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Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Lachancea fermentati Lachancea waltii Saccharomyces cerevisiae Dictyostelium discoideum

PROVIDER: GSE246637 | GEO | 2025/01/13

REPOSITORIES: GEO

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Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [shotgun_sequencing]

Project description:Natural plasmids are common in prokaryotes, but few have been documented in eukaryotes. The natural 2µ plasmid present in budding yeast Saccharomyces cerevisiae is one of the most well characterized. This highly stable genetic element coexists with its host for millions of years, efficiently segregating at each cell division through a mechanism that remains poorly understood. Using proximity ligation (Hi-C, Micro-C) to map the contacts between the 2µ and yeast chromosomes under dozens of different biological conditions, we found that the plasmid tether preferentially on regions with low transcriptional activity, often corresponding to long inactive genes. Common players in chromosome structure such as members of the structural maintenance of chromosome complexes (SMC) are not involved in these contacts which depend instead on a nucleosomal signal associated with a depletion of RNA Pol II. These contacts are stable throughout the cell cycle and can be established within minutes. This strategy may involve other types of DNA molecules and species other than S. cerevisiae, as suggested by the binding pattern of the natural plasmid along the silent regions of the chromosomes of Dictyostelium discoideum.

2025-01-21 | GSE287201 | GEO

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [ChIP-seq]

Project description:Natural plasmids are common in prokaryotes, but few have been documented in eukaryotes. The natural 2µ plasmid present in budding yeast Saccharomyces cerevisiae is one of the most well characterised. This highly stable genetic element coexists with its host for millions of years, efficiently segregating at each cell division through a mechanism that remains poorly understood. Using proximity ligation (Hi-C, Micro-C) to map the contacts between the 2µ and yeast chromosomes under dozens of different biological conditions, we found that the plasmid tether preferentially on regions with low transcriptional activity, often corresponding to long inactive genes. Common players in chromosome structure such as members of the structural maintenance of chromosome complexes (SMC) are not involved in these contacts, which depend instead on a nucleosomal signal associated with a depletion of RNA Pol II. These contacts are stable throughout the cell cycle and can be established within minutes. This strategy may involve other types of DNA molecules and species other than S. cerevisiae, as suggested by the binding pattern of the natural plasmid along the silent regions of the chromosomes of Dictyostelium discoideum.

2025-01-13 | GSE246636 | GEO

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [RNA-seq]

2025-01-13 | GSE274259 | GEO

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [Hi-C]

2025-01-13 | GSE246635 | GEO

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal

Project description:Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal

| PRJNA1034022 | ENA

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [shotgun_sequencing]

Project description:Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [shotgun_sequencing]

| PRJNA1211605 | ENA

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [ChIP-seq]

Project description:Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [ChIP-seq]

| PRJNA1034023 | ENA

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [Hi-C]

Project description:Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [Hi-C]

| PRJNA1034026 | ENA

Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [RNA-seq]

Project description:Anchoring of parasitic plasmids to inactive regions of eukaryotic chromosomes through nucleosome signal [RNA-seq]

| PRJNA1145470 | ENA

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.

Project description:A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these "seed" nucleosomes--together with trans-acting factors--may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.

| S-EPMC4617968 | biostudies-literature

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