ThCHART of roX2 lncRNA [DNA]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA492139 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7879640.fastq.gz | Fastqsanger.gz | |||
| SRR7879650.fastq.gz | Fastqsanger.gz | |||
| SRR7879641.fastq.gz | Fastqsanger.gz | |||
| SRR7879651.fastq.gz | Fastqsanger.gz | |||
| SRR7879642.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 21 |
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
Project description:Proteomic analysis on lncRNA associated proteins . Functional role of DNA-PK .
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
| PRJNA307252 | ENA
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.
| MSV000090292 | MassIVE
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:The three-stranded DNA-RNA triplex hybridization is involved in various biological processes, including gene expression regulation, DNA repair, and chromosomal stability. However, the DNA-RNA triplex mediating mechanisms underlying tumorigenesis remain to be fully elucidated. In gastric cancer, we performed ChIRP-MS in order to further capture the trimer-forming lncRNA binding protein.
2024-09-20 | PXD056041 | Pride
Project description:Although non-coding RNAs (ncRNAs) have been proposed to play important roles in nuclear organization with three-dimensional (3D) conformation and gene transcription regulation, exploring the targeting and diffusion patterns of ncRNAs on chromatin has been challenging because it requires a technique that can simultaneously detect high-affinity sites and their higher-order contacts in 3D structures. Here we developed a new method, RNA-associated chromatin DNA-DNA interactions (RDD) in solution, which enables genome-wide detection of genomic binding sites and high-resolution chromatin interactions for a specific ncRNA. Using RDD to investigate the well-known ncRNA roX2 that involved in Drosophila dosage compensation, we not only recapitulate roX2 targeting chromatin sites but also reveal the landscape of chromatin DNA-DNA contacts at various resolutions from loops, domains to territories. We further show that roX2 anchors at the target gene TES and spreads around as a 'boot-like' structure for maintaining gene activity, where tethered daisy-chain chromatin loops, bridging to TSS to dock RNAPII-related contact hubs to achieve a precise twofold expression of male X-linked genes, further crossing active domains to form distinct hubs to exhibit the condensed properties of roX2 in high-throughput sequencing. These results provide a genome-wide 3D model for explaining the mechanism of ncRNA roX2 involved dosage compensation in Drosophila. Together, we demonstrate the high specificity and robustness of the RDD method to capture RNA-associated chromatin DNA-DNA interactome, which provides topological insights into the mechanism of gene transcription regulation by ncRNAs.
2024-05-21 | GSE207720 | GEO
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