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The intrinsically disordered region of the E3 ubiquitin ligaseTRIP12 induces the formation of chromatin condensates and interferes withDNA damage response.

ABSTRACT: The intrinsically disordered region of the E3 ubiquitin ligaseTRIP12 induces the formation of chromatin condensates and interferes withDNA damage response.

PROVIDER: PRJNA1038777 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26784755_1.fastq.gz	Fastqsanger.gz
	SRR26784755_2.fastq.gz	Fastqsanger.gz
	SRR26784756_1.fastq.gz	Fastqsanger.gz
	SRR26784756_2.fastq.gz	Fastqsanger.gz
	SRR26784757_1.fastq.gz	Fastqsanger.gz

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The intrinsically disordered region of the E3 ubiquitin ligaseTRIP12 induces the formation of chromatin condensates and interferes withDNA damage response.

Project description:Chromatin compaction is crucial for the expression and the integrity of the genome. We previously showed that the nuclear HECT-type E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) is tightly associated to chromatin. Overexpressed in several types of cancers, we explored herein the consequences of TRIP12 overexpression on chromatin homeostasis. First, we established the proxisome of TRIP12 by BioID and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that an overexpression of TRIP12, via its intrinsically disordered region, leads to the formation of chromatin condensates enriched in heterochromatin epigenetic marks. We further discovered that the formation of TRIP12 mediated-chromatin condensates is highly dynamic and driven by a mechanism of polymer-polymer phase separation (PPPS). Chromatin condensates formation is dependent not only on the concentration, the length of TRIP12-IDR but also electrostatic interactions. Chromatin compaction is a determinant parameter in several biological processes. Indeed, we measured that the formation of TRIP12 mediated-chromatin condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response (DDR) by inhibiting the accumulation of Mediator DNA Damage Checkpoint (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular processes.

2023-11-11 | GSE247490 | GEO

The intrinsically disordered region of the E3 ubiquitin ligase TRIP12 induces the formation of chromatin condensates and interferes with DNA damage response.

Project description:The intrinsically disordered region of the E3 ubiquitin ligase TRIP12 induces the formation of chromatin condensates and interferes with DNA damage response.

| PRJNA1013901 | ENA

Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq datasets)

Project description:RNA granules are cellular condensates that contain RNAs and proteins. The mechanism that drive the recruitment of many mRNAs to RNA granules are not fully understood. Here we characterize the assembly and transcriptome of the germ (P) granules of C. elegans. We find that mRNAs are recruited into P granules by condensation with the intrinsically-disordered protein MEG-3. MEG-3 binds ~500 mRNAs in C. elegans embryos in a sequence-independent manner that favors mRNAs with low ribosome coverage. Translational stress causes additional mRNAs to localize to P granules and translational activation correlates with P granule exit for two mRNAs coding for germ cell fate regulators. MEG-3/RNA condensates assembled in vitro are gel-like and trap mRNAs in a non-dynamic state. Our observations reveal similarities between P granules and stress granules and identify gelation with intrinsically-disordered proteins as a sequence-independent mechanism to enrich low-translation mRNAs in RNA granules

2019-12-01 | GSE139879 | GEO

Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (iCLIP results)

2019-12-01 | GSE139878 | GEO

Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq and ribosome profiling)

2019-12-01 | GSE139880 | GEO

An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq]

Project description:Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBalpha, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse Liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBalpha condensates are located at high-order transcriptional repressive hubs in the Liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBalpha. This work demonstrates physiological circadian protein condensates containing REV-ERBalpha whose IDR is required for hub formation and the control of rhythmic gene expression.

2024-11-05 | GSE242901 | GEO

Androgen receptor condensates as drug targets

Project description:Transcription factors are among the most attractive therapeutic targets but are considered largely undruggable. Here we provide evidence that small molecule-mediated partitioning of the androgen receptor, an oncogenic transcription factor, into phase-separated condensates has therapeutic effect in prostate cancer. We show that the phase separation capacity of the androgen receptor is driven by aromatic residues and short unstable helices in its intrinsically disordered activation domain. Based on this knowledge, we developed tool compounds that covalently attach aromatic moieties to cysteines in the receptors’ activation domain. The compounds enhanced partitioning of the receptor into condensates, facilitated degradation of the receptor, inhibited androgen receptor-dependent transcriptional programs, and had antitumorigenic effect in mouse models of prostate cancer and castration resistant prostate cancer. These results establish a generalizable framework to target the phase-separation capacity of intrinsically disordered regions in oncogenic transcription factors and other disease-associated proteins with therapeutic intent.

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Multiple regulatory intrinsically disordered motifs control FOXO4 transcription factor binding and function

Project description:Transcription factors harbour defined intrinsically disordered regulatory regions, which raises the question of how they mediate binding to structured co-regulators and how this regulates activity. Here, we present a detailed molecular regulatory mechanism of Forkhead box O4 (FOXO4) by the structured transcriptional co-regulator β-catenin. We find that the largely disordered FOXO4 C-terminal region, which contains its transactivation domain binds β-catenin through two defined interaction sites, and this is regulated by combined PKB/AKT- and CK1-mediated phosphorylation. Binding of β-catenin competes with the auto-inhibitory interaction of the FOXO4 disordered region with its DNA-binding forkhead domain, and thereby enhances FOXO4 transcriptional activity. Furthermore, we show that binding of the β-catenin inhibitor protein ICAT is compatible with FOXO4 binding to β-catenin, suggesting that ICAT acts as a molecular switch between anti-proliferative FOXO and pro-proliferative Wnt/TCF/LEF signalling. Together these data illustrate how the interplay of intrinsically disordered regions, post-translational modifications and co-factor binding contribute to transcription factor function. Highlights • The interaction network between FOXO4 and β-catenin was deciphered • FOXO4 auto-inhibition interferes with DNA binding and is counter-acted by β-catenin • FOXO4 exists in multiple conformations regulated by phosphorylation and co-factors • ICAT switches between FOXO4 and TCF/LEF transcription factors

2022-04-15 | PXD026263 | Pride

Synthetic biomolecular condensates enhance translation from a target mRNA in living cells

Project description:Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here, we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain, and a synthetic intrinsically disordered protein, an elastin-like polypeptide, that can bind and sequester a target mRNA transcript. In protocells, sequestration of a target mRNA largely limits its translation. Conversely, in E. Coli, sequestration of the same target mRNA increases its translation. We characterize the Pum2-ELP condensate system using microscopy, biophysical and biochemical assays, and RNA-seq. This approach enables modulation of cell function via the formation of synthetic biomolecular condensates that upregulate the expression of a target protein.

2024-11-30 | GSE277409 | GEO

Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria

Project description:Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria

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