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Analysis by Mnase-seq of the chromatin structure of wild type cells and cells in which chromatin structure is perturbed (histone H4 depletion) in the presence or absence of the kleisin subunit of cohesin, Scc1

ABSTRACT: The main objective of this study is to determine how cohesin influences chromatin structure and chromatin assembly during DNA replication

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE121067 | GEO | 2019/08/06

REPOSITORIES: GEO

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Genome-wide profiling of Scc1 subunit in wild type cells and in cells in which chromatin structure is perturbed (histone H4 depletion).

Project description:The main objective of this study is to determine how chromatin assembly during DNA replication influences cohesin deposition

2019-08-06 | GSE121004 | GEO

Analysis by Mnase-seq of the chromatin structure of wild type cells and cells in which chromatin structure is perturbed (histone H4 depletion) in the presence or absence of the kleisin subunit of cohesin, Scc1

Project description:Analysis by Mnase-seq of the chromatin structure of wild type cells and cells in which chromatin structure is perturbed (histone H4 depletion) in the presence or absence of the kleisin subunit of cohesin, Scc1

| PRJNA495502 | ENA

Distinct developmental function of two Caenorhabditis elegans homologs of the cohesin subunit Scc1/Rad21.

Project description:Cohesin, which mediates sister chromatid cohesion, is composed of four subunits, named Scc1/Rad21, Scc3, Smc1, and Smc3 in yeast. Caenorhabditis elegans has a single homolog for each of Scc3, Smc1, and Smc3, but as many as four for Scc1/Rad21 (COH-1, SCC-1/COH-2, COH-3, and REC-8). Except for REC-8 required for meiosis, function of these C. elegans proteins remains largely unknown. Herein, we examined their possible involvement in mitosis and development. Embryos depleted of the homolog of either Scc3, or Smc1, or Smc3 by RNA interference revealed a defect in mitotic chromosome segregation but not in chromosome condensation and cytokinesis. Depletion of SCC-1/COH-2 caused similar phenotypes. SCC-1/COH-2 was present in cells destined to divide. It localized to chromosomes in a cell cycle-dependent manner. Worms depleted of COH-1 arrested at either the late embryonic or the larval stage, with no indication of mitotic dysfunction. COH-1 associated chromosomes throughout the cell cycle in all somatic cells undergoing late embryogenesis or larval development. Thus, SCC-1/COH-2 and the homologs of Scc3, Smc1, and Smc3 facilitate mitotic chromosome segregation during the development, presumably by forming a cohesin complex, whereas COH-1 seems to play a role important for development but unrelated to mitosis.

| S-EPMC194888 | biostudies-literature

High Sensitivity Profiling of Chromatin Structure by MNase-SSP.

Project description:A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data.

| S-EPMC6582983 | biostudies-literature

Wapl releases Scc1-cohesin and regulates chromosome structure and segregation in mouse oocytes.

Project description:Cohesin is essential for genome folding and inheritance. In somatic cells, these functions are both mediated by Scc1-cohesin, which in mitosis is released from chromosomes by Wapl and separase. In mammalian oocytes, cohesion is mediated by Rec8-cohesin. Scc1 is expressed but neither required nor sufficient for cohesion, and its function remains unknown. Likewise, it is unknown whether Wapl regulates one or both cohesin complexes and chromosome segregation in mature oocytes. Here, we show that Wapl is required for accurate meiosis I chromosome segregation, predominantly releases Scc1-cohesin from chromosomes, and promotes production of euploid eggs. Using single-nucleus Hi-C, we found that Scc1 is essential for chromosome organization in oocytes. Increasing Scc1 residence time on chromosomes by Wapl depletion leads to vermicelli formation and intra-loop structures but, unlike in somatic cells, does not increase loop size. We conclude that distinct cohesin complexes generate loops and cohesion in oocytes and propose that the same principle applies to all cell types and species.

| S-EPMC7147110 | biostudies-literature

Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1.

Project description:Sister chromatid cohesion is mediated by cohesin, whose Smc1, Smc3, and kleisin (Scc1) subunits form a ring structure that entraps sister DNAs. The ring is opened either by separase, which cleaves Scc1 during anaphase, or by a releasing activity involving Wapl, Scc3, and Pds5, which bind to Scc1 and open its interface with Smc3. We present crystal structures of Pds5 from the yeast L. thermotolerans in the presence and absence of the conserved Scc1 region that interacts with Pds5. Scc1 binds along the spine of the Pds5 HEAT repeat fold and is wedged between the spine and C-terminal hook of Pds5. We have isolated mutants that confirm the observed binding mode of Scc1 and verified their effect on cohesin by immunoprecipitation and calibrated ChIP-seq. The Pds5 structure also reveals architectural similarities to Scc3, the other large HEAT repeat protein of cohesin and, most likely, Scc2.

| S-EPMC4793087 | biostudies-literature

Functional characterization of cohesin subunit SCC1 in Trypanosoma brucei and dissection of mutant phenotypes in two life cycle stages.

Project description:In yeast and metazoa, structural maintenance of chromosome (SMC) complexes play key roles in chromosome segregation, architecture and DNA repair. The main function of the cohesin complex is to hold replicated sister chromatids together until segregation at anaphase, which is dependent on proteolytic cleavage of the cohesin subunit SCC1. Analysis of trypanosomatid genomes showed that the core cohesin and condensin complexes are conserved, but SMC5/6 is absent. To investigate the functional conservation of cohesin in eukaryotes distantly related to yeast and metazoa, we characterized the Trypanosoma brucei SCC1 orthologue. TbSCC1 is expressed prior to DNA synthesis at late G1, remains in the nucleus throughout S- and G2-phases of the cell cycle and disappears at anaphase. Depletion of SCC1 by RNAi or expression of a non-cleavable SCC1 resulted in karyokinesis failure. Using the dominant negative phenotype of non-cleavable SCC1 we investigated checkpoint regulation of cytokinesis in response to mitosis failure at anaphase. In the absence of chromosome segregation, procyclic trypanosomes progressed through cytokinesis to produce one nucleated and one anucleate cell (zoid). In contrast, cytokinesis was incomplete in bloodstream forms, where cleavage was initiated but cells failed to progress to abscission. Kinetoplast duplication was uninterrupted resulting in cells with multiple kinetoplasts and flagella.

| S-EPMC2610385 | biostudies-literature

Crosstalk between chromatin structure, cohesin activity and transcription.

Project description:BackgroundA complex interplay between chromatin and topological machineries is critical for genome architecture and function. However, little is known about these reciprocal interactions, even for cohesin, despite its multiple roles in DNA metabolism.ResultsWe have used genome-wide analyses to address how cohesins and chromatin structure impact each other in yeast. Cohesin inactivation in scc1-73 mutants during the S and G2 phases causes specific changes in chromatin structure that preferentially take place at promoters; these changes include a significant increase in the occupancy of the - 1 and + 1 nucleosomes. In addition, cohesins play a major role in transcription regulation that is associated with specific promoter chromatin architecture. In scc1-73 cells, downregulated genes are enriched in promoters with short or no nucleosome-free region (NFR) and a fragile "nucleosome - 1/RSC complex" particle. These results, together with a preferential increase in the occupancy of nucleosome - 1 of these genes, suggest that cohesins promote transcription activation by helping RSC to form the NFR. In sharp contrast, the scc1-73 upregulated genes are enriched in promoters with an "open" chromatin structure and are mostly at cohesin-enriched regions, suggesting that a local accumulation of cohesins might help to inhibit transcription. On the other hand, a dramatic loss of chromatin integrity by histone depletion during DNA replication has a moderate effect on the accumulation and distribution of cohesin peaks along the genome.ConclusionsOur analyses of the interplay between chromatin integrity and cohesin activity suggest that cohesins play a major role in transcription regulation, which is associated with specific chromatin architecture and cohesin-mediated nucleosome alterations of the regulated promoters. In contrast, chromatin integrity plays only a minor role in the binding and distribution of cohesins.

| S-EPMC6647288 | biostudies-literature

Mapping the differential distribution of the cohesin subunit Scc1 in Trypanosoma brucei brucei.

Project description:Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where Scc1 is deposited. This was achieved by deletion of one Scc1 allele and N-terminal tagging of the second Scc1 allele with a Ty1-tag. During the ChIP experiment, the DNA was crosslinked and cells were permeabilized with digitonin. DNA was fragmented by sonication with a Covaris instrument. DNA bound to Ty1-Scc1 was pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and the DNA was purified and prepared for Illumina sequencing.

2018-11-06 | GSE119071 | GEO

Genome-wide profiling of Scc1 subunit in wild type cells and in cells in which chromatin structure is perturbed (histone H4 depletion).

Project description:Genome-wide profiling of Scc1 subunit in wild type cells and in cells in which chromatin structure is perturbed (histone H4 depletion).

| PRJNA495336 | ENA

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