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Nucleosomal DNA has topological memory

ABSTRACT: Nucleosomal DNA has topological memory

PROVIDER: PRJNA950463 | ENA |

REPOSITORIES: ENA

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Nucleosomal DNA has topological memory

Project description:One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculated the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we placed each nucleosome in a circular minichromosome and performed Topo-seq, a high-throughput procedure to inspect the topology of circular DNA libraries in one gel electrophoresis. We found that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (∆Lk=-1.29), intergenic regions (∆Lk=-1.23), rDNA genes (∆Lk=-1.24) and telomeric regions (∆Lk=-1.07). Nucleosomes near the transcription start and termination sites also exhibit singular DNA topologies. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.

2023-06-05 | GSE228623 | GEO

FoxP3 Pulldown-seq (Nucleosomal DNA)

Project description:FoxP3 Pulldown-seq (Nucleosomal DNA)

| PRJNA1018996 | ENA

Cohesin causes replicative DNA damage by trapping DNA topological stress

Project description:DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological stress linked damage in these regions. At cohesin enriched centromeres cohesin activity causes the accumulation of DNA damage, RF rotation and precatenation, confirming that cohesin dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.

2020-03-03 | GSE131558 | GEO

FoxP3 Pulldown-seq (Nucleosomal DNA)

Project description:To investigate the interactions between FoxP3 and chromatinized templates, particularly assessing whether FoxP3 can still bind significantly to TnG-repeat DNA, we conducted FoxP3 pulldown experiments using nucleosomal DNA. Consitent with the result using naked genomic DNA, the results highlighted TnG repeats as one of the most significant motifs in these interactions.

2023-10-09 | GSE243605 | GEO

The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress [ChIP-seq]

Project description:Tof1/Timeless, protects eukaryotic cells from DNA replication stress as part of the Fork Protection Complex (FPC). Tof1 supports rapid DNA replication, fork pausing, and resolution of DNA topological stress. Here, we show that disruption of FPC function through loss of either Tof1 or Mrc1 results in DNA damage in long replicons. Despite increasing DNA damage in long replicons, loss of either Tof1 or Mrc1 concurrently reduces DNA damage in regions prone to damage caused by DNA topological stress, indicating that the rapid replication promoted by the FPC fosters completing DNA replication at the cost of increased vulnerability to DNA topological stress. Supporting this we find that a tof1 mutation that selectively inhibits DNA topological stress resolution increases DNA damage in contexts prone to DNA topological stress. Our data indicates that the FPC balances rapid replication with recruitment of topoisomerase I to resolve the topological stress generated by increased DNA unwinding.

2024-10-21 | GSE239965 | GEO

Cohesin causes replicative DNA damage by trapping DNA topological stress

Project description:Cohesin causes replicative DNA damage by trapping DNA topological stress

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The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress [TrAEL-seq]

2024-10-21 | GSE239966 | GEO

Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

Project description:In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open up the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.

2016-09-20 | GSE84910 | GEO

Transcription profiling of Saccharomyces cerevisiae genomic DNA, nucleosomal DNA and the yeast strain to analyse diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure

Project description:Genomic DNA from Saccharomyces cerevisiae W303-1A was isolated along with nucleosomal DNA from W303-1A and the yeast strain GAL:orc2-1. Nucleosomal DNA was isolated following a 2h release from a nocodazole block in which the medium was changed from galactose (YPAG) to glucose (YPAD).

2010-04-25 | E-MEXP-2369 | biostudies-arrayexpress

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern.

2012-01-01 | GSE33986 | GEO

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