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DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [TMP-seq]

ABSTRACT: DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [TMP-seq]

PROVIDER: PRJNA1205668 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31871221_1.fastq.gz	Fastqsanger.gz
	SRR31871221_2.fastq.gz	Fastqsanger.gz
	SRR31871222_1.fastq.gz	Fastqsanger.gz
	SRR31871222_2.fastq.gz	Fastqsanger.gz
	SRR31871223_1.fastq.gz	Fastqsanger.gz

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DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [TMP-seq]

Project description:Hypoxic stress responses are crucial for cellular and organismal survival and provoke gene regulation in diverse biological pathways including cell cycle progression and energy metabolism. Here, we identified that topoisomerase IIβ (TOP2B) regulates DNA topology and transcription in hypoxiainducible genes (HIGs) in a DNA-PK-dependent manner. Cellular, mutational, and genomic analyses showed antagonistic relation between TOP2B and DNA-PK. TOP2B associates with HIGs and represses transcription by suppressing negative supercoiling formation under normoxic conditions.Under hypoxia, TOP2B is released, whereas DNA-PK and HIF1a are recruited to and activate HIGs.Intriguingly, DNA-PK is responsible for TOP2B to be repressive because DNA-PK knockout overturns both TOP2B activity and release and increases the expression of a number of HIGs. Mutational and genomic analyses confirmed that DNA-PK phosphorylates TOP2B at T1403 to stimulate TOP2B catalysis for DNA topological relaxation, which is important for controlled HIG transcription. Collectively, our findings suggest a novel role of TOP2B and DNA-PK-mediated TOP2B regulation as important transcriptional elements in HIG expression. We propose that TOP2B catalysis modulated by protein phosphorylation is coordinated with transcriptional activation and determines DNA topology to stimulate Pol II transcription in response to hypoxic stresses.

2025-01-26 | GSE285699 | GEO

DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]

2025-01-26 | GSE285698 | GEO

DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]

Project description:DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]

| PRJNA1205669 | ENA

Integrative Structural Model of DNA-PK Synapsis

Project description:In non-homologous end joining repair of DNA double strand breaks, DNA dependent protein kinase catalytic subunit (DNA-PKcs) and Ku70/80 binds the free DNA ends forming the holoenzyme DNA-PK. DNA-PK synapses across the break to tether the broken ends in the initial long range synaptic complex. We generated an integrative structural model of DNA-PK synapsis at a precision of 13.5Å with crosslinking mass spectrometry (XL-MS) restraints. While our hydrogen deuterium exchange (HX) analysis revealed an allosteric axis in DNA-PK connecting DNA binding (including the plug domain) to the kinase domain. Our model presents a symmetrical synapsis primarily through head to head interactions and protection of the DNA by previously uncharacterized a plug domain. The offset of the DNA in our model allows access to downstream processing enzymes, while the combination of DNA binding and kinase loading creates a tensed state that could have roles in the re-arrangement/dissociation of DNA-PKcs as the repair process progresses.

2021-01-20 | PXD017931 | Pride

DNA topoisomerase and supercoil accumulation across yeast genome

Project description:DNA topoisomerases assist DNA replication & transcription events by controlling supercoiling alterations. We investigated supercoil distribution across the yeast genome and compared with the accumulation of RNA pol2 and DNA topoisomerases particularly in S-phase. Our data indicate that Top2 along with Hmo1 maintain negative supercoil at gene boundaries by stabilizing alternative DNA structures. To understand how DNA superhelical tension accumulates across the genome we have adopted previously described method [Naughton C et al., 2013] to budding yeast where a biotin molecule was attached to TMP via a linker (bTMP). The Chip on chip analysis for proteins was carried out as described (Bermejo R et al., 2009). For RNA-DNA hybrids DRIP-chip is carried out as described previously (Chan YA et al., 2014). Supercoiled regions are then compared with RNA pol2 (RPB3-chip), DNA Topoisomerase (Top1-chip) & RNA-DNA hybrid (DRIP-chip).

2018-07-02 | GSE114410 | GEO

Pleiotropic impact of DNA-PK in cancer and implications to therapeutic strategies

Project description:DNA-dependent protein kinase catalitic subunit (DNA-PK) is associated with aggressive disease. DNA-PK plays a role in transcriptional regulation of cancer-relevent pathways but it is not well understood. This study uses transcriptomic analyses to understand the transcriptional role of DNA-PK in castration resistent prostate cancer (CRPC) upon DNA-PK inhibition

2019-08-11 | GSE116765 | GEO

Haemming et al. A lncRNA integrates a DNA-PK-mediated DNA damage response and vascular senescence

Project description:Proteomic analysis on lncRNA associated proteins . Functional role of DNA-PK .

2019-10-04 | MSV000084424 | MassIVE

Chromosome end protection by RAP1-mediated inhibition of DNA-PK

Project description:During classical non-homologous end joining (cNHEJ), DNA-dependent protein kinase (DNA-PK) encapsulates free DNA ends, forming a recruitment platform for downstream end-joining factors including Ligase 4 (LIG4). DNA-PK can also bind telomeres, but does not initiate cNHEJ at this position. How the end joining process is regulated in this context-specific manner is currently unclear. Here we show that the Shelterin components TRF2 and RAP1 form a complex with DNA-PK that directly represses its end joining function at telomeres. Biochemical experiments and cryo-electron microscopy reveal that when bound to TRF2, RAP1 establishes a network of interactions with KU and DNA that prevents DNA-PK from recruiting LIG4. In cells, RAP1 is redundant with the APOLLO nuclease in repressing cNHEJ at chromosome ends, demonstrating that the inhibition of DNA-PK prevents telomere fusions in parallel with overhang-dependent mechanisms. Our experiments show that the end joining function of DNA-PK is specifically and directly repressed at telomeres, describing a molecular mechanism for the maintenance of individual linear chromosomes in mammalian cells.

2025-02-25 | PXD047643 | Pride

Selective DNA-PK inhibition enhances chemotherapy and ionizing radiation activity in soft-tissue sarcomas

Project description:Purpose: Patients with advanced soft-tissue sarcomas (STSs) exhibit a poor prognosis and have few therapeutic options. DNA-dependent protein kinase catalytic subunit (DNA-PK) is a multifunctional serine—threonine protein kinase that plays a crucial role in DNA double-strand damage repair via nonhomologous end joining (NHEJ). Experimental design: To investigate the therapeutic potential of DNA-PK targeting in STS, we first evaluated the prognostic value of DNA-PK expression in two large cohorts of patients with STS. We then used the potent and selective DNA-PK inhibitor AZD7648 compound to investigate the antitumor effect of the pharmacological inhibition of DNA-PK in vitro via MTT, apoptosis, cell cycle, and proliferation assays. In vivo studies were performed with patient-derived xenograft models to evaluate the effects of AZD7648 in combination with chemotherapy or ionizing radiation on tumor growth. The mechanisms of sensitivity and resistance to DNA-PK inhibition were investigated by using a genome-wide CRISPR-Cas9 positive screen. Results: DNA-PK overexpression is significantly associated with poor prognosis in patients with sarcomas. Selective pharmacological inhibition of DNA-PK strongly synergizes with radiation- and doxorubicin-based regimen in sarcoma models. By using a genome-wide CRISPR-Cas9 positive screen, we identified genes involved in sensitivity to DNA-PK inhibition. Conclusion: DNA-PK inhibition deserves clinical investigation to improve response to current therapies in patients with sarcoma

2023-09-25 | GSE243758 | GEO

Nucleosomal DNA has topological memory

Project description:Nucleosomal DNA has topological memory

| PRJNA950463 | ENA