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Chemo- versus immuno-precipitation of G-quadruplex-DNA (G4- DNA): a direct comparison of the efficiency of the antibody BG4 versus the small-molecule ligands TASQs for G4 affinity capture

ABSTRACT: Chemo- versus immuno-precipitation of G-quadruplex-DNA (G4- DNA): a direct comparison of the efficiency of the antibody BG4 versus the small-molecule ligands TASQs for G4 affinity capture

PROVIDER: PRJNA823482 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18614800_1.fastq.gz	Fastqsanger.gz
	SRR18614800_2.fastq.gz	Fastqsanger.gz
	SRR18614801_1.fastq.gz	Fastqsanger.gz
	SRR18614801_2.fastq.gz	Fastqsanger.gz
	SRR18614802_1.fastq.gz	Fastqsanger.gz

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Chemo- versus immuno-precipitation of G-quadruplex-DNA (G4- DNA): a direct comparison of the efficiency of the antibody BG4 versus the small-molecule ligands TASQs for G4 affinity capture

Project description:The reliability of the BG4-IP-seq protocol, along with the straightforward access to rice genomic DNA, makes this system ideal for comparing the pull-down efficiency of the antibody BG4 versus the small-molecular baits BioTASQ and BioCyTASQ. These two TASQs (for template-assembled synthetic G-quartets) are biotinylated biomimetic ligands that were successfully employed for fishing G4-RNAs out from human cell lysates, in a protocol referred to as G4RP-seq, which belong to the toolbox of seq-based techniques used to interrogate G4-RNA prevalence, comprising rG4-seq, DMS-seq, Keth-seq and SHALiPE-seq. We reasoned that the ability of TASQs to isolate G4-DNA deserves both to be investigated and to be compared to that of BG4. We thus report here on these investigations. which provides the very first comparison of the efficiency of the immuno- versus chemo- precipitation of G4s, under strictly identical experimental conditions.

2023-08-10 | GSE200171 | GEO

Expression data from G0 versus G4/G5 CMP/GMP

Project description:Telomere dysfunctional CMP/GMP have deregulated pathways that are associated with DNA damage signaling We compared differentially expressed genes in the G4/G5 CMP relative to the G0 control to identify pathways that may affect CMP differentiation. Bone marrow CMP and GMP cells were sorted from two paired pools of G0 TERTER/+ or G4/G5 TERTER/ER mice (5,000-20,000 cells per sample) using the Influx Cell Sorter. Every paired pool includes CMP or GMP sorted from 4 age and gender matched G0 or G4/G5 mice. RNA from the respective sorted cells was extracted using Trizol (Ambion) and profiled on 2100 Bioanalyzer (Agilent). Gene expression profiling was performed at the Sequencing and Non-coding RNA Program at MD Anderson Cancer Center. Briefly, the GeneChip® 3 IVT Express Kit (Affymetrix) was used to generate biotin-labeled cRNA, which were purified and fragmented, before target hybridization on the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix) according to the manufacturer's instructions. Affymetrix raw data (CEL files) were normalized using Affymetrix Microarray Suite (MAS) version 5.0 using a TGT=100. Paired pools used in the study were: CMP pool 1: G0-1 and G4/5-1 CMP pool 2: G0-2 and G4/G5-2 GMP pool 1: G0-1 and G4/G5-1 GMP pool 2: G0-2 and G4/G5-2

2015-04-09 | E-GEOD-62278 | biostudies-arrayexpress

G4-dependent DNA loops regulate gene expression [RNA-seq]

Project description:RNAPII is mainly responsible for mRNA transcription and plays a vital role in gene expression. In light of the above results showing that cellular G4s are highly correlated with RNAPII-mediated DNA loops, we performed the RNA-seq to evaluate how G4-dependent long-range DNA interactions modulate gene expression. We revealed that PDS treatment modulates the expression of not only genes with G4 in their promoters, but also those with promoters being connected with distal G4 through RNAPII-linked long-range DNA interactions.

2023-09-13 | GSE222207 | GEO

Expression data from G0 versus G4/G5 CMP/GMP

2015-04-09 | GSE62278 | GEO

G4 Quadruplex Binding Proteins

Project description:In this study we discover proteins that bind to G4 quadruplex DNA structure. We use modified c-myc quadruplex as a bait, and compare it to the control bait - T15 oligo. We use spectral counts and G-test to determine significant binders. T15 and G4 datafiles are uploaded

2016-07-07 | PXD003501 | Pride

PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA

Project description:Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood. We developed a zinc finger nuclease translocation reporter (ZITR) and screened for factors that modulate rearrangements in human cells. We identified UBC9 and RAD50 as suppressors and 53BP1, DDB1, and PARP3 as promoters of chromosomal rearrangements across human cell types. We focused on poly(ADP)ribose polymerase 3 (PARP3) as it is dispensable for murine viability and has druggable catalytic activity. We found that PARP3 regulated G quadruplex (G4) DNA in response to DNA damage, which suppressed repair by nonhomologous end-joining and homologous recombination. Chemical stabilization of G4 DNA in PARP3-/- cells led to widespread DNA double-strand breaks and synthetic lethality. We propose a model in which PARP3 suppresses G4 DNA and facilitates DNA repair by multiple pathways.

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HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability

Project description:G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.

2024-08-13 | GSE247967 | GEO

Geobacillus sp. G4 strain:G4

Project description:Geobacillus sp. G4 strain:G4 Genome sequencing

| PRJNA1124973 | ENA

Timeless collaborates with DDX11 to ensure processive replication of G4-forming DNA [RNA-seq]

Project description:Regions of DNA with the potential to form secondary structure pose a frequent and significant impediment to DNA replication that must be actively countered by cells in order to preserve genetic and epigenetic integrity. The fork protection complex (FPC), a conserved group of replisome-associated proteins, comprising Timeless, plays an important role in maintaining efficient replisome function. A previously unappreciated DNA binding domain in the C terminus of Timeless, which exhibits specificity towards G4 structures, acts in collaboration with the DDX11 helicase to ensure replication of G4 structures in vivo and maintenance of genetic and epigenetic stability. Using RNA-seq experiments, we show that (i) Timeless and DDX11 share common gene targets, (ii) the promoter of Timeless- and DDX11-dependent genes are enriched in G4 structures in the vicinity of their promoter and (iii) both Timeless and DDX11 share a common set of gene targets with the FANCJ helicase known to maintain epigenetic stability in the vicinity of G4 structures.

2020-07-01 | GSE139256 | GEO

Identification of human proteins interacting with locked G4 structures

Project description:G4 are noncanonical secondary structures consist in stacked tetrads of Hoogsteen hydrogen-bonded guanines bases. An essential feature of G-quadruplexes is their intrinsic polymorphic nature. Indeed, depending on the length and the composition of the sequence, as well as the environmental conditions (including the nature and concentration of metal cations, and local molecular crowding), a G-quadruplex-forming sequence can adopt different topologies in which the strands are in parallel or antiparallel conformations, with the co-existence of different types of loops (lateral, diagonal or propeller) with variable lengths. The impact of G4 on cellular metabolism is associated with protein or enzymatic factors that promote, inhibits or resolve these structures. Thus, the major impact of G4 on the human cell metabolism is associated with genetic defects affecting proteins that counteract their formation. Although a large number of proteins able to bind and/or "to resolve" G-quadruplex structures have been identified in vitro, less is known about their mode of interaction with G-quadruplex, their specificity versus the topology and finally their specificity for G4 structures relatively to G-rich single-stranded sequences. In this study we aimed to identify and characterize human proteins interacting with locked G4 structures.

2021-07-16 | PXD021003 | Pride

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