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Genome-wide mapping of native G-loops in living cells

ABSTRACT: Genome-wide mapping of native G-loops in living cells

PROVIDER: PRJNA1071642 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27820407_1.fastq.gz	Fastqsanger.gz
	SRR27820407_2.fastq.gz	Fastqsanger.gz
	SRR27820408_1.fastq.gz	Fastqsanger.gz
	SRR27820408_2.fastq.gz	Fastqsanger.gz
	SRR27820409_1.fastq.gz	Fastqsanger.gz

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Genome-wide mapping of native G-loops in living cells

Project description:G-quadruplex (G4) are four‑stranded DNA secondary structures that form in guanine‑rich regions of the genome, which can enhance or repress gene expression. An R-loop is a special triple-stranded nucleic acid structure formed when nascent RNA invades double-stranded DNA (dsDNA) during transcription. G-loops are constituted by one or more DNA G4 on one strand and a stable RNA/DNA hybrid on the other. We developed the HepG4-seq for mapping the native G4s and the HBD-seq for mapping native R-loops. We combined the HepG4-seq and HBD-seq to profile the genomic native G-loops, which are regions co-occupied by both native G4s and R-loops, in both HEK293 cells and mouse embryonic stem cells (mESCs).

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Project description:We adapted the nuclease-targeting approach CUT&RUN (Skene & Henikoff, eLife 2017) to map R-loops in vivo. We show that this approach accurately identifies R-loops that are sensitive to both Actinomycin D and RNase H and largely overlap with previously identified regions containing R-loops. We also show that MapR can identify R-loops genome-wide from much smaller input material than existing techniques.

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