Regulation of yeast chromosome III architecture and mating-type switching by a Sir2/condensin-bound region of the recombination enhancer
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PROVIDER: PRJNA358414 | ENA |
REPOSITORIES: ENA
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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
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 | GSE92714 | GEO
Project description:Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR. The Recombination Enhancer (RE), located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III. Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains. We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells. Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding. In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types. The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching.
2015-11-20 | GSE73890 | GEO
Project description:Yeast chromosome III contains the mating type loci that provide a paradigm for long-range interactions between distant loci. Yeast switch mating type by gene conversion between the MAT locus and either of two silent loci (HML or HMR) on opposite ends of the chromosome. This long-range process is mating type-specific so that MATa cells choose HML as template, while MATα cells use HMR. The Recombination Enhancer (RE), located on the left arm regulates this process. One long-standing hypothesis is that switching is guided by mating type-specific, and possibly RE-dependent three-dimensional folding of chromosome III. Here we used Hi-C, 5C, and live cell imaging to characterize the conformation of chromosome III in both mating types in non-switching strains. We discovered a mating type-specific difference in the folding of the left arm: in MATa cells the left arm is located closely to the centromere-proximal portion of the chromosome as well as to MAT, whereas it is more extended away in MATα cells. Deletion analysis showed that a 1 kb subregion within the RE, which is not necessary during switching, abolished mating type-dependent chromosome folding. In this mutant the conformation of chromosome III is the same in both mating types, but distinct from the wild type MATa or MATα conformations, indicating that the RE induces conformational changes in both mating types. The RE is therefore a composite element with one subregion essential for selecting the appropriate donor during switching, and a separate region involved in modulating chromosome conformation prior to switching. This submission contain 2 biological replicates of Hi-C experiments done in MATa and MATalpha cells in Saccharamycese cerevisiae. It also contains 3 biological replicates of 13 5C experiments in various mutants in MATa and MATalpha cells.
2015-11-20 | E-GEOD-73890 | biostudies-arrayexpress
Project description:As a successful commensal and pathogen of humans, Candida albicans encounters a wide range of environmental changes. Among them, ambient pH is an important factor, which changes frequently and affects many biological processes in this species. The ability to adapt to pH changes is tightly linked with pathogenesis and morphogenesis. In this study, we report that pH has a profound effect on white-opaque switching and sexual mating in C. albicans. Acidic pHs promote white-to-opaque switching but repress sexual mating of opaque cells. The cAMP signaling and Rim101-mediated pH sensing pathways are involved in the regulation of pH-regulated white-opaque switching. Interestingly, white and opaque cells of the cyr1/cyr1 mutant, which is defective in producing cAMP, show distinct growth defects under acidic and alkaline conditions. Phr2 could play a major role in acidic pHs-induced opaque cell formation. We further discover that acidic pH conditions repress sexual mating due to the failure of activation of the Ste2-mediated a-pheromone response pathway. The effects of pH changes on phenotypic switching and sexual mating could be a balance behavior between host adaptation and sexual reproduction.
2015-12-30 | GSE67101 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-05-23 | GSE92717 | GEO
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
Project description:It has been proposed that the ancestral fungus was mating competent and homothallic. However, many mating competent fungi were initially classified as asexual because their mating capacity was hidden behind layers of regulation. For efficient in vitro mating, the essentially obligate diploid ascomycete pathogen C. albicans has to homozygose its mating type locus from MTLa/α to MTLa/a or MTLα/α, and then undergo an environmentally controlled epigenetic switch to the mating competent opaque form. These requirements greatly reduce the potential for C. albicans mating. Deletion of the YciI domain gene OFR1 bypasses the need for C. albicans cells to homozygose the mating type locus prior to switching to the opaque form and mating, and allows homothallic mating of MTL heterozygous strains. This bypass is carbon source dependent and does not occur when cells are grown on glucose. Transcriptional profiling of ofr1 mutant cells shows that in addition to regulating cell type and mating circuitry, Ofr1 is needed for proper regulation of histone and chitin biosynthesis gene expression. It appears that OFR1 is a key regulator in C. albicans, and functions in part to maintain the cryptic mating phenotype of the pathogen. Distruption of OFR1 gene which encodes a Yci1 related domain in Candida ablicans (MTLa/α) is shown to have white-opaque switching related and mating related gene expression. The expression of histone genes are also positively regulated in some conditions.
2015-12-29 | GSE75780 | GEO
Project description:Sir2 and the homologous proteins, Hst1, Hst2, Hst3, and Hst4 from Saccharomyces cerevisiae are NAD+-dependent histone deacetylases of the sirtuin protein family. Sir2 functions in transcriptional silencing at the silent mating-type loci, telomeres, and rDNA locus, but also promotes replicative lifespan. To gain a better understanding of the chromatin-regulatory roles carried out by Sir2 and the Hst proteins, we performed ChIP-sequencing analysis on all five sirtuins and Sum1, the DNA binding partner for Hst1. Sir2, Hst1, and Sum1 were abundantly, and functionally co-enriched at several major targets, including the telomeric repeats, where they were required for maintaining proper telomere repeat length. At tRNA target genes they were required for efficient cohesin and condensin deposition. Across the open reading frames of glycolytic and ribosomal protein genes, Sir2 and Hst1 functioned in NAD+-dependent transcriptional repression at the diauxic shift, directly linking Sir2 to glucose metabolism, which could have implications for longevity. Six factors and Input ChIP-seq samples were analyzed in Saccharomyces eerevisiae.
2013-05-10 | E-GEOD-41415 | biostudies-arrayexpress
Project description:Sir2 and the homologous proteins, Hst1, Hst2, Hst3, and Hst4 from Saccharomyces cerevisiae are NAD+-dependent histone deacetylases of the sirtuin protein family. Sir2 functions in transcriptional silencing at the silent mating-type loci, telomeres, and rDNA locus, but also promotes replicative lifespan. To gain a better understanding of the chromatin-regulatory roles carried out by Sir2 and the Hst proteins, we performed ChIP-sequencing analysis on all five sirtuins and Sum1, the DNA binding partner for Hst1. Sir2, Hst1, and Sum1 were abundantly, and functionally co-enriched at several major targets, including the telomeric repeats, where they were required for maintaining proper telomere repeat length. At tRNA target genes they were required for efficient cohesin and condensin deposition. Across the open reading frames of glycolytic and ribosomal protein genes, Sir2 and Hst1 functioned in NAD+-dependent transcriptional repression at the diauxic shift, directly linking Sir2 to glucose metabolism, which could have implications for longevity.
2013-05-10 | GSE41415 | GEO