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A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq]

ABSTRACT: A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq]

PROVIDER: PRJNA678751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13068917.fastq.gz	Fastqsanger.gz
	SRR13068918.fastq.gz	Fastqsanger.gz
	SRR13068919.fastq.gz	Fastqsanger.gz
	SRR13068920.fastq.gz	Fastqsanger.gz
	SRR13068921.fastq.gz	Fastqsanger.gz

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A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq]

Project description:The relationship between chromatin and transcription was investigated through condensin, a key regulator of higher order chromatin structure. We use rapid conditional condensin depletion in nocodozole arrested cells in budding yeast S. cerevisiae cells to study condensin’s role in transcriptional regulation. We use TT-Chemseq to assess global RNA levels through a S. pombe spike-in, and found that condensin depletion leads to upregulation of global transcription. We also found transcriptional changes in response to environmental stimuli are subdued by condensin depletion.

2021-05-21 | GSE161581 | GEO

A role for condensin in mediating transcriptional adaptation to environmental stimuli.

Project description:A role for condensin in mediating transcriptional adaptation to environmental stimuli.

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A role for condensin in mediating transcriptional adaptation to environmental stimuli. [RNA-Seq]

Project description:A role for condensin in mediating transcriptional adaptation to environmental stimuli. [RNA-Seq]

| PRJNA678750 | ENA

A role for condensin in mediating transcriptional adaptation to environmental stimuli. [RNA-Seq]

2021-05-21 | GSE161580 | GEO

A role for condensin in mediating transcriptional adaptation to environmental stimuli.

Project description:Nuclear organisation shapes gene regulation; however, the principles by which three-dimensional genome architecture influences gene transcription are incompletely understood. Condensin is a key architectural chromatin constituent, best known for its role in mitotic chromosome condensation. Yet at least a subset of condensin is bound to DNA throughout the cell cycle. Studies in various organisms have reported roles for condensin in transcriptional regulation, but no unifying mechanism has emerged. Here, we use rapid conditional condensin depletion in the budding yeast Saccharomyces cerevisiae to study its role in transcriptional regulation. We observe a large number of small gene expression changes, enriched at genes located close to condensin-binding sites, consistent with a possible local effect of condensin on gene expression. Furthermore, nascent RNA sequencing reveals that transcriptional down-regulation in response to environmental stimuli, in particular to heat shock, is subdued without condensin. Our results underscore the multitude by which an architectural chromosome constituent can affect gene regulation and suggest that condensin facilitates transcriptional reprogramming as part of adaptation to environmental changes.

| S-EPMC8200293 | biostudies-literature

A role for condensin in mediating transcriptional adaptation to environmental stimuli.

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

2021-05-21 | GSE161582 | GEO

Project description:tt

| PRJEB51254 | ENA

Condensin II complex mediates interactions of histone gene loci

Project description:Condensin complexes are known for their importance in chromosome condensation during mitosis. However, condensin II binds to the geome during interphase as well. The role of condensin II in genome organization in mammalian interphase nuclei is not characterized. Since condensin II binds to the promoters of the transcriptionally active promoters in interphase genome, the aim of this study is to uncover its role in mediating chromatin interactions between active gene promoters such as histone gene loci.

2017-06-01 | GSE80219 | GEO

Condensin II Activation by the centromeric protein M18BP1

Project description:Condensin I and condensin II promote drastic spatial compaction (condensation) of the genome upon mitotic entry. Condensin I binds chromatin only after dissolution of the nuclear envelope in prophase. Conversely, condensin II is nuclear throughout the cell cycle and initiates chromosome condensation. Previous studies demonstrated that MCPH1 inhibits condensin II to prevent chromosome condensation during interphase. Mechanisms that promote condensin II activation in early mitosis likely exist but are currently unknown. Through genetic and proteomic approaches, we identify M18BP1, a protein previously associated with centromere identity, as a factor required for condensin II localization to chromatin during mitosis. To activate and localize condensin II, M18BP1 directly binds the CAP-G2 subunit. M18BP1 and MCPH1 compete for CAP-G2 binding, and CDK1 phosphorylation promotes replacement of MCPH1 with M18BP1 to activate condensin II upon mitotic entry. Our results identify a fundamental and evolutionarily conserved mechanism of condensin II activation.

2025-07-09 | PXD051886 | Pride

Environmental interactions and epistasis are revealed in the proteomic responses to complex stimuli

Project description:Ultimately, the genotype of a cell and its interaction with the environment determine the cell’s biochemical state. While the cell’s response to a single stimulus has been studied extensively, a conceptual framework to model the effect of multiple environmental stimuli applied concurrently is not as well developed. In this study, we developed the concepts of environmental interactions and epistasis to explain the responses of the S. cerevisiae proteome to simultaneous environmental stimuli. We hypothesize that, as an abstraction, environmental stimuli can be treated as analogous to genetic elements. This would allow modeling of the effects of multiple stimuli using the concepts and tools developed for studying gene interactions. Mirroring gene interactions, our results show that environmental interactions play a critical role in determining the state of the proteome. We show that individual and complex environmental stimuli behave similarly to genetic elements in regulating the cellular responses to stimuli, including the phenomena of dominance and suppression. Interestingly, we observed that the effect of a stimulus on a protein is dominant over other stimuli if the response to the stimulus involves the protein. Using publicly available transcriptomic data, we find that environmental interactions and epistasis regulate transcriptomic responses as well.

2015-07-20 | PXD002371 | Pride

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