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Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence (SS-Seq)

ABSTRACT: Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence (SS-Seq)

PROVIDER: PRJNA642235 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12097651.fastq.gz	Fastqsanger.gz
	SRR12097652.fastq.gz	Fastqsanger.gz
	SRR12097653.fastq.gz	Fastqsanger.gz
	SRR12097654.fastq.gz	Fastqsanger.gz
	SRR12097655.fastq.gz	Fastqsanger.gz

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Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence (SS-Seq)

Project description:We developed an efficient method to map DNA supercoils that quantifies genome-wide incorporation of biotinylated psoralen using high throughput DNA sequencing and applied it to C. elegans. We discovered that GC-rich regions flanked by sharp GC/AT boundaries delineate the extent of negative supercoiling at transcription start sites, the regions of DNA accessibility and the positioning of nucleosomes. We also discovered that promoters with either paused or non-paused RNA polymerase II (Pol II) exhibit the same level of supercoiling, revealing that supercoiling at transcription start sites is neither the cause nor consequence of Pol II pausing. Furthermore, we found that a condensin complex that mediates X-chromosome dosage compensation in C. elegans creates local negative supercoils at its high-occupancy binding sites on X but does not create large domains of supercoiling across X to achieve dosage compensation. We also developed a new high-throughput method to map single-stranded DNA and alternative DNA structures, including Z DNA. The approach combines potassium permanganate footprinting and a technique to sequence rare double-stranded breaks. We discovered that GC-rich regions flanked by sharp GC/AT boundaries determine the width of single-stranded DNA regions at transcription start sites. Moreover, AT-rich sequences bordered by a change in GC content delineate Z DNA at transcription end sites and in introns as well as non-B DNA at trans-splicing acceptor sites that comprise the 5' ends of most mature mRNAs in C. elegans. Our analysis suggests that a sharp transition in GC content rather than the GC content by itself creates alternative DNA structures.

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Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence

Project description:Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence

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Genome-wide mapping of DNA supercoils, single-stranded DNA, and Z DNA in C. elegans using new high-throughput methods reveals the delineation of DNA structure by DNA sequence (BP-Seq)

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RNA Polymerase-II-generated DNA supercoils destabilize nucleosomes

Project description:The twin supercoiled domain model posits that, as RNA Polymerase II (Pol II) transcribes a gene, it generates negative and positive supercoils upstream and downstream respectively, but little is known about the functional consequence in vivo of the resulting torsional strain. Here we provide a method for high resolution mapping of DNA supercoils using next-generation sequencing, and show that the level of supercoiling is correlated with gene expression in Drosophila cells. Inhibition of topoisomerases, enzymes that relieve torsional strain, leads to accumulation of supercoils surrounding gene bodies and of Pol II at the transcription start sites. Topoisomerase I inhibition results in increased nascent RNA transcripts with Topoisomerase II inhibition shows little change in nascent RNA levels. Despite these different effects on transcription, inhibition of either enzyme results in increased nucleosome turnover within gene bodies, suggesting that torsional stress contributes to destabilizing nucleosomes ahead of Pol II. 12 paired-end samples and 8 single-end samples were sequenced and analyzed.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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