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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE198162 | GEO | 2023/03/23

REPOSITORIES: GEO

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

Project description: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.

2023-03-23 | GSE198161 | GEO

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

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

| PRJNA813880 | ENA

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

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

| PRJNA813885 | ENA

Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III.

Project description:Despite recent advances in single-molecule and structural analysis of condensin activity in vitro, mechanisms of functional condensin loading and loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae, the most prominent condensin loading site is the rDNA locus on chromosome XII, but its repetitiveness deters rigorous analysis of individual genes. An equally prominent non-rDNA condensin site is located on chromosome III (chrIII). It lies in the promoter of a putative non-coding RNA gene called RDT1, which is in a segment of the recombination enhancer (RE) that dictates MATa-specific chrIII organization. Here, we unexpectedly find that condensin is recruited to the RDT1 promoter in MATa cells through hierarchical interactions with Fob1, Tof2, and cohibin (Lrs4/Csm1), a set of nucleolar factors that also recruit condensin to the rDNA. Fob1 directly binds to this locus in vitro, while its binding in vivo depends on an adjacent Mcm1/α2 binding site that provides MATa cell specificity. We also uncover evidence for condensin-driven loop extrusion anchored by Fob1 and cohibin at RDT1 that unidirectionally extends toward MATa on the right arm of chrIII, supporting donor preference during mating-type switching. S. cerevisiae chrIII therefore provides a new platform for the study of programmed condensin-mediated chromosome conformation.

| S-EPMC10132618 | biostudies-literature

Recruiting a microtubule-binding complex to DNA directs chromosome segregation in budding yeast.

Project description:Accurate chromosome segregation depends on the kinetochore, which is the complex of proteins that link microtubules to centromeric DNA. The kinetochore of the budding yeast Saccharomyces cerevisiae consists of more than 80 proteins assembled on a 125-bp region of DNA. We studied the assembly and function of kinetochore components by fusing individual kinetochore proteins to the lactose repressor (LacI) and testing their ability to improve segregation of a plasmid carrying tandem repeats of the lactose operator (LacO). Targeting Ask1, a member of the Dam1-DASH microtubule-binding complex, creates a synthetic kinetochore that performs many functions of a natural kinetochore: it can replace an endogenous kinetochore on a chromosome, bi-orient sister kinetochores at metaphase during the mitotic cycle, segregate sister chromatids, and repair errors in chromosome attachment. We show the synthetic kinetochore functions do not depend on the DNA-binding components of the natural kinetochore but do require other kinetochore proteins. We conclude that tethering a single kinetochore protein to DNA triggers assembly of the complex structure that directs mitotic chromosome segregation.

| S-EPMC2752306 | biostudies-literature

Stability, structure and complexity of yeast chromosome III.

Project description:The complete sequence of yeast chromosome III provides a model for studies relating DNA sequence and structure at different levels of organisation in eukaryotic chromosomes. DNA helical stability, intrinsic curvature and sequence complexity have been calculated for the complete chromosome. These features are compartmentalised at different levels of organisation. Compartmentalisation of thermal stability is observed from the level delineating coding/non-coding sequences, to higher levels of organisation which correspond to regions varying in G + C content. The three-dimensional path reveals a symmetrical structure for the chromosome, with a densely packed central region and more diffuse and linear subtelomeric regions. This interspersion of regions of high and low curvature is reflected at lower levels of organisation. Complexity of n-tuplets (n = 1 to 6) also reveals compartmentalisation of the chromosome at different levels of organisation, in many cases corresponding to the structural features. DNA stability, conformation and complexity delineate telomeres, centromere, autonomous replication sequences (ARS), transposition hotspots, recombination hotspots and the mating-type loci.

| S-EPMC310056 | biostudies-other

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

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

2019-05-23 | GSE92717 | GEO

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

Scc2 regulates gene expression by recruiting cohesin to the chromosome as a transcriptional activator during yeast meiosis.

Project description:To tether sister chromatids, a protein-loading complex, including Scc2, recruits cohesin to the chromosome at discrete loci. Cohesin facilitates the formation of a higher-order chromosome structure that could also influence gene expression. How cohesin directly regulates transcription remains to be further elucidated. We report that in budding yeast Scc2 is required for sister-chromatid cohesion during meiosis for two reasons. First, Scc2 is required for activating the expression of REC8, which encodes a meiosis-specific cohesin subunit; second, Scc2 is necessary for recruiting meiotic cohesin to the chromosome to generate sister-chromatid cohesion. Using a heterologous reporter assay, we have found that Scc2 increases the activity of its target promoters by recruiting cohesin to establish an upstream cohesin-associated region in a position-dependent manner. Rec8-associated meiotic cohesin is required for the full activation of the REC8 promoter, revealing that cohesin has a positive feedback on transcriptional regulation. Finally, we provide evidence that chromosomal binding of cohesin is sufficient for target-gene activation during meiosis. Our data support a noncanonical role for cohesin as a transcriptional activator during cell differentiation.

| S-EPMC3113765 | biostudies-literature

Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.

Project description:The recent determination of the complete sequence of chromosome III from the yeast Saccharomyces cerevisiae allows, for the first time, the investigation of the long range primary structure of a eukaryotic chromosome. We have found that, against a background G+C level of about 35%, there are two regions (one in each chromosome arm) in which G+C values rise to over 50%. This effect is seen in silent sites within genes, but not in noncoding intergenic sequences. The variation in G+C content is not related to differential selection of synonymous codons, and probably reflects mutational biases. That the intergenic regions do not exhibit the same phenomenon is particularly interesting, and suggests that they are under substantial constraint. The yeast chromosome may be a model of the structure of the human genome, since there is evidence that it is also a mosaic of long regions of different base compositions, reflected in wide variation of G+C content at silent sites among genes. Two possible causes of this regional effect, replication timing, and recombination frequency, are discussed.

| S-EPMC309089 | biostudies-other

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