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S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min

ABSTRACT: Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation in absence of telomere silencing.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE18241 | GEO | 2009/12/01

SECONDARY ACCESSION(S): PRJNA123505

REPOSITORIES: GEO

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S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in M-NM-^Ttop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation in absence of telomere silencing. Two-condition experiment: delta top1 delta sir3-TOPA vs delta top1 delta sir3 top2-ts-TOPA. 2 time points: 0min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2009-12-01 | E-GEOD-18241 | biostudies-arrayexpress

Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Îtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation. Two-condition experiment: delta top1-TOPA vs delta top1 top2-ts-TOPA. 3 time points: 0min, 30min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2010-05-19 | E-GEOD-18240 | biostudies-arrayexpress

Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation.

2009-12-01 | GSE18240 | GEO

Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Îtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Two-condition experiment, JCW25 vs top2-ts-TOPA (JCW26). 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2010-05-18 | E-GEOD-18605 | biostudies-arrayexpress

Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress

2009-12-03 | GSE18605 | GEO

Mammalian telomeres reforged with non-telomeric sequences

Project description:Telomere is a highly refined system for maintaining the stability of linear chromosomes. Most telomeres rely on simple repetitive sequences and telomerase enzymes, but in some species or telomerase-defective situations, alternative telomere lengthening (ALT) mechanism is utilized to protect chromosomal ends. Telomere loss can induce telomere recombination by which specific sequences can be recruited into telomeres. However, canonical telomeric repeat-based telomeres have been found in mammals. Here, we show that mammalian telomeres can also be completely reconstituted using a non-telomeric unique sequence. We found that a specific subtelomeric element, named as mouse template for ALT (mTALT), is utilized for repairing telomeric DNA damage and composing new telomeric sequences in mouse embryonic stem cells. We found a high-level of non-coding mTALT transcript despite the heterochromatic nature of mTALT-based telomere. After ALT activation, the increased HMGN1, a non-histone chromosomal protein, contributed to maintaining telomere stability by regulating telomeric transcriptions. Our findings reveal novel molecular features of potential telomeric sequences which can reconstitute telomeres during cancer formation and evolution.

2020-07-17 | MSV000085772 | MassIVE

End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination

Project description:Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the nematode Ascaris to study the timing of PDE breaks and examine the DSBs and their end processing. Using END-seq, we characterize the DSB ends and demonstrate that DNA breaks are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3’ overhangs before the addition of telomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB in Ascaris is likely due to the sequestration of the eliminated DNA into micronuclei, preventing their ends from telomere healing. Additional DNA breaks occur within the eliminated DNA in both Ascaris and Parascaris, ensuring chromosomal breakage and providing a fail-safe mechanism for nematode PDE.

2024-03-15 | GSE260958 | GEO

ZNF365 promotes stability of fragile sites and telomeres

Project description:Critically short telomeres activate cellular senescence or apoptosis, as mediated by the tumor suppressor p53, but in the absence of this checkpoint response, telomere dysfunction engenders chromosomal aberrations and cancer. Here, analysis of p53-regulated genes activated in the setting of telomere dysfunction identified Zfp365 (ZNF365 in humans) as a direct p53 target that promotes genome stability. Germline polymorphisms in the ZNF365 locus are associated with increased cancer risk, including those associated with telomere dysfunction. On the mechanistic level, ZNF365 suppresses expression of a subset of common fragile sites (CFS) including telomeres. In the absence of ZNF365, defective telomeres engage in aberrant recombination of telomere ends, leading to increased telomere sister chromatid exchange (T-SCE) and formation of anaphase DNA bridges, including ultra-fine DNA bridges (UFB), and ultimately increased cytokinesis failure and aneuploidy. Thus, the p53-ZNF365 axis contributes to genomic stability in the setting of telomere dysfunction.

2013-08-01 | GSE44599 | GEO

Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability

Project description:Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here we show that, in Schizosaccharomyces pombe, the telomere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelterin, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA sequences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by controlling nucleosome occupancy and genome stability.

2018-10-19 | GSE121502 | GEO

m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors [II]

Project description:Telomerase-negative tumors can maintain telomere length by alternative lengthening of telomeres (ALT) but the mechanism of telomere maintenance in ALT cells is not well understood. A significant portion of the relapse Neuroblastoma (NB) tumors are positive for ALT which suggests better dissecting the ALT mechanism could provide novel therapeutic opportunities. TERRA RNA which is derived from the telomere ends is localized to telomeres in R-loop dependent manner and is essential for telomere maintenance. In the present study, we provide evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA RNA by methyl transferase METTL3 is essential for telomere maintenance in ALT cells and loss of TERRA m6A/METTL3 leads to accumulation of DNA damage over telomere. Our data suggest that m6A modification in TERRA RNA is required for R-loop formation and telomere targeting of TERRA. We observed that R-loop enriched TERRA is abundantly m6A modified and m6A mediated recruitment of hnRNPA2B1 to TERRA RNA is essential for R-loop formation. Together our study suggests that m6A-mediated R-loop formation could be a widespread mechanism utilized by other chromatin-interacting lncRNAs. We also show treating ALT positive NB cells with small molecule METTL3 inhibitor leads to compromised telomere targeting of TERRA and accumulation of DNA damage over telomere, suggesting METTL3 inhibition could be a therapeutic opportunity for ALT positive NB.

2023-12-13 | GSE219212 | GEO

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