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MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq & DRIP-seq)

ABSTRACT: MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq & DRIP-seq)

PROVIDER: PRJNA1087397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28336000.fastq.gz	Fastqsanger.gz
	SRR28336001.fastq.gz	Fastqsanger.gz
	SRR28336002.fastq.gz	Fastqsanger.gz
	SRR28336003.fastq.gz	Fastqsanger.gz
	SRR28336004.fastq.gz	Fastqsanger.gz

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Similar Datasets

MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq & DRIP-seq)

Project description:MePCE is a multifunctional protein that regulates the Positive Transcription Elongation Factor b (P-TEFb) partitioning between the nucleosol and chromatin. While the role of MePCE in sequestering P-TEFb in the nucleoplasm through the 7SK ribonuclear protein complex (RNPc) is well understood, its functions on chromatin remain obscure. In order to address this gap in our knowledge, we performed mass spectrometry of MePCE interactors on chromatin. Our analysis revealed that chromatin-associated-MePCE mainly interacts with factors involved in R-loop processing and DNA repair factors. Consistent with this initial finding, MePCE is rapidly recruited to laser-mediated DNA damage and AsiSI-mediated DNA double stranded breaks (DSBs). Moreover, MePCE depletion specifically impairs DSB repair by homologous recombination (HR). To explore the molecular mechanism behind the observed HR defect, we took advantage of an inducible AsiSI system to analyze the effect of MePCE depletion in DSB repair factor recruitment and R-loop levels at over 100 genomic site-specific DSBs. Consistent with impaired HR, MePCE depletion decreases RAD51 loading and enhances R-loop levels specifically at DSBs. Analysis of R-loop protein complexes by mass spectrometry revealed that in addition to decreasing specific R-loop processing factors and chromatin remodelers, MePCE depletion increased the interaction with R-loops of the other constitutive member of the 7SK RNPc, LARP7, which is degraded by BRCA1/BARD1 upon DSB. Overall, our results uncover dynamic regulation of the 7SK RNPc at DSBs during the repair process and explain the recently observed synthetic lethality of MePCE and BRCA1 deficiency.

2025-05-23 | GSE261535 | GEO

MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq)

2025-05-23 | GSE289797 | GEO

MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (RNA-Seq)

2025-05-23 | GSE289796 | GEO

MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq)

Project description:MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq)

| PRJNA1224821 | ENA

MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (RNA-Seq)

Project description:MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (RNA-Seq)

| PRJNA1224822 | ENA

LARP3, LARP7, and MePCE are Involved in the Early Stage of Human Telomerase RNA Biogenesis

Project description:Human telomerase assembly is a highly dynamic process. Using biochemical approaches, we found that LARP3 and LARP7/MePCE are involved in the early stage and that their binding to hTR is destabilized when the mature hTR is produced. LARP3 plays a negative role in preventing the processing of the 3′-extended long (exL) form and binding of LARP7 and MePCE. Interestingly, the tertiary structure of the exL form prevents LARP3 binding and facilitates hTR biogenesis. Supporting this process, LARP3 at low levels promotes hTR maturation, increases telomerase activity, and elongates telomeres. LARP7 and MePCE knockdown inhibits the conversion of the 3′-extended short (exS) form into mature hTR and the cytoplasmic accumulation of hTR, resulting in telomere shortening. Our data suggest that LARP3 and LARP7/MePCE mediate the processing of hTR precursors and thus control the production of functional telomerase.

2024-07-25 | GSE262590 | GEO

DRIP-sequencing U2OS

Project description:DRIP-sequencing U2OS

| PRJNA533125 | ENA

Senataxin resolves R-loops forming at DNA double strand breaks to prevent translocations

Project description:DNA Double Strands Breaks (DSBs) are highly detrimental since they can lead to mutations and chromosomes rearrangements (amplification, deletion, translocation and chromosome loss). Here, we set to assess the role of senataxin, a RNA:DNA helicase involved in the regulation of transcription and the maintenance of genome integrity, at sites of DNA Double Strand Breaks. We performed ChIP-Seq mapping of senataxin before and after damage, genome-wide DNA:RNA hybrids (DRIP) mapping before and after damage. We also performed RNA-Seq and RNA pol II mapping (total and phosphorylated on serine 2 of the CTD) by ChIP-Seq in undamaged cells to discriminate between damage in active versus inactive regions.

2018-02-20 | E-MTAB-6318 | biostudies-arrayexpress

Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin

Project description:The switch of RNAP II from the paused to the productive transcription elongation state is a pivotal regulatory step requiring specific phosphorylations catalyzed by the P-TEFb kinase. Nucleosolic P-TEFb activity is inhibited by its interaction with the ribonuclear protein complex built around the 7SK small nuclear RNA (7SK snRNP). MePCE is the RNA methyltransferase that methylates and stabilizes 7SK in the nucleosol. Here we report that MePCE also binds chromatin through the tail of histone H4 to serve as a P-TEFb activator at specific genes important for cellular identity. Notably, this histone binding abolishes MePCE’s RNA methyltransferase activity towards 7SK, explaining why MePCE-bound P-TEFb on chromatin may not be associated with the full 7SK snRNP and is competent for RNAP II activation. Overall, our results suggest that a crosstalk between the histone binding and RNA methylation activities of MePCE regulates P-TEFb activation on chromatin in a 7SK- and Brd4-independent manner.

2018-02-05 | GSE108830 | GEO

DRIP-seq files for: DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci

Project description:Determining the role of DDX17 in the formation of DNA:RNA-hybrids around active DNA double-strand breaks (DSBs) using DRIP-seq in the damaged induced via AsiSI (DIvA) cell system that induced DSBs at known genomic loci in response to hydroxytamoxifen (OHT) treatment via and AsiSI enzyme fused to an oestrogen receptor. Sequencing was done using either control or DDX17 siRNA, and mock or 4 hours 300nM OHT treatment. Paired-end 150 cycles was completed on an Illumina NextSeq 500 and library prep was completed using the NEB NEBNext Ultra II library prep kit.

2022-11-08 | E-MTAB-10814 | biostudies-arrayexpress

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