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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Hi-C]

ABSTRACT: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Hi-C]

PROVIDER: PRJNA896585 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22130067_1.fastq.gz	Fastqsanger.gz
	SRR22130067_2.fastq.gz	Fastqsanger.gz
	SRR22130068_1.fastq.gz	Fastqsanger.gz
	SRR22130068_2.fastq.gz	Fastqsanger.gz
	SRR22130069_1.fastq.gz	Fastqsanger.gz

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

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Project description:In eukaryotes, DNA-associated protein complexes co-evolve with genomic sequence to orchestrate chromatin folding into functional chromosomes. Here, we investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of co-evolutions. Using bacterial genomes integrated into S. cerevisiae, which diverged from yeast up to 1.5 billion years ago, we show that nucleosomes, cohesins and the transcriptional machinery can lead to the formation of two different chromatin archetypes, one being transcribed and the other silent. These two archetypes also form on eukaryotic exogenous sequences, and depend on sequence composition. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalisation reminiscent of the organization of vertebrate nuclei. Our findings represent a significant advance in understanding the primary molecular mechanisms that govern the co-option or silencing of DNA sequences integrated into foreign genomes during natural horizontal gene transfers, or in synthetic genomics projects.

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [ChIP-Seq]

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Project description:Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [RNA-Seq]

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Mnase-Seq]

Project description:Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Mnase-Seq]

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2025-02-14 | GSE217016 | GEO

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [RNA-Seq]

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Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

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

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Comparison of Hi-C results using in-solution versus in-nucleus ligation

Project description:Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications. We created Hi-C libraries by two different methods, in-solution ligation and in-nucleus ligation, from two biological replicates each of mouse foetal liver cells (mouse-1 and mouse-2) and human ES cells (human-1 and human-2) or the mixture of these two species. We also sequenced a random ligation library prepared by reversal of the cross-links and purification of the DNA prior to ligation.

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