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Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in HEK-293T Cells

ABSTRACT: Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in HEK-293T Cells

PROVIDER: PRJEB73859 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12743900_1.fastq.gz	Fastqsanger.gz
	ERR12743900_2.fastq.gz	Fastqsanger.gz
	ERR12743901_1.fastq.gz	Fastqsanger.gz
	ERR12743901_2.fastq.gz	Fastqsanger.gz
	ERR12743902_1.fastq.gz	Fastqsanger.gz

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Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in HEK-293T Cells

Project description:Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. We systematically engineered light-inducible transcription factor condensates with different material properties and analyzed their influence on transcription activation. When transcription factor condensates were transformed into solid-like gels, we observed a reduced activation of gene expression. We wanted to evaluate the impact that the condensate formation of the transcription factor RelA had on its endogenous promoters using expression data. To this aim, HEK-293T cells were transfected either with empty vector (1-3) or eGFP-RelA (4-6) or eGFP-RelA, Cry2olig-mCh-FUSN-NLS-NbGFP and Cry2olig-mCh-FUSN-NLS, along with an NF-κB-responsive SEAP reporter (7-9). In each of the three groups of transfected cells, 8 h after transfection, 3 samples were kept in the dark (D) and 3 under blue light illumination (BL, 5 μmol m-² s-1) for 24 h prior to RNA extraction. RNA-seq libraries from the 18 samples were sequenced by BGI on a DNBSEQ platform using paired-end chemistry with a read length of 100 base pairs each. Each strand was sequenced across two separate lanes (L03, L04), generating a total of 4 FASTQ files per sample.

2024-04-01 | E-MTAB-13905 | biostudies-arrayexpress

Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

Project description:It remains largely unclear how material properties of biomolecular condensates impact physiological and pathological processes such as cancer. Here we show that AKAP95, a nuclear protein involved in gene regulation, plays an important role in tumorigenesis through directly regulating mRNA splicing. We show that AKAP95, through an intrinsic disordered region (IDR), forms liquid-like droplets in vitro and dynamic foci in nucleus. We have also identified key residues in IDR whose mutations to different residues perturb AKAP95 condensation in opposite directions. Importantly, the biological activity of AKAP95 in splice regulation is affected by either disruption of liquid condensation or enhancing the gelation of the assembly. We then show that the ability of AKAP95 in overcoming oncogene-induced senescence requires AKAP95 in an appropriate window of liquidity. These results thus link phase separation to tumorigenesis and uncover an important role of regulating the material property of protein condensates in disease including cancer.

2020-05-06 | GSE122308 | GEO

nsp1 acts on HEK-293T

Project description:nsp1 acts on HEK-293T

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Tumorigenic effects of TLX over-expression in HEK 293T cells

Project description:Transcriptomic profiling to investigate the effect of TLX overexpression with an inducible vector system in the HEK 293T cell line

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Effect of depletion of C17orf80 on mtDNA transcription in HEK-293T cells

Project description:Effect of depletion of C17orf80 on mtDNA transcription in HEK-293T cells

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DNA methylation profiling for HEK-293T cells transfected with GFP and DMEΔ

Project description:Methylome data obtained from human embryonic kindey (HEK)-293T cells expressing a GFP (293T-GFP) or a truncated form of Arabidopsis DEMETER (DME) 5-methylcytosine (5mC) DNA glycosylase (293T-DMEΔ) analyzed on a Human Methylation 450K BeadChip platform (Illumina). These methylation array data revealed genome-wide DNA methylation patterns of the 293T-GFP cells (without direct 5mC excision activity) and 293T-DMEΔ cells (with artificially implemented direct 5mC excision activity).

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ASFV I73R acts on HEK-293T

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Role of BACH1 in HEK 293T cells

Project description:This SuperSeries is composed of the following subset Series: GSE28050: Expression data from knockdown of BACH1 in HEK 293T cells GSE28051: Genome-wide map of BACH1 binding in HEK293T cells Refer to individual Series

2011-05-12 | E-GEOD-28053 | biostudies-arrayexpress

Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

Project description:Material properties of biomolecular condensates regulates RNA splicing and tumorigenesis

| PRJNA504562 | ENA

Gene expression data for HEK-293T cells transfected with GFP control and plant derived DNA demethylase DMEΔ

Project description:Expression profiles of human embryonic kidney (HEK)-293T cells expressing a GFP (293T-GFP) or a truncated form of Arabidopsis DEMETER (DME) 5-methylcytosine (5mC) DNA glycosylase (293T-DMEΔ) analyzed on an Affymetrix Human Genome U133 Plus 2.0 Array Platform. These array data revealed differentially expressed genes (DEGs) between the 293T-GFP cells (without direct 5mC excision activity) and 293T-DMEΔ cells (with artificially implemented direct 5mC excision activity).

2017-09-20 | GSE96863 | GEO

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