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DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

ABSTRACT: DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

PROVIDER: PRJNA433837 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6708981.fastq.gz	Fastqsanger.gz
	SRR6708982.fastq.gz	Fastqsanger.gz
	SRR6708983.fastq.gz	Fastqsanger.gz
	SRR6708984.fastq.gz	Fastqsanger.gz

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DREAM-seq, an endonucleases-assisted mapping of R-loops: MCF-7

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DREAM-seq, an endonucleases-assisted mapping of R-loops

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DREAM-seq, an endonucleases-assisted mapping of R-loops

Project description:Genome-wide identification of R-loops almost uniquely relies on antibody based pull-down, a method that shows sequence and structural biases. Here we describe a novel approach – DREAM-seq – centered around the use of endonuclease digestions. Unstimulated and stimulated B cells showed that R-loops are more widespread than anticipated, mostly covering all actively transcribed genes.

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Mapping of TOP1cc and R-loops im MCF-7 after TOP1 KD and/or RNase H OE [CHiP_DRIP_Seq]

Project description:DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employed DRIP-seq and ChIP-seq to map the change in TOP1cc and R-loops after the depletion of TOP1 and R-loops, to comprehensively investigate the interplay between transcription, DSBs, Topoisomerase 1 (TOP1), and R-loops. Our findings revealed the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops, indicating their crucial involvement in transcription-associated genomic instability. Depletion of R-loops and TOP1 specifically reduced DSBs at highly expressed genes, uncovering their pivotal roles in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides novel insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development. Notably, our study highlights the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations, shedding light on the potential for targeted therapeutic strategies. Overall, these findings deepen our understanding of the regulatory mechanisms governing DSBs in hypertranscribed genes associated with carcinogenesis, opening avenues for future research and therapeutic interventions.

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Project description:Expression of DREAM in dorsal root ganglia and spinal cord is related to endogenous control mechanisms of acute and chronic pain. In primary sensory trigeminal neurons high levels of endogenous DREAM protein are preferentially localized in the nucleus, suggesting a major transcriptional role. Here, we show that DREAM participates in the control of trigeminal pain perception through the regulation of prodynorphin and BDNF. Furthermore, genome-wide analysis of trigeminal neurons in daDREAM transgenic mice revealed that cathepsin L (CTSL) and the monoglyceride lipase (MGLL) are new DREAM downstream targets and have a role in the regulation of trigeminal nociception.

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