Saccharomyces cerevisiae
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PROVIDER: PRJNA101013 | ENA |
REPOSITORIES: ENA
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Project description:Nucleosome organization determines local chromatin structure and changes in nucleosome occupancy during the cell cycle are correlated with nuclear functions. We used oligonucleotide tiling arrays to analyze the cell cycle dependence of nucleosome occupancy at cohesin binding sites in yeast chromosomes. Processed data included in Series table. Data processing: To improve the signal to noise ratio, the raw data were first processed with dCHIP with its PM/MM difference model and invariant set normalization method, using the entire dataset. 8251 out of the total 92812 probe pairs were excluded from further analysis because they either have multiple hits in the genome or the signal from the genomic hybridization was too weak (cutoff at (PM-MM)/MM < 0.25). After Gaussian smoothing (s =75 bp), the data were normalized by that of the genomic DNA. These values were then converted to log2 scale. The mean was then computed for each array. To facilitate comparisons, the different datasets were rescaled to have the same mean with log2 value of 0. The log2 ratio along the four chromosomes at all the cell cycle stages are included. The ID represents "Chromosome No_chromosomal coordinate". Keywords: time course Yeast cells were arrested at G1/S boundary with alpha factor, then released for 15 min, 40 min, 65 min and 95 min respectively. Cells were collected at each time points, then mononucleosomal DNA was purified and hybridized to Affymetrix oligonucleotide tiling arrays. Total genomic DNA was hybridized as normalization signal.
2010-05-26 | E-GEOD-8130 | biostudies-arrayexpress
Project description:Nucleosome organization determines local chromatin structure and changes in nucleosome occupancy during the cell cycle are correlated with nuclear functions. We used oligonucleotide tiling arrays to analyze the cell cycle dependence of nucleosome occupancy at cohesin binding sites in yeast chromosomes. Processed data included in Series table. Data processing: To improve the signal to noise ratio, the raw data were first processed with dCHIP with its PM/MM difference model and invariant set normalization method, using the entire dataset. 8251 out of the total 92812 probe pairs were excluded from further analysis because they either have multiple hits in the genome or the signal from the genomic hybridization was too weak (cutoff at (PM-MM)/MM < 0.25). After Gaussian smoothing (s =75 bp), the data were normalized by that of the genomic DNA. These values were then converted to log2 scale. The mean was then computed for each array. To facilitate comparisons, the different datasets were rescaled to have the same mean with log2 value of 0. The log2 ratio along the four chromosomes at all the cell cycle stages are included. The ID represents "Chromosome No_chromosomal coordinate". Keywords: time course
2008-03-11 | GSE8130 | GEO
Project description:Cohesin-dependent compaction of mitotic chromosomes in budding yeast
| PRJNA344307 | ENA
Project description:FACT mediates cohesin function on chromatin Cohesin is a key regulator of genome architecture with roles in sister chromatid cohesion and the organisation of higher-order structures during interphase and mitosis. The recruitment and mobility of cohesin complexes on DNA are restricted by nucleosomes. Here we show that cohesin role in chromosome organization requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects cohesin stability on chromatin reducing its accumulation at pericentric regions and binding on chromosome arms. Using Hi-C, we show that cohesin-dependent TAD (Topological Associated Domains)-like structures in G1 and metaphase chromosomes are disrupted in the absence of FACT. Surprisingly, sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our results uncover a role for FACT in genome organisation by facilitating cohesin dependent compartmentalization of chromosomes into loop domains.
2019-10-03 | PXD014896 | Pride
Project description:Genome wide maps of nucleosome occupancy in yeast have been produced through deep sequencing of nuclease-protected DNA. These maps have been obtained from crosslinked chromatin in vivo at varying phosphate concentrations (no phoshate and 10mM phosphate concentration). Here, we analyze these maps in combination with existing TF binding data (Harbison et al., Nature, 2004, 431(7004):99-104), and with new gene expression experiments reported here (GSE26770). We also confirm previous conclusions that the intrinsic,sequence dependent binding of nucleosomes helps determine the localization of TF binding sites.
2011-08-01 | GSE26392 | GEO
Project description:Sister chromatid cohesion is mediated by cohesin but the process of cohesion establishment during S phase is still enigmatic. Recent data indicate that in mammalian cells, cohesin binding to chromatin is dynamic in G1 but becomes stabilized during S phase. Whether the regulation of chromosomal cohesin turn-over is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behaviour. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, implying that repeated loading cycles maintain cohesin binding. Cohesin retention on G1 chromosomes was improved by deletion of wpl, the fission yeast ortholog of mammalian WAPL, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl is non-essential, indicating that a change in wpl-dependent cohesin turnover is not integral to the mechanism of cohesion establishment. Instead we find that cohesin instability is down-regulated during S phase in a reaction independent of DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence. Keywords: ChIP-chip Experiments in budding and fission yeast have shown that the cohesin loading factors are dispensable for viability in G2, when cohesion has been established (Bernard et al., 2006; Ciosk et al., 2000). In fission yeast, inactivation of the loading machinery at that time no longer affects cohesin binding to chromosomes (Bernard et al., 2006). In mammalian cells, about one-third of nuclear cohesin becomes stably bound to chromatin in G2 (Gerlich et al., 2006). Since the binding of cohesin to chromosomes appears labile in G1, but stabilized in G2, we asked how cohesin becomes stable during the intervening S phase. Spreads showed that Rad21 was only slightly decreased in HU arrested cells after inactivation of the cohesin loading factors Mis4 or Ssl3. In this series we analyzed whether cohesin association was equally stabilised at all its association sites along chromosome arms. Rad21 binding was therefore analyzed on a chromosome-wide scale by ChIP followed by hybridization to an oligonucleotide tiling array covering chromosomes 2 and 3. We compared the Rad21 binding pattern in HU arrested wild-type versus ssl3-29 cells after the shift to the restrictive temperature. Four 50 kb regions from chromosome 2 are shown in Figure 5, and the complete chromosome 2 in Supplemental Fig.2 (based on samples GSM209708 & GSM209722 compared to the SUP sample GSM209740, provisional accession numbers). This showed that cohesin peaks remained indistinguishable in their relative height and positions whether or not Ssl3 was inactivated. We conclude that, unlike in G1, the loading machinery is dispensable for the stable binding of cohesin to chromosomes in S phase cells. The experiment was repeated twice with slightly changed parameters (16B12 vs 12CA5 anti-HA antibody, 8.5h vs 9h HU arrest at 20C, 3h at 36C vs 3h at 37C inactivation in HU, see samples for details).
2007-11-30 | E-GEOD-8450 | biostudies-arrayexpress
Project description:Cohesin holds sister chromatids together to enable their accurate segregation in mitosis. How, and where, cohesin binds to chromosomes are still poorly understood, and recent genome-wide surveys have revealed an apparent disparity between its chromosomal association patterns in different organisms. Here, we present the high-resolution analysis of cohesin localisation along fission yeast chromosomes. This reveals that several determinants, thought specific for distinct organisms, come together to shape the overall distribution. Cohesin is detected at chromosomal loading sites, characterised by the cohesin loader Mis4/Ssl3, in regions of strong transcriptional activity. Cohesin also responds to transcription by downstream translocation and accumulation at convergent transcriptional terminators surrounding the loading sites. As cells enter mitosis, a fraction of cohesin leaves chromosomes in a cleavage-independent reaction, while a substantial pool of cohesin dissociates when it is cleaved at anaphase onset. As a unique feature, centromeric cohesin spreads out onto chromosome arms during mitosis as the heterochromatin protein Swi6 dissociates from centromeres. Together, this allows us to suggest conserved mechanisms for chromosomal cohesin binding in eukaryotes. After DNA replication in S phase, sister chromatids are held together by the cohesin complex. This allows DNA break repair by homologous recombination in G2 and bipolar attachment of the spindle to sister kinetochores in mitosis. At anaphase onset, sister chromatid cohesion is resolved to trigger chromosome segregation. Cohesin is an essential, conserved protein complex consisting of at least five subunits, Psm1, Psm3, Rad21, Psc3 and Pds5 in fission yeast (orthologs of budding yeast Smc1, Smc3, Scc1, Scc3 and Pds5, respectively). Chromatin immunoprecipitations against three different subunits of the cohesin complex, fused to two different epitope tags (Rad21-Pk9 -> GSM333001, Rad21-HA3 -> GSM333004, Psc3-Pk9 -> GSM333005 and Pds5-Pk9 -> GSM333006), yielded a reproducible binding pattern between approximately half of all available convergently transcribed gene pairs (in the following called convergent sites). The pattern was almost indistinguishable between exponentially growing cell populations (GSM333004, GSM333005, GSM333006) and cells arrested in G2 using the thermosensitive cdc25-22 mutation (GSM333001). To understand why some, but not all, convergent sites are bound by cohesin, we analysed whether fission yeast cohesin responds to Pol II transcription by downstream translocation, like in budding yeast. As an example, we analysed cohesin at the convergent site between the rad21 and pof3 genes. rad21 expression is high during G1 and S phase, but low in G2. In cells arrested in G2 using the cdc25-22 allele, only a small cohesin peak was detectable that largely overlapped with the rad21 ORF (GSM333001). In contrast, in cells arrested in G1 using the cdc10-129 allele, the rad21 ORF was clear of cohesin and instead a large cohesin peak accumulated downstream of rad21 (GSM333007). It has been suggested that transcriptional readthrough at convergent sites promotes double stranded RNA-dependent heterochromatin formation, which in turn underlies cohesin recruitment. We therefore tested whether the heterochromatin protein Swi6, thought to recruit cohesin, played a role in generating the observed cohesin pattern. We grew wild type and swi6Î cells in synthetic medium lacking thiamine, conditions under which the nmt2 gene is transcribed at the nmt2/avn2 convergent site that has been studied as an example. In contrast to the prediction, the cohesin pattern along chromosome arms, including the nmt2/avn2 convergent site, remained unchanged in swi6Î cells (GSM333008). We detected only small amounts of cohesin at the nmt2/avn2 convergent site, a class 1 convergent site following the above classification. At the centromeric repeats, cohesin levels were reduced in the absence of Swi6. These findings are consistent with previous reports implicating Swi6 in cohesin recruitment to centromeric heterochromatin, but not chromosome arms. To compare cohesinâs pattern to its likely sites of chromosomal loading, we analysed the localisation of the cohesin loader subunits Mis4 and Ssl3. The two subunits showed a largely overlapping pattern of binding. Chromatin immunoprecipitation was performed against epitope-tagged Mis4-Pk9 (GSM333163) and Ssl3-Pk9 (GSM334196) from exponentially proliferating cells. As a control, cells without epitope-tagged protein were grown under identical conditions and processed in parallel for chromatin immunoprecipitation with an α-Pk antibody (GSM333230). The untagged control sample yielded trace amounts of immunoprecipitated DNA, which after amplification led to several strong peaks often in intergenic low complexity regions. Several of these peaks overlapped with Mis4/Ssl3 peaks, which were excluded from the analysis. Peaks in low complexity regions were not observed in chromatin immunoprecipitates of cohesin subunits (compare GSM333001). In the search for an underlying determinant of Mis4/Ssl3 binding sites, we noticed a striking correlation with tRNA and ribosomal protein genes. Mis4/Ssl3 binding sites at tRNA genes overlapped with the binding profile of the Pol III transcription factor TFIIIC subunit Sfc6 (GSM334198), while at ribosomal protein genes it colocalised with the forkhead domain containing protein Fhl1 (GSM334307). Fhl1 is a possible fission yeast ortholog of the transcription factor Fhl1 that controls ribosomal protein gene expression in budding yeast. We found Sfc6 also associated with ribosomal protein genes, and Fhl1 with tRNA genes, though with weaker signal intensities. We do not currently know whether Sfc6 contributes to transcriptional control of ribosomal protein genes, and Fhl1 to that of tRNA genes, or whether the weaker levels of association may reflect indirect association, mediated by interactions between ribosomal protein and tRNA gene loci. Similar to budding yeast, Mis4/Ssl3 binding sites are also binding sites for the chromosomal condensin complex (GSM334197), which may mediate such interactions. Having identified the binding sites of the Mis4/Ssl3 cohesin loader, we wanted to analyse its relationship with the cohesin distribution along chromosome arms. If Mis4/Ssl3 cohesin loading sites promote cohesin binding in their surrounding, deletion of a loading site should alter this pattern. To test this, we deleted a 489 bp sequence, containing two adjacent tRNA genes that form a Mis4/Ssl3 and cohesin binding site, on the left arm of chromosome 2. In response to the deletion, Mis4/Ssl3 binding to this locus disappeared (GSM334308). Cohesin was also no longer detected at this site (GSM334309), consistent with the notion that cohesin loading had been disrupted. However, the cohesin distribution at convergent sites surrounding the former loading site remained unchanged. This suggests that establishment of the cohesin pattern did not depend on a specific Mis4/Ssl3 binding site. Despite the tRNA deletion, residual Mis4/Ssl3 remained detectable in the vicinity of this site (GSM334308). Cohesin loading by Mis4/Ssl3 might therefore be less restricted to its peaks of binding than the pattern suggests. Alternatively, other determinants, e.g. gene orientation and their transcriptional activity, might define cohesin distribution at this locus. We next addressed how cohesin on fission yeast chromosomes responds to loss of sister chromatid cohesion during mitosis and whether cohesin removal in mitosis affected certain regions of the chromosome more than others. In order to follow cohesin through mitosis, we arrested a cell population in G2 using the thermosensitive cdc25-22 mutation and released the culture into synchronous mitotic progression at permissive temperature.The cohesin pattern remained largely unchanged throughout G2, metaphase and anaphase, although the height of peaks along chromosome arms decreased. This suggests that cohesin is not removed from a subset of its binding sites during mitosis, but that its association among most binding sites was uniformly reduced. A noticeable change to the cohesin pattern during mitosis became apparent around centromeres. Over a region of approximately 50 kb surrounding the centromeres, cohesin appeared to spread along chromosome arms, showing little preference for convergent sites. The spreading started as cells entered metaphase (GSM334316) and became most pronounced during anaphase (GSM334317). We also observed a similar, although less pronounced, spreading around centromeres in cells arrested in G1 using the cdc10-129 thermosensitive mutation (GSM333007). This suggests that spreading of cohesin around centromeres is cell cycle stage specific. Cohesin is enriched at the centromeric repeat regions (GSM333001), tethered by the heterochromatin protein Swi6, possibly after being loaded at core centromere sequences, where we observed strong Mis4/Ssl3 accumulation (GSM333163 & GSM334196). In mitosis, Swi6 levels are reduced after aurora B kinase-dependent phosphorylation of histone H3, and it reaccumulates as cells enter the subsequent S phase. To test whether loss of Swi6-dependent
2010-05-14 | E-GEOD-13517 | biostudies-arrayexpress
Project description: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
2008-07-21 | GSE12149 | GEO
Project description:Genome wide maps of nucleosome occupancy in yeast have been produced through deep sequencing of nuclease-protected DNA. These maps have been obtained from crosslinked chromatin in vivo at varying phosphate concentrations (no phoshate and 10mM phosphate concentration). Here, we analyze these maps in combination with existing TF binding data (Harbison et al., Nature, 2004, 431(7004):99-104), and with new gene expression experiments reported here (GSE26770). We also confirm previous conclusions that the intrinsic,sequence dependent binding of nucleosomes helps determine the localization of TF binding sites. High-throughput sequencing of yeast nucleosomal DNA at varying phosphate concentration. Yeast S. cerevisiae (strain: PHO4-MYC::TRP1; CBF1-3HA::LEU2) in log phase was grown in PNB medium with no phosphate for 3 hours and then shifted to various phosphate concentration (0mM and 10 mM) for 80 minutes. After micrococcal nuclease treatment, reverse crosslink and gel purification mononucleosome were isolated. The sequencing by Illumina Solexa following manufacturer protocol has provided mononucleosomal maps in yeast genome (Oct. 2003 SGD/sacSer1 genome release) at two phosphate concentrations (starvation and normal).
2011-08-01 | E-GEOD-26392 | biostudies-arrayexpress
Project description:The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. However, nucleosome number in cells was considered fixed, and no condition was described where nucleosome number was reduced. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker and variant histones, and a correspondingly reduced number of nucleosomes. Yeast nhp6 mutants lacking NHP6A and –B proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform, and our results can be modelled assuming that different nucleosomal sites compete for the available histones: sites with high affinity are almost always packaged into nucleosomes both in wt and nucleosome-depleted cells, whereas sites with low affinity are less frequently packaged in nucleosome-depleted cells. We suggest that by modulating the occupancy of nucleosomes histone availability may constitute a novel layer of epigenetic regulation.
2011-05-19 | GSE23711 | GEO