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Genome-wide profiling of DNA G-quadruplexes in living neurons

ABSTRACT: Genome-wide profiling of DNA G-quadruplexes in living neurons

PROVIDER: PRJNA789551 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17248200_1.fastq.gz	Fastqsanger.gz
	SRR17248200_2.fastq.gz	Fastqsanger.gz
	SRR17248201_1.fastq.gz	Fastqsanger.gz
	SRR17248201_2.fastq.gz	Fastqsanger.gz
	SRR17248202_1.fastq.gz	Fastqsanger.gz

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Genome-wide profiling of DNA G-quadruplexes in living neurons

Project description:We report a genome-wide mapping of DNA G-quadruplexes and histone modifications in living neurons. We used primary cultured neurons from the fetus mouse cortex. Cultured cells were treated with 2 µM Ara-C at DIV3 to prevent the proliferation of mitotic cells and were harvested at DIV10. For iG4 CUT&Tag, a BG4-expressing plasmid was transfected by electroporation at DIV0.

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Project description:The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.

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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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