DNA-RNA three-stranded hybrids: from the telomere to the genome (human dataset)
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ABSTRACT:
PROVIDER: PRJNA602142 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10914726_1.fastq.gz | Fastqsanger.gz | |||
| SRR10914726_2.fastq.gz | Fastqsanger.gz | |||
| SRR10914727_1.fastq.gz | Fastqsanger.gz | |||
| SRR10914727_2.fastq.gz | Fastqsanger.gz | |||
| SRR10914728_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:DNA-RNA three-stranded hybrids: from the telomere to the genome (mouse dataset)
| PRJNA602143 | ENA
Project description:DNA-RNA three-stranded hybrids: from the telomere to the genome
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Project description:The origin and possible functions of local three-stranded DNA-RNA hybrid regions in the mammalian genome is still a matter of discussion. R-loops have been so far essentially detected by immunodetection of the DNA-RNA hybrid regions (DRIP assay). This powerful and easy to implement method relies on recognition by a unique monoclonal antibody and may not detect all the hybrid regions. Starting from simple logical steps, we developed a preparative method that allows detection and physical isolation of stable DNA-RNA triplexes in a complex genome. A modification of the popular TRIzol extraction procedure first identifies RNAs stably bound to DNA in RNaseH-sensitive complexes, which can be isolated and further characterized by RNA-seq. We first tested the efficiency of the approach by a search for a generalized three-stranded state of the human and mouse telomeres. While such a structure is suggested by the complementarity of the long chromosomal CCCTAA repeats and the noncoding RNA TERRA, it was only in one class of cancer cells that telomeric R-loops were so far evidenced by DRIP assay. The proposed method allowed us to generalize to the mouse and human genomes the notion of terminal R-loop complexes with TERRA molecules synthesized from local promoters. When further applied to murine sperm genome, it evidenced a reproducible genome-wide profile of RNA complexes.
2021-06-30 | GSE143918 | GEO
Project description:The origin and possible functions of local three-stranded DNA-RNA hybrid regions in the mammalian genome is still a matter of discussion. R-loops have been so far essentially detected by immunodetection of the DNA-RNA hybrid regions (DRIP assay). This powerful and easy to implement method relies on recognition by a unique monoclonal antibody and may not detect all the hybrid regions. Starting from simple logical steps, we developed a preparative method that allows detection and physical isolation of stable DNA-RNA triplexes in a complex genome. A modification of the popular TRIzol extraction procedure first identifies RNAs stably bound to DNA in RNaseH-sensitive complexes, which can be isolated and further characterized by RNA-seq. We first tested the efficiency of the approach by a search for a generalized three-stranded state of the human and mouse telomeres. While such a structure is suggested by the complementarity of the long chromosomal CCCTAA repeats and the noncoding RNA TERRA, it was only in one class of cancer cells that telomeric R-loops were so far evidenced by DRIP assay. The proposed method allowed us to generalize to the mouse and human genomes the notion of terminal R-loop complexes with TERRA molecules synthesized from local promoters. When further applied to murine sperm genome, it evidenced a reproducible genome-wide profile of RNA complexes.
2021-06-30 | GSE143917 | GEO
Project description:Super killer (SKI) complex is a well-known cytoplasmic 3′ to 5′ mRNA decay complex that functions with the exosome to degrade excessive and aberrant mRNAs. Recently, SKIV2L, the 3′ to 5′ RNA helicase of the human SKI (hSKI) complex has been implicated with the extraction of mRNA at stalled ribosomes, tackling aberrant translation. Here, we show that SKIV2L and TTC37 of the hSKI complex are present within the nucleus, localise on chromatin and at some telomeres during the G2 cell cycle phase. In cells, SKIV2L prevents telomere replication stress shown as fragile telomeres and increases the stability of telomere DNA-RNA hybrids in G2 of the cell cycle whereas its absence decreases the amount of those structures. We further demonstrate that purified hSKI complex binds telomeric DNA and RNA substrates in vitro. Moreover, SKIV2L association with telomeres is dependent on DNA-RNA hybrids but its helicase activity is dispensable for its telomeric function. Taken together, our results provide a nuclear function for SKIV2L of the hSKI complex in overcoming replication stress at telomeres mediated by its recruitment to DNA-RNA hybrid structures in G2 and thus maintaining telomere stability.
2024-10-03 | PXD046955 | Pride
Project description:Telomeres are the ends of linear chromosomes and consist of repetitive double- and single-stranded DNA sequences. Telomeres are bound by dedicated protein complexes, such as shelterin in mammals. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to screen for proteins binding to C. elegans telomeres, and identified TEBP-1 and TEBP-2, two paralogs that associate to telomeres in vitro and in vivo. TEBP-1 and TEBP-2 form a telomeric complex with the known single-stranded telomere-binding proteins POT-1, POT-2, and MRT-1. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp 2 mutants display shorter telomeres and a mortal germline, a phenotype characterized by transgenerational germline deterioration. Notably, tebp 1;tebp-2 double mutant animals are synthetic sterile, with germlines showing signs of severe mitotic and meiotic arrest. These results define the first telomere-binding complex of C. elegans, including TEBP-1 and TEBP-2, two double-stranded telomere binders required for fertility.
2021-03-09 | PXD019241 | Pride
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-06-30 | GSE143919 | GEO
Project description:We used microarrays to analyze the prevalence of signalling induced by acute telomere dysfunction (as induced by TRF2DBDM expression = Dataset 1) and in TERC- compared to TERC+ HCC (Dataset 2). Keywords: acute telomere dysfunction, hepatocellular cancer
2006-07-01 | GSE4627 | GEO
Project description:Telomere variant sequences encode a genetic blueprint for allele-specific telomere length (dataset 2)
| PRJNA1455523 | ENA
Project description:At critically short telomeres TERRA RNA-DNA hybrids become stabilized and drive homology-directed repair (HDR) to delay replicative senescence. However, even at long- and intermediate-length telomeres, not subject to HDR, transient TERRA RNA-DNA hybrids form, suggestive of additional roles. Here, we report that hybrids at telomeres prevent resection by the Exo1 nuclease when telomeres become non-functional. We employed the well-characterized cdc13-1 allele, where telomere resection can be induced in a temperature dependent manner, to demonstrate that ssDNA generation at telomeres is either prevented or augmented when RNA-DNA hybrids are stabilized or destabilized, respectively. The viability of cdc13-1 cells is affected by the presence or absence of hybrids accordingly. These results give insights into an additional role of TERRA at dysfunctional telomeres suggesting that it not only affects replicative senescence rates through HDR activation at critically short telomeres, but may also affect resection rates at intermediate length telomeres in pre-senescent cells.
2023-01-18 | PXD034986 | Pride