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Chemical profiling of DNA G-quadruplex-interacting proteins in live cells

ABSTRACT: Chemical profiling of DNA G-quadruplex-interacting proteins in live cells

PROVIDER: PRJNA693305 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13485918.fastq.gz	Fastqsanger.gz
	SRR13485919.fastq.gz	Fastqsanger.gz
	SRR13485920.fastq.gz	Fastqsanger.gz
	SRR13485921.fastq.gz	Fastqsanger.gz
	SRR13485922.fastq.gz	Fastqsanger.gz

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Chemical profiling of DNA G-quadruplex-interacting proteins in live cells

Project description:DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential for understanding the underlying regulatory mechanisms on a molecular level. Here, we describe a novel co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in cellular chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We show the robustness of CMPP on proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we identify hundreds of putative G4-interacting proteins from various functional classes. Next, we observe high G4 binding affinity and selectivity for several G4 interactors in vitro and confirm direct G4 interactions for one of the top candidates in chromatin. Our studies provide a chemical approach to map protein interactions of specific nucleic acid features in living cells.

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Chemical profiling of DNA G-quadruplex-interacting proteins in live cells.

Project description:DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential to understand the underlying regulatory mechanisms on a molecular level. Here we describe a co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in native chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We first showed the robustness of CMPP by proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we then identified hundreds of putative G4-interacting proteins from various functional classes. Next, we confirmed a high G4-binding affinity and selectivity for several newly discovered G4 interactors in vitro, and we validated direct G4 interactions for a functionally important candidate in cellular chromatin using an independent approach. Our studies provide a chemical strategy to map protein interactions of specific nucleic acid features in living cells.

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

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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.

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