Ontology highlight
ABSTRACT:
PROVIDER: PRJNA374924 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identification of splice variants and RNA binding partners of STAT3-induced long noncoding RNAs (STAiRs) in multiple myeloma
| PRJNA376176 | ENA
Project description:Interleukin 6 (IL-6) activates the transcription factor signal transducer and activator of transcription 3 (STAT3). We previously identified several STAT3-induced long noncoding RNAs (STAiRs) in INA-6 multiple myeloma cells (Hackermüller et al. 2014). Here, we analyze five STAiRs by CAPTURE- and ChIRP-RNA-sequencing, a pulldown of a target RNA by transcript tiling oligonucleotides. The CAPTURE technique allows the identification of different STAiR splice variants and shall give rise to the transcript architecture. ChIRP, a method first published by Chu et al 2011, is the original method on which the CAPTURE approach is based on and enables the identification of RNAs interacting with our STAiRs.
2017-08-01 | GSE95131 | GEO
Project description:STAiR18, an mRNA-like STAT3-induced long noncoding RNA shows ubiquitous expression. RNAi-mediated knockdown of STAiR18 led to a dramatic decrease in INA-6 cell vitality. Furthermore, STAiR18 knockdown reduced the STAT3 RNA and protein levels in these cells, suggesting a positive feedback loop between STAT3 and its target ncRNA STAiR18. Microarray analyses of INA-6 cells after STAiR18 or STAT3 knockdown revealed overlapping changes of transcription patterns indicating a close functional interplay between the two molecules. Taken together, STAiR18 represents a novel noncoding RNA that is likely to play an important role for the oncogenic function of the STAT3 pathway. STAT3- and STAiR18-dependent gene expression in human multiple myeloma cell line INA-6 was measured 40 hours after transfection with either a negative control siRNA, an siRNA to STAT3 or an siRNA to STAiR18. Four independent experiments were performed for each siRNA approach, yielding 12 approaches in total.
2016-07-17 | E-GEOD-71092 | biostudies-arrayexpress
Project description:Knockdown of STAiR18, an IL-6/STAT3-induced long noncoding RNA, in INA-6 multiple myeloma cells
| PRJNA290335 | ENA
Project description:Detection of RNA–DNA binding sites in long noncoding RNAs
| PRJNA489807 | ENA
Project description:RBFOX2 controls the splicing of a large number of transcripts implicated in cell differentiation and development. Parsing RNA-binding protein datasets, we uncover that RBFOX2 can interact with hnRNPC, hnRNPM and SRSF1 to regulate splicing of a broad range of splicing events using different sequence motifs and binding modes. Using immunoprecipitation, specific RBP knockdown, RNA-seq and splice-sensitive PCR, we show that RBFOX2 can target splice sites using three binding configurations: single, multiple or secondary modes. In the single binding mode RBFOX2 is recruited to its target splice sites through a single canonical binding motif, while in the multiple binding mode RBFOX2 binding sites include the adjacent binding of at least one other RNA binding protein partner. Finally, in the secondary binding mode RBFOX2 likely does not bind the RNA directly but is recruited to splice sites lacking its canonical binding motif through the binding of one of its protein partners. These dynamic modes bind distinct sets of transcripts at different positions and distances relative to alternative splice sites explaining the heterogeneity of RBFOX2 targets and splicing outcomes.
2021-06-23 | GSE140679 | GEO
Project description:Epigenetic dysregulation is a common feature of acute myeloid leukemia (AML). Recently it has become clear that long noncoding RNAs (lncRNAs) can play a key role in epigenetic regulation, and consequently also dysregulation. Currently, our understanding of the requirements and roles of lncRNAs in AML is still limited. Using CRISPRi screening, we identified the lncRNA SGOL1-AS1 as an essential regulator of survival in THP-1 AML cells. We use RNA affinity purification using a biotinylated bait to pull down binding partners of the lncRNA, SGOL1-AS1. The identified proteins show a signficant enrichment for chromatin-modifying proteins involved in gene repression and chromosome organization.
2023-06-12 | PXD034329 | Pride
Project description:Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple cancer types. The expression of CONCR is cell cycle-regulated, and it is required for cell cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication. These findings suggest a novel mechanism of action for CONCR in the modulation of DDX11 enzymatic activity, unveiling the direct involvement of a lncRNA in the establishment of sister chromatid cohesion. Characterization of the function of the long noncoding RNA CONCR. Analysis of DDX11 chromatin binding by ChIP-seq in the presence or absence of CONCR.
2016-08-03 | E-GEOD-81600 | biostudies-arrayexpress
Project description:It is widely recognized that the missing heritability of many human diseases is partially due to noncoding genetic variants, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals, and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multi-granular information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell-stage-specific regulatory roles three top novel regulatory elements on our list, respectively in the RET, RASGEF1A and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the affects the binding of the gliogenesis regulator NFIA, with a corresponding down-regulation of multiple genes in the same topologically associating domain.
2020-08-30 | GSE154972 | GEO
Project description:A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma
| PRJNA430521 | ENA