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Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch

ABSTRACT: Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch

PROVIDER: PRJNA1089188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28380300_1.fastq.gz	Fastqsanger.gz
	SRR28380300_2.fastq.gz	Fastqsanger.gz
	SRR28380301_1.fastq.gz	Fastqsanger.gz
	SRR28380301_2.fastq.gz	Fastqsanger.gz
	SRR28380302_1.fastq.gz	Fastqsanger.gz

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Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch

Project description:Transcriptional regulation is a dynamic process that coordinates diverse cellular activities, and the use of small molecules to perturb gene expression has propelled our understanding of the fundamental regulatory mechanisms. However, small molecules typically lack the spatiotemporal precision required in highly non-invasive, controlled settings. Here, we present the development of a cell-permeable small-molecule DNA G-quadruplex (G4) binder, termed G4switch, that can be reversibly toggled on and off by visible light. We have biophysically characterised the light-mediated control of G4 binding in vitro, followed by cellular, genomic mapping of G4switch to G4 targets in chromatin to confirm G4-selective, light-dependent binding in a cellular context. By deploying G4switch in living cells, we show spatiotemporal control over the expression of a set of G4-containing genes and G4-associated cell proliferation. Our studies demonstrate a chemical tool and approach to interrogate the dynamics of key biological processes directly at the molecular level in cells.

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Project description:The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA. Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

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Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [control]

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