Ontology highlight
ABSTRACT:
PROVIDER: PRJNA847751 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19612315.fastq.gz | Fastqsanger.gz | |||
| SRR19612316.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Modular domains of lncRNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here we present HiChIRP, a method leveraging novel bioorthogonal chemistry and customized 3C conditions, that enables interrogation of chromatin architecture focused around a specific RNA of interest down to ~10 copies per cell. HiChIRP of three nuclear RNAs reveal insights into promoter interactions (7SK), telomere biology (TERC), and inflammatory gene regulation (lincRNA-EPS).
2018-12-04 | GSE115524 | GEO
Project description:Vault RNAs (vRNAs) are evolutionarily conserved small non-coding RNAs transcribed by RNA polymerase lll. Initially described as components of the vault particle, they have since also been described as noncanonical miRNA precursors and as riboregulators of autophagy. As central molecules in these processes, vRNAs have been attributed numerous biological roles including regulation of cell proliferation and survival, response to viral infections, drug resistance, and animal development. Yet, their impact to mammalian physiology remains largely unexplored. To study vault RNAs in vivo, we generated a mouse line with a conditional Vaultrc5 loss of function allele. Because Vaultrc5 is the sole murine vRNA, this allele enables the characterization of the physiological requirements of this conserved class of small regulatory RNAs in mammals. Using this strain, we show that mice constitutively null for Vaultrc5 are viable and histologically normal but have a slight reduction in platelet counts pointing to a potential role for vRNAs in hematopoiesis. This work paves the way for further in vivo characterizations of this abundant but mysterious RNA molecule. Specifically, it enables the study of the biological consequences of constitutive or lineage-specific Vaultrc5 deletion and of the physiological requirements for an intact Vaultrc5 during normal hematopoiesis or in response to cellular stresses such as oncogene expression, viral infection, or drug resistance.
2024-06-11 | GSE269048 | GEO
Project description:There is increasing evidence that the architecture of long non-coding RNAs – just like that of proteins – is hierarchically organized into independently folding sub-modules with distinct functions. Studies characterizing the cellular activities of such modules, however, are rare. The lncRNA growth arrest specific 5 (Gas5) is a key regulator of cell survival in response to stress and nutrient availability. We used SHAPE-MaP to probe the structure of Gas5 in vitro and in cellulo. The results show that Gas5 contains three separate structural modules including the previously predicted steroid receptor binding hairpin motif. Functional assays show that the newly identified modules act independently in leukemic T cells. The 5’ terminal module with low secondary structure content affects basal survival and slows the cell cycle, whereas the highly structured core module mediates the effects of mTOR inhibition on cell growth. Disruption of specific secondary structures within the modules abolish their function in cells. These results highlight the central role of Gas5 in regulating cell survival and reveals how a single lncRNA transcript utilizes a modular structure-function relationship to respond to a variety of cellular stresses under various cellular conditions.
2021-04-07 | PXD018584 | Pride
Project description:Ewing sarcoma a rare pediatric tumor characterized by EWSR1-ETS fusions. We performed expression profiling of both miRNA and mRNA from the same Ewing's sarcoma tumors. We propose a novel statistical measure of non-linear dependence between miRNA and mRNA expression, In order to infer miRNA-target interactions. This approach, That we name antagonism pattern detection, Is based on the statistical recognition of a triangular-shaped pattern in miRNA-target expression profiles. This pattern is observed in miRNA-target expression measurements since their simultaneously elevated expression is statistically under-represented in the case of miRNA silencing effect. The proposed method enables miRNA target prediction to strongly rely on cellular context and physiological conditions reflected by expression data. Total RNAs issued of 39 Ewing tumors were used for mRNA and miRNA microarray analyses. The microRNA data were collected using the Illumina human-6 V1 BeadChip.
2012-06-11 | E-GEOD-37370 | biostudies-arrayexpress
Project description:Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellelar functions and dynamics upon changing environmental condictions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical ncRNAs and ~11% of long ncRNA (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responces. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured noncoding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. Duplicate gPAR-CLIP libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. polyA RNAs were isolated for all conditions. Total RNA were isolated from log phase growth conditions. Sucrose gradient fractionation was performed: some RNAs were isolated from the "light" fraction (lighter than 40S ribosome) and some from the "heavy" fraction. gPAR-CLIP libraries were used to determine regions of RNA bound by proteins.
2013-07-15 | E-GEOD-48888 | biostudies-arrayexpress
Project description:Ewing sarcoma a rare pediatric tumor characterized by EWSR1-ETS fusions. We performed expression profiling of both miRNA and mRNA from the same Ewing's sarcoma tumors. We propose a novel statistical measure of non-linear dependence between miRNA and mRNA expression, In order to infer miRNA-target interactions. This approach, That we name antagonism pattern detection, Is based on the statistical recognition of a triangular-shaped pattern in miRNA-target expression profiles. This pattern is observed in miRNA-target expression measurements since their simultaneously elevated expression is statistically under-represented in the case of miRNA silencing effect. The proposed method enables miRNA target prediction to strongly rely on cellular context and physiological conditions reflected by expression data. Expression profiling of Ewing sarcoma samples in the frame of the CIT program from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). Total RNAs issued of 39 Ewing tumors were used for mRNA and miRNA microarray analyses. The mRNA data were collected using the Affymetrix GeneChip HG-U133A and Affymetrix GeneChip HG-U133Plus2.
2012-06-11 | E-GEOD-37371 | biostudies-arrayexpress
Project description:Nuclear Argonaute proteins, guided by their bound small RNAs, orchestrate heterochromatin formation at transposon insertions and repetitive genomic loci. The molecular mechanisms that, besides recruiting heterochromatin effector proteins, are required for this silencing process are poorly understood. Here, we show that the SFiNX complex, the central silencing mediator downstream of nuclear Piwi-piRNA complexes in Drosophila, enables co-transcriptional silencing via the formation of molecular condensates. Condensate formation is stimulated by nucleic acid binding and requires SFiNX to form a homodimer. The dynein light chain dLC8, a highly conserved dimerization hub protein, mediates homo-dimerization of SFiNX. Point mutations preventing dLC8-mediated SFiNX dimerization result in transposon de-repression and sterility. dLC8’s function can be bypassed with a heterologous dimerization domain, suggesting that dimerization is a constitutive rather than a regulated feature of SFiNX. We propose that nucleic-acid stimulated condensate formation enables co-transcriptional silencing through the retention of the target RNA at chromatin, thereby allowing effector proteins to establish heterochromatin at the target locus.
2021-02-12 | PXD022010 | Pride
Project description:Bacterial RNase III cleaves long dsRNA at preferred sites
| PRJNA491502 | ENA
Project description:Long noncoding RNAs (lncRNAs) are an important class of transcripts that regulate gene expression on many levels, yet their mechanisms of action remain poorly understood. Previous studies have indicated that these RNAs can serve as modular scaffolds to recruit a variety of protein complexes and coordinate their distinct functions. XIST, a founding member of the lncRNA family, controls the inactivation of an entire X chromosome in placental mammals. Here we develop and integrate several orthogonal structure-interaction analysis methods to demonstrate that XIST RNA-protein complex folds into a modular architecture that is conserved in evolution. The discrete XIST RNA domains interact with distinct sets of effector proteins to orchestrate the X chromosome inactivation (XCI). The modular architecture plays an essential role, in addition to the sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and establishes a paradigm for mechanistic studies of lncRNA functions.
2020-04-23 | GSE126716 | GEO
Project description:Long noncoding RNAs (lncRNAs) are an important class of transcripts that regulate gene expression on many levels, yet their mechanisms of action remain poorly understood. Previous studies have indicated that these RNAs can serve as modular scaffolds to recruit a variety of protein complexes and coordinate their distinct functions. XIST, a founding member of the lncRNA family, controls the inactivation of an entire X chromosome in placental mammals. Here we develop and integrate several orthogonal structure-interaction analysis methods to demonstrate that XIST RNA-protein complex folds into a modular architecture that is conserved in evolution. The discrete XIST RNA domains interact with distinct sets of effector proteins to orchestrate the X chromosome inactivation (XCI). The modular architecture plays an essential role, in addition to the sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and establishes a paradigm for mechanistic studies of lncRNA functions.
2020-04-23 | GSE126715 | GEO