ThCHART of roX2 lncRNA [DNA]
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ABSTRACT:
PROVIDER: PRJNA492139 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress. Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.
2020-03-11 | GSE120217 | GEO
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2019-10-04 | MSV000084424 | MassIVE
Project description:Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress. Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin. This SuperSeries is composed of the SubSeries listed below.
2020-03-11 | GSE120220 | GEO
Project description:LncRNA DINO guides DNA damage signaling
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Project description:P53 inactivation occurs in about 50% of human cancers, where p53-driven p21 activity is devoid and p27 becomes essential for the establishment of the G1/S checkpoint upon DNA damage. Here, we show that the E2F1-responsive lncRNA LIMp27 selectively represses p27 expression and contributes to proliferation, tumorigenicity, and treatment resistance in p53-defective colon adenocarcinoma (COAD) cells. LIMp27 competes with p27 mRNA for binding to cytoplasmically localized hnRNA0, which otherwise stabilizes p27 mRNA leading to cell cycle arrest at the G0/G1 phase. In response to DNA damage, LIMp27 is upregulated in both wild-type and p53-mutant COAD cells, whereas cytoplasmic hnRNPA0 is only increased in p53-mutant COAD cells due to translocation from the nucleus. Moreover, high LIMp27 expression is associated with poor survival of p53-mutant but not wild-type p53 COAD patients. These results uncover a lncRNA mechanism that promotes p53-defective cancer pathogenesis and suggest that LIMp27 may constitute a target for the treatment of such cancers.
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Project description:We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by lncRNA H19 knockdown in myotubes. Following H19 knockdown, we observed extensive genome-wide mthylation pattern changes relative to siCon cells, with some genes showing incresed methylation, others showing decreased methylation, and a third group with no significant change. Myotubes differentiated from mouse C3H myoblasts were transfected with either control siRNA or siH19, 48h later, cellular genomic DNA was extracted and subjected to genome-scale DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).
2015-11-09 | E-GEOD-73013 | biostudies-arrayexpress
Project description:Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress. Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of a lncRNAs on chromatin.
2020-03-11 | GSE137401 | GEO
Project description:The hereditary information encoded in DNA sequence is intrinsically susceptible to alterations, being continually threatened by a variety of genotoxic perturbations. To safeguard the stability of the genome, eukaryotic cells have evolved a set of sophisticated surveillance system that controls several aspects of the cellular response, including the detection of DNA lesions, a temporary cell cycle arrest, regulation of transcription, and the repair of the damaged DNA. However, it is still poorly understood how the DNA damage checkpoints and stalled RNAPII molecules convert a very limited amount of molecular-level information (even a single DNA lesion) in the context of an otherwise genome into regulation that halts and resumes the cell-cycle engine in a coordinated way. In this study, we reveal a map of extensive lncRNA transcription during DDR by using synchronized cells, leading to the unexpected identification of a poorly characterized mammalian lncRNA-ZFAS1. We describe that ZFAS1 functions as a key player of cellular response to DNA damage in both human and rodent cells by fine tuning RNAPII kinetics, suggesting a lncRNA-dependent transcriptional regulatory axis that maintains genomic stability upon DNA damage in mammalian cells.
2023-08-03 | GSE239616 | GEO
Project description:The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we designed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-rich sequences and tandem stem-loop structures. In vitro, the helicase binds and remodels many RNAs beyond its main target, roX2. Unwinding of roX2 by the helicase triggers their selective association with the DCC, via the MSL2 subunit. Whereas the core DCC alone does not show intrinsic RNA binding specificity, the presentation of remodeled roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of MSL2. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
2020-05-27 | GSE143455 | GEO