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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]

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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

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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

TT-Seq captures the human transient transcriptome

Project description:A large portion of the genome is transcribed but many of the resulting RNAs live only transiently and can generally not be mapped. Here we develop transient transcriptome sequencing (TT-Seq), a protocol that maps transcriptionally active regions in a nearly uniform manner and allows for unbiased monitoring of cellular RNA synthesis activity. Application of TT-Seq to human K562 cells recovers stable mRNAs and long intergenic non-coding RNAs, and additionally maps over 10,000 transient RNAs including enhancer RNAs, antisense RNAs, promoter-associated upstream antisense and convergent RNAs. TT-Seq also provides RNA half-lives, and reveals that transient RNAs are short and lack U1 motifs and secondary structure. TT-Seq further uncovers transcription termination sites and reveals a universal DNA motif for RNA polymerase II release.

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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.

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