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

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

PROVIDER: PRJNA896581 | ENA |

REPOSITORIES: ENA

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

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

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

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.

2025-02-14 | GSE217019 | GEO

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

2025-02-14 | GSE217018 | GEO

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

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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.

2025-02-14 | GSE217022 | GEO

Sequence composition dictates chromatin assembly, activity, folding and compartmentalization [CRAC-seq]

Project description:Genomic sequences co-evolve with chromatin-associated proteins to ensure that long DNA molecules are folded in the nucleus in an orderly and functional manner. In eukaryotes, this multiscale folding involves several molecular complexes and structures, ranging from nucleosomes to large cohesin-mediated DNA loops. To explore the causal relationships between the DNA sequence composition and the spontaneous loading and activity of these complexes, we circumvented the boundaries imposed by the evolved, fine-tuning of chromosome regulation by using yeast strains that carry artificial bacterial chromosomes that have diverged from eukaryotic sequences for over 1.5 billion years. By combining this chimeric? synthetic genomics approach with a deep learning-based in silico analysis, we show that sequence composition precisely dictates the whole spectrum of chromatin assembly, transcriptional activity, folding, and compartmentalization in a given cellular context. These results are a first step to understand the molecular events at stake during synthetic chromosome engineering as well as natural horizontal gene transfers.

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