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A nucleolar condensin-recruiting complex that regulates yeast chromosome III structure [ChIP-Seq]

ABSTRACT: Purpose: To identify cohibin-dependent condensin binding sites throughout the yeast genome. Conclusions: This ChIP-seq experiment showed that the condensin subunit, Brn1, was depleted from the RDT1 promoter in an lrs4Δ mutant strain. The experiment also showed that the Lrs4 subunit of the cohibin complex is highly enriched at the RDT1 promoter on chromosome III.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE198161 | GEO | 2023/03/23

REPOSITORIES: GEO

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Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III [Micro-C seq]

Project description:Purpose: This study was designed to determine the mechanism of condensin and Sir2 recruitment to the RDT1 promoter region of S. cerevisiae chromosome III, and to test whether preventing condensin recruitment by deleting the key factors, Fob1 and Lrs4, significantly alters the conformation of chromosome III. Conclusions: Conformational changes in chromosome III and loss of CEN12-rDNA looping in chromosome XII observed in lrs4? and fob1? mutants.

2023-03-23 | GSE198148 | GEO

Shugoshin biases chromosomes for biorientation through condensin recruitment to the pericentromere

Project description:To protect against aneuploidy, chromosomes must attach to microtubules from opposite poles (“biorientation”) prior to their segregation during mitosis. Biorientation relies on the correction of erroneous attachments by the aurora B kinase, which destabilizes kinetochore-microtubule attachments that lack tension. Incorrect attachments are also avoided because sister kinetochores are intrinsically biased towards capture by microtubules from opposite poles. Here we show that shugoshin acts as a pericentromeric adaptor that plays dual roles in biorientation in budding yeast. Shugoshin maintains the aurora B kinase at kinetochores that lack tension, thereby engaging the error correction machinery. Shugoshin also recruits the chromosome-organising complex, condensin, to the pericentromere. Pericentromeric condensin biases sister kinetochores towards capture by microtubules from opposite poles. Overall, shugoshin integrates a bias to sister kinetochore capture with error correction to enable chromosome biorientation. Our findings uncover the molecular basis of the bias to sister kinetochore capture and expose shugoshin as a pericentromeric hub controlling chromosome biorientation. Two experiments: Experiment A: Sgo1 is required for condensin localization in the pericentromere. Sample 1: Wild type input DNA Sample 2: Wild type Brn1-6HA ChIP DNA, Sample 3 sgo1D input DNA, Sample 4 sgo1D Brn1-6HA ChIP DNA; Experiment B: Sgo1 is not required for cohesin localization in the periecentromere: Sample 5: wild type input DNA, Sample 6 Wild type Scc1-6HA ChIP DNA, Sample 7, sgo1D input DNA, Sample 8 sgo1D Scc1-6HA ChIP DNA. 1 replicate of each repeat

2014-01-08 | E-GEOD-53856 | biostudies-arrayexpress

Calibrated Sgo1 and Brn1 ChIP-seq for wild type strains arrested in metaphase without tension

Project description:Genome binding/occupancy profiling of Sgo1 and the condensin subunit Brn1 by high throughput sequencing. S. pombe is included as the calibration genome.

2020-01-13 | GSE128236 | GEO

Calibrated Scc1, Sgo1 and Brn1 ChIP-seq in metaphase with and without tension, in strains where convergent genes at pericentromere borderes are rearranged into a tandem orientation

Project description:Genome binding/occupancy profiling of Sgo1 and the condensin subunit Brn1 by high throughput sequencing. S. pombe is included as the calibration genome.

2020-01-13 | GSE128227 | GEO

A nucleolar condensin-recruiting complex that regulates yeast chromosome III structure

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-03-23 | GSE198162 | GEO

Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer [HiC-Seq]

Project description:Saccharomyces cerevisiae switches its mating type (MATa or MATalpha) through gene conversion using one of two possible donors, HMLalpha or HMRa, both of which are maintained by the SIR silencing complex as heterochromatic cassettes on opposing ends of chromosome III. In MATa cells, HMLalpha on the left arm is preferentially chosen as the donor through a mechanism requiring a cis-acting sequence called the recombination enhancer (RE). The left half of the RE is required for this donor preference activity, whereas the right half has been implicated in regulating chromosome III structure. In this study we have identified a MATa-specific Sir2 and condensin binding site within the right half of the RE that maintains chromosome III in a switching-competent conformation by preventing MATa from interacting with the default HMRa donor on the right arm. Within the RE, Sir2 strongly represses transcription of a small MATa-specific gene of unknown function (RDT1). Upon expression of HO endonuclease to induce the switching process, Sir2 redistributes from the RE to the double-stranded DNA break site at MATa, thus derepressing RDT1 transcription to coincide with the timing of mating-type switching. Condensin is also displaced from the RE in response to the HO-induced break, likely contributing to the transient change in chromosome III conformation required for effective switching without disruption of HML and HMR heterochromatin.

2019-05-23 | GSE92715 | GEO

Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer [ChIP-Seq]

2019-05-23 | GSE92714 | GEO

Genome-wide distribution of the three condensin complexes in C. elegans

Project description:Condensins are multi-subunit protein complexes that regulate chromosome structure throughout cell-cycle. Metazoans contain two types of condensin complexes (I and II) with essential and distinct functions. In C. elegans a third type of condensin (IDC) functions as part of the X chromosome dosage compensation complex1,2. We mapped genome-wide binding sites of the three condensin types in C. elegans embryos. Characteristics of condensin binding are similar between condensin types. ChIP-seq profiles of C. elegans subunits of the three condensins in 3-6 replicates from mixed stage embryos, controls are included, and RNA-Seq profiles of C. elegans in 5 replicates from mixed staged embryos. Additionally, ChIP-seq profiles of the condensin II subunit KLE-2 in 6 replicates from L3 with controls, and RNA-Seq profiles of KLE-2 mutants in 3 replicates each from L3.

2013-09-16 | E-GEOD-45678 | biostudies-arrayexpress

Condensin II inactivation in interphase does not affect chromatin folding or gene expression

Project description:Condensin complexes have been proposed to play a prominent role in interphase chromatin organization and control of gene expression. Here, we report that the deletion of the central condensin II kleisin subunit Ncaph2 in differentiated mouse hepatocytes does not lead to significant changes in chromosome organization or in gene expression. Both observations challenge current views that implicate condensin in interphase chromosomal domain formation and in enhancer-promoter interactions. Instead, we suggest that the previously reported effects of condensin perturbation may result from their structural role during mitosis, which might indirectly impact the re-establishment of interphase chromosomal architecture after cell division.

2019-05-05 | GSE122157 | GEO

Transcriptome analysis of condensin II knockdown cells

Project description:Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. Condensin II is present in the nucleus throughout the cell cycle, including interphase. The aim of these experiments is to investigate the changes of gene expression in knockdown of NCAPH2, a condensin II subunit, in mouse embryonic stem cells compared to their control cells.

2017-06-01 | GSE80041 | GEO

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