The budding yeast heterochromatic protein Sir3 modulates genome-wide gene expression through transient direct contacts with euchromatin
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE246043 | GEO | 2025/10/20
REPOSITORIES: GEO
Similar Datasets
Project description:The SIR complex (Silent Information Regulator) is the building block of heterochromatic structures that silence underlying genes. It is well established that the silenced state is epigenetically inherited but it is not known how the SIR complex is maintained through cell divisions in optimal or variable growth conditions. The biological function of heterochromatin located in subtelomeric regions is also unclear since heterochromatin coverage appears to be limited to a few kbps near chromosome ends and the expression of subtelomeric genes is only marginally affected in the absence of the SIR complex. We use a three-pronged approach to address these questions. First, Nanopore-MetID, an in vivo foot printing technique similar to DamID that uses nanopore sequencing technology, identified over a thousand new transient contacts between Sir3 and euchromatic genes that are not detectable by ChIP-seq and revealed a previously undocumented low-density mode of Sir3 binding to subtelomeric regions that extends 15kbps downstream of subtelomeric SIR nucleation sites. Second, our measurements of genome-wide Sir3 exchange rates after exit from starvation show that heterochromatin is a highly dynamic structure in optimal growth conditions. Third, “spike-in” RNA-seq time course experiments in the same conditions reveal that Sir3 modulates global mRNA levels in correlation with fluctuations in nutrient availability. We now propose that subtelomeric regions serve as Sir3 hubs from which Sir3 is brought over to distal sites down the chromosome arm where it transiently contacts euchromatic genes in its path. We hypothesize that contacts between Sir3 and actively transcribed genes facilitate the removal of stalled transcription complexes and allow for optimal genome-wide transcription, which gives wt cells a competitive advantage over sir3Δ cells when nutrients are limited.
2025-10-20 | GSE246042 | GEO
Project description:The SIR complex (Silent Information Regulator) is the building block of heterochromatic structures that silence underlying genes. It is well established that the silenced state is epigenetically inherited but it is not known how the SIR complex is maintained through cell divisions in optimal or variable growth conditions. The biological function of heterochromatin located in subtelomeric regions is also unclear since heterochromatin coverage appears to be limited to a few kbps near chromosome ends and the expression of subtelomeric genes is only marginally affected in the absence of the SIR complex. We use a three-pronged approach to address these questions. First, Nanopore-MetID, an in vivo foot printing technique similar to DamID that uses nanopore sequencing technology, identified over a thousand new transient contacts between Sir3 and euchromatic genes that are not detectable by ChIP-seq and revealed a previously undocumented low-density mode of Sir3 binding to subtelomeric regions that extends 15kbps downstream of subtelomeric SIR nucleation sites. Second, our measurements of genome-wide Sir3 exchange rates after exit from starvation show that heterochromatin is a highly dynamic structure in optimal growth conditions. Third, “spike-in” RNA-seq time course experiments in the same conditions reveal that Sir3 modulates global mRNA levels in correlation with fluctuations in nutrient availability. We now propose that subtelomeric regions serve as Sir3 hubs from which Sir3 is brought over to distal sites down the chromosome arm where it transiently contacts euchromatic genes in its path. We hypothesize that contacts between Sir3 and actively transcribed genes facilitate the removal of stalled transcription complexes and allow for optimal genome-wide transcription, which gives wt cells a competitive advantage over sir3Δ cells when nutrients are limited.
2025-10-20 | GSE246041 | GEO
Project description:The budding yeast heterochromatic protein Sir3 modulates genome-wide gene expression through transient direct contacts with euchromatin
| PRJNA1031167 | ENA
Project description:The budding yeast heterochromatic protein Sir3 modulates genome-wide gene expression through transient direct contacts with euchromatin (ChIP-Seq)
| PRJNA1031170 | ENA
Project description:The budding yeast heterochromatic protein Sir3 modulates genome-wide gene expression through transient direct contacts with euchromatin (RNA-Seq)
| PRJNA1031171 | ENA
Project description:We have previously shown that yeast TFIID provides coactivator function on the promoters of ribosomal protein-encoding genes (RPGs) by making direct contact with the transactivator repressor activator protein 1 (Rap1). Further, our structural studies of assemblies generated with purified Rap1, TFIID, and TFIIA on RPG enhancer-promoter DNA indicate that Rap1-TFIID interaction induces dramatic conformational rearrangements of enhancer-promoter DNA and TFIID-bound TFIIA. These data indicate a previously unknown yet critical role for yeast TFIIA in the integration of activator-TFIID contacts with promoter conformation and downstream preinitiation complex formation and/or function. Here we describe the use of systematic mutagenesis to define how specific TFIIA contacts contribute to these processes. We have verified that TFIIA is required for RPG transcription in vivo and in vitro, consistent with the existence of a critical Rap1-TFIIA-TFIID interaction network. We also identified essential points of contact for TFIIA and Rap1 within the Rap1 binding domain of the Taf4 subunit of TFIID. These data suggest a mechanism for how interactions between TFIID, TFIIA, and Rap1 contribute to the high rate of transcription initiation seen on RPGs in vivo.
| S-EPMC3743499 | biostudies-literature
Project description:Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3-5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between distant regions, including the rDNA, telomeres, and internal Sir3-bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach, we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, Sir4), Sir2 activity, or chromosome context. Altogether, these data suggest that Sir3 acts as a molecular bridge that stabilizes long-range interactions.
| S-EPMC7919453 | biostudies-literature
Project description:Chromatin domains are believed to spread via a polymerization-like mechanism in which modification of a given nucleosome recruits a modifying complex, which can then modify the next nucleosome in the polymer. In this study, we carry out genome-wide mapping of the Sir3 component of the Sir silencing complex in budding yeast during a time course of establishment of heterochromatin. Sir3 localization patterns do not support a straightforward model for nucleation and polymerization, instead showing strong but spatially delimited binding to silencers, and weaker and more variable Ume6-dependent binding to novel secondary recruitment sites at the seripauperin (PAU) genes. Genome-wide nucleosome mapping revealed that Sir binding to subtelomeric regions was associated with overpackaging of subtelomeric promoters. Sir3 also bound to a surprising number of euchromatic sites, largely at genes expressed at high levels, and was dynamically recruited to GAL genes upon galactose induction. Together, our results indicate that heterochromatin complex localization cannot simply be explained by nucleation and linear polymerization, and show that heterochromatin complexes associate with highly expressed euchromatic genes in many different organisms.
| S-EPMC3061035 | biostudies-literature
Project description:Chromatin immunoprecipitation of Sir3 applied with tilling array chip ( ChIP on chip of Sir3) analysis demonstrated that Changes of conventional and dynamical Genome-wide localization of Sir3 in Saccharomyces cerevisiae during different growth stages
2013-07-01 | GSE39437 | GEO
Project description:Chromatin immunoprecipitation of Sir3 applied with tilling array chip ( ChIP on chip of Sir3) analysis demonstrated that Changes of conventional and dynamical Genome-wide localization of Sir3 in Saccharomyces cerevisiae during different growth stages comparison the genome-wide localization of Sir3 of logarithmic phase younger cells vs of stationary phase older cells
2013-07-01 | E-GEOD-39437 | biostudies-arrayexpress