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Global Run-On sequencing (GRO-seq) of HeLa cells under CDK9 inhibitor tratment to study elongation checkpoints at both ends of RNA polymerase II-transcribed genes.

ABSTRACT: Global Run-On sequencing (GRO-seq) of HeLa cells under CDK9 inhibitor tratment to study elongation checkpoints at both ends of RNA polymerase II-transcribed genes.

PROVIDER: PRJEB8651 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR769522_1.fastq.gz	Fastqsanger.gz
	ERR769522_2.fastq.gz	Fastqsanger.gz
	ERR769523_1.fastq.gz	Fastqsanger.gz
	ERR769523_2.fastq.gz	Fastqsanger.gz
	ERR769524_1.fastq.gz	Fastqsanger.gz

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Global Run-On sequencing (GRO-seq) of HeLa cells under CDK9 inhibitor tratment to study elongation checkpoints at both ends of RNA polymerase II-transcribed genes.

Project description:Global Run-On sequencing (GRO-seq) was carried out on nuclei isolated from HeLa cells after 30 minutes of treatment with CDK9 inhibitors KM05382 and DRB and from two untreated controls. Libraries of nascent RNAs were generated and sequenced using Illumina Hi-seq technology. GRO-seq reads were processed, deduplicated, mapped to human genome and normalised to reads in the 5’ ETS of the 45S rRNA gene.

2015-02-26 | E-MTAB-3360 | biostudies-arrayexpress

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes.

Project description:Transcription through early-elongation checkpoints requires phosphorylation of negative transcription elongation factors (NTEFs) by the cyclin-dependent kinase (CDK) 9. Using CDK9 inhibitors and global run-on sequencing (GRO-seq), we have mapped CDK9 inhibitor-sensitive checkpoints genome wide in human cells. Our data indicate that early-elongation checkpoints are a general feature of RNA polymerase (pol) II-transcribed human genes and occur independently of polymerase stalling. Pol II that has negotiated the early-elongation checkpoint can elongate in the presence of inhibitors but, remarkably, terminates transcription prematurely close to the terminal polyadenylation (poly(A)) site. Our analysis has revealed an unexpected poly(A)-associated elongation checkpoint, which has major implications for the regulation of gene expression. Interestingly, the pattern of modification of the C-terminal domain of pol II terminated at this new checkpoint largely mirrors the pattern normally found downstream of the poly(A) site, thus suggesting common mechanisms of termination.

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Unique vulnerability of RAC1-mutant melanoma to combined inhibition of CDK9 and immune checkpoints

Project description:Unique vulnerability of RAC1-mutant melanoma to combined inhibition of CDK9 and immune checkpoints

| PRJNA1042851 | ENA

A PP2A-Integrator complex fine-tunes transcription by opposing CDK9

Project description:Gene expression by RNA Polymerase II (RNAPII) is tightly controlled by Cyclindependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The RNAPII pausing checkpoint, engaged after transcription initiation, is controlled by CDK9 to regulate transcription in metazoans. We discovered that CDK9-mediated RNAPII pause-release is functionally opposed by a protein phosphatase 2A (PP2A) complex. PP2A dynamically competes for key CDK9 substrates, DSIF and RNAPIICTD, and is recruited to transcription pausing sites by the Integrator complex subunit INTS6. INTS6 depletion confers resistance to CDK9 inhibition in a variety of normal and tumor cell lines. Loss of INTS6 abolishes the Integrator-PP2A association leading to unrestrained CDK9 activity, which amplifies transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill MLLrearranged leukemias and solid tumors and provide therapeutic benefit in vivo. These data demonstrate that finely-tuned gene expression relies on the balance of kinase and phosphatase activity at the pausing checkpoint.

2022-08-12 | PXD022962 | Pride

Unique vulnerability of RAC1-mutant melanoma to combined inhibition of CDK9 and immune checkpoints

Project description:RAC1P29S is the third most prevalent hotspot mutation in sun-exposed melanoma. RAC1 alterations in cancer are correlated with poor prognosis, resistance to standard chemotherapy, and insensitivity to targeted inhibitors. Although RAC1P29S mutations in melanoma and RAC1 alterations in several other cancers are increasingly evident, the RAC1-driven biological mechanisms contributing to tumorigenesis remain unclear. Lack of rigorous signaling analysis has prevented identification of alternative therapeutic targets for RAC1P29S-harboring melanomas. To investigate the RAC1P29S-driven effect on downstream molecular signaling pathways, we generated an inducible RAC1P29S expression melanocytic cell line and performed RNA-sequencing (RNA-seq) coupled with multiplexed kinase inhibitor beads and mass spectrometry (MIBs/MS) to establish enriched pathways from the genomic to proteomic level. Our proteogenomic analysis identified CDK9 as a potential new and specific target in RAC1P29S-mutant melanoma cells.In vitro, CDK9 inhibition impeded the proliferation of in RAC1P29S-mutant melanoma cells and increased surface expression of PD-L1 and MHC Class I proteins.In vivo, combining CDK9 inhibition with anti-PD-1 immune checkpoint blockade significantly inhibited tumor growthonly in melanomas that expressed the RAC1P29Smutation. Collectively, these results establish CDK9 as a novel target in RAC1-driven melanoma that can further sensitize the tumor to anti-PD-1 immunotherapy.

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A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [3UTR-seq]

Project description:Gene expression by RNA Polymerase II (RNAPII) is tightly controlled by Cyclin-dependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The RNAPII pausing checkpoint, engaged after transcription initiation, is controlled by CDK9 to regulate transcription in metazoans. We discovered that CDK9-mediated RNAPII pause-release is functionally opposed by a protein phosphatase 2A (PP2A) complex. PP2A dynamically competes for key CDK9 substrates, DSIF and RNAPII-CTD, and is recruited to transcription pausing sites by the Integrator complex subunit INTS6. INTS6 depletion confers resistance to CDK9 inhibition in a variety of normal and tumor cell lines. Loss of INTS6 abolishes the Integrator-PP2A association leading to unrestrained CDK9 activity, which amplifies transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill MLL-rearranged leukemias and solid tumors and provide therapeutic benefit in vivo. These data demonstrate that f inely-tuned gene expression relies on the balance of kinase and phosphatase activity at the pausing checkpoint.

2021-05-23 | GSE163802 | GEO

A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [ChIP-seq]

2021-05-23 | GSE163804 | GEO

A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 [4sU-seq]

2021-05-23 | GSE163803 | GEO

Profiling active transcription in MDA-MB-231 cells using global run-on assays (GRO-seq)

Project description:GRO-seq was performed to identify transcribed RNAs in MDA-MB-231 cells.

2023-02-15 | GSE186641 | GEO

Expression profiling of HeLa cell line treated with CDK9 inhibitor

Project description:CDK9 is the kinase subunit of P-TEFb that enables RNA polymerase (Pol) II to transit from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to the lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9’s activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb’s loss of activity, only the simultaneous inhibition of CDK9 and MYC can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy. We used microarrays to examine the global impact on gene expression by imhibiting CDK9 at different time durations. HeLa cell lines treated with CDK9 inhibitor at different time points

2015-06-17 | E-GEOD-60952 | biostudies-arrayexpress

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