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

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

PROVIDER: PRJNA678750 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13068900.fastq.gz	Fastqsanger.gz
	SRR13068901.fastq.gz	Fastqsanger.gz
	SRR13068902.fastq.gz	Fastqsanger.gz
	SRR13068903.fastq.gz	Fastqsanger.gz
	SRR13068904.fastq.gz	Fastqsanger.gz

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

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

| PRJNA678745 | ENA

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

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

| PRJNA678751 | ENA

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. [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

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 plays a role in both interphase nuclei and premature chromosome condensation

Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.

2017-05-03 | E-GEOD-74892 | biostudies-arrayexpress

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

Genome-wide analysis of condensin binding sites in vertebrate genome

Project description:The condensin complex is well known to be essential for correct packaging and segregation of chromosomes during mitosis and meiosis in all eukaryotes. To date, the genome wide location and the nature of condensin binding sites has remained elusive in vertebrate systems. A detailed knowledge of condensin binding sites is essential to understand the as-yet enigmatic function of this complex and to define its greater role in chromosome architecture. To address this, we have used next generation sequencing to map condensin I in chicken DT40 cells. Unexpectedly, we found condensin I binds predominately to promoter sequences in mitotic cells. We also found a striking enrichment at both centromeres and telomeres, highlighting the importance of the complex in chromosome segregation. Taken together, the results show condensin I is largely absent from heterochromatic regions. These results reveal for the first time the condensin I binding sites in the vertebrate genome, and demonstrate the importance of the complex in genome segregation and suggest a novel function in gene regulation. Condensin associated DNA from chicken DT40 cells were affinity purified using streptavidin and deep sequenced by Illumina Hiseq2000

2013-10-03 | E-GEOD-45552 | biostudies-arrayexpress

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