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Identification of G-quadruplex-interacting Proteins in Living Cells using an artificial G4-targeting Biotin ligase

ABSTRACT: Identification of G-quadruplex-interacting Proteins in Living Cells using an artificial G4-targeting Biotin ligase

PROVIDER: PRJNA926896 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23198432_1.fastq.gz	Fastqsanger.gz
	SRR23198432_2.fastq.gz	Fastqsanger.gz
	SRR23198433_1.fastq.gz	Fastqsanger.gz
	SRR23198433_2.fastq.gz	Fastqsanger.gz
	SRR23198434_1.fastq.gz	Fastqsanger.gz

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Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase

Project description:G-quadruplexes (G4s) are noncanonical nucleic acid structures pivotal to cellular processes and disease pathways. Deciphering G4-interacting proteins is imperative for unraveling G4's biological significance. In this study, we developed a G4-targeting biotin ligase named G4PID, meticulously assessing its binding affinity and specificity both in vitro and in vivo. Capitalizing on G4PID, we devised a tailored approach termed G-quadruplex-interacting proteins specific biotin-ligation procedure (PLGPB) to precisely profile G4-interacting proteins.

2024-05-24 | PXD045634 | Pride

Identification of G-quadruplex-interacting Proteins in Living Cells using an artificial G4-targeting Biotin ligase

Project description:We engineering a G4-targeted biotin ligase probe (G4PID), which consists of three parts, RHAU23 at the C-terminus, miniTurbo at the N-terminus, and a flexible linker in the middle to prevent the disturbance of the two functional moieties. We used eCLIP to verified the G4s affinity of G4PID. We also used eCLIP method to verify the direct G4 interaction of Splicing factor 3B subunit 4 (SF3B4) in cellular transcriptome.

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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

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G4 quadruplex landscape and its regulation revealed by a new antibody capture method

Project description:Currently, the identification of G4 quadruplexes in vivo depends on a published and widely used G4-ChIP protocol (PMID: 29470465) that uses the anti-G4 antibody to captures the quadruplexes like regular chromatin. This method is challenged by some false positives and false negatives in G4-quadruplex capture. We have developed an antibody capture G4-ChIP (AbC G4-ChIP) method to overcome these challenges. The AbC G4-ChIP achieves (i) minimized in vitro artifacts during the incubation steps, and (ii) capture of G4-quadruplexes which are not protein-bound. We have applied the AbC G4-ChIP to study the regulatory effect of a CGG-repeat binding protein CGGBP1 on G4-quadruplex formation. The AbC G4-ChIP identifies inter-strand G/C-skew as a sequence property associated with CGGBP1-regulated G4-quadruplexes.

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LiveG4ID-seq identifies the chromatin G-quadruplex landscape in living cells

Project description:G-quadruplex (G4) structures exist in single-stranded DNA of chromatins and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, we fused BG4 antibody and GFP-tag to construct a live-cell G4 identifier (LiveG4ID). We first displayed its function as a high-specificity chromatin G4 probe in living cells by Dox-induced expression LiveG4ID in HEK293T cells and detecting its cellular localization, biocompatibility and G4-binding specificity. By coupling LiveG4ID with CUT&Tag technology, we established LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells. LiveG4ID-seq can identify more chromatin G4 motifs than traditional CUT&Tag and ChIP-seq methods. Using LiveG4ID-seq, we profiled the dynamic landscape of chromatin G4 structures during the cell cycle. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future study on chromatin G4 structures.

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Project description:The effect of bisquinolinium compounds PhenDC3 and 360A genome wide gene expression changes modulated via promoter based G-quadruplex (G4) motifs. The total RNA was extracted after treating HeLa S3 cells with 10 ÂµM of no molecule (DMSO), 8979A (control molecule), PhenDC3 (G4 specific molecule) or 360A (G4 specific molecule) for 48 hrs in triplicate.

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Project description:G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.

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G4-RNA binding proteins from K562

Project description:G-quadruplex RNA pulldown followed by mass spectrometry. G4A4 oligoribonucleotide (5’-AAAAAAGGGGAAAAGGGGAAAAGGGGAAAAGGGGAAAAAA-3’) was biotinylated and folded in either K+ or Li+ containing buffers, causing folding of G-quadruplex (K+) or destabilization of the secondary structure (Li+). G4A4 pulldown was used to identify G4-RNA binding proteins from K562 human cell line nuclear extracts, interacting in structure-dependent manner.

2024-02-20 | PXD041154 | Pride

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

RNA-Seq to assess the transcriptional effects of G quadruplex stabilization by the G4 ligand PhenDC3 in HT-1080 cells

Project description:G-quadruplex motifs are frequently located near TSS and in the first introns of transcribed genes. We investigated the role that G4 structures play in transcription by stabilizing G4 DNA with the selective G4 ligand PhenDC3 in the HT-1080 human fibrosarcoma cell line. After treatment of triplicate samples with PhenDC3 or a negative control (DMSO carrier only), we performed RNA-Seq after poly-dT selection to assess changes in gene expression. Heme is an essential cofactor for many enzymes, but free heme is toxic and its levels are tightly regulated. G-quadruplexes bind heme avidly in vitro, raising the possibility that they may sequester heme in vivo. If so, then treatment that displaces heme from quadruplexes is predicted to induce expression of genes involved in iron and heme homeostasis. Here we show that PhenDC3, a G-quadruplex ligand structurally unrelated to heme, displaces quadruplex-bound heme in vitro and alters transcription in cultured human cells, up-regulating genes that support heme degradation and iron homeostasis, and most strikingly causing a 30-fold induction of heme oxidase 1, the key enzyme in heme degradation. We propose that G-quadruplexes sequester heme to protect cells from the pathophysiological consequences of free heme. This identifies a new function for G-quadruplexes and a new mechanism for protection of cells from heme.

2016-01-31 | GSE60630 | GEO

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