of Nipbl at the Nipbl-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at Nipbl-occupied sites at CpG islands probably due to reduced cohesin translocation along chromosomes and fewer cohesin peaks colocalize with CTCF.

2021-05-27 | GSE145966 | GEO

Cohesin releases DNA through asymmetric ATPase-driven ring opening

Project description:Cohesin stably holds together the sister chromatids from S phase until mitosis. To do so, cohesin must be protected against its cellular antagonist Wapl. Eco1 acetylates cohesinâs Smc3 subunit, which locks together the sister DNAs. We used yeast genetics to dissect how Wapl drives cohesin from chromatin and identified mutants of cohesin that are impaired in ATPase activity but remarkably confer robust cohesion that bypasses the need for the cohesin protectors Eco1 in yeast and Sororin in human cells. We uncover an unexpected functional asymmetry within the heart of cohesinâs highly conserved ABC-like ATPase machinery and show that an activity associated with one of cohesinâs two ATPase sites drives DNA release from cohesin rings. This key mechanism is conserved from yeast to humans. We propose that Eco1 locks cohesin rings around the sister chromatids by counteracting an asymmetric cohesin-associated ATPase activity. Effect of mutations in Smc1 and Smc3 on cohesin loading onto chromosomes

2016-02-18 | E-GEOD-76891 | biostudies-arrayexpress

RNA Seq analysis of SCC2 mutations R787G and G1242V at 9 hours following SCC2 depletion in Saccharomyces cerevisiae

Project description:The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 function as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate localization of the Scc2-Scc4 cohesin loader. Here we identify a broad range of Scc2- chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in recruitment of the cohesin loader. We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and decreased binding of Scc2 at RNA Pol II transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in direct recruitment of Scc2 to RNA pol II transcribed genes. We identified two mutations in the evolutionarily conserved HEAT domain of SCC2 that result in significantly reduced growth, scc2R787G and scc2G1242V. This experiment uses RNA-Seq analysis to study the effect of these mutations on gene expression.

2022-05-25 | GSE201192 | GEO

RNA Seq analysis of SCC2 mutations R787G and G1242V at 3 hours following SCC2 depletion in Saccharomyces cerevisiae

2022-05-25 | GSE201191 | GEO

ChIP Seq Analysis of SCC2 in the Presence or Absence of MED14 in Saccharomyces cerevisiae

Project description:The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 function as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate localization of the Scc2-Scc4 cohesin loader. Here we identify a broad range of Scc2- chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in recruitment of the cohesin loader. We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and decreased binding of Scc2 at RNA Pol II transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in direct recruitment of Scc2 to RNA pol II transcribed genes. We identified two mutations in the evolutionarily conserved HEAT domain of SCC2 that result in significantly reduced growth, scc2R787G and scc2G1242V. This experiment uses ChIP Seq to examine global localization of Scc2 in the presence or absence of MED14.

2022-05-25 | GSE201193 | GEO

Transcriptome analysis of mouse embryonic fibroblasts of NIPBL-haploinsufficient mice

Project description:Cohesinopathies are characterized by mutations in the cohesin complex. Mutations in NIPBL, a cohesin loader, result in Cornelia de Lange syndrome (CdLS). CdLS is a congenital genetic disorder distinguished by craniofacial dysmorphism, abnormal upper limb development, delayed growth, severe cognitive retardation, and multiple organ malformations.It has been suggested that CdLS is caused by defects in the cohesin network that alter gene expression and genome organization. However, the precise molecular etiology of CdLS is largely unclear. To gain insights, we sequenced mRNAs isolated from mouse embryonic fibroblasts of both WT and NIPBL-haploinsufficient mice and compared their transcriptomes.

2015-10-01 | GSE64706 | GEO

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