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Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [Temp_Stress_circ]

ABSTRACT: Circular RNAs are a large class of stable RNAs generated by backsplicing that accumulate with age in neural tissue. To determine the reason for this accumulation, we profiled circRNAs from fly heads at six timepoints during their lifespan. We found that the global levels of circRNAs increase linearly with age and that circRNAs are excellent age-markers. At the individual level, we found that most circRNAs increase their levels with age, and this increase does not correlate with changes on overall transcription, the levels of the mRNA counterparts, changes in intron retention, or splicing of the host gene, demonstrating that the increase is not due to biogenesis. In addition, a sustained stimulus, like transient exposure to higher or lower temperatures, leads to increases (but no decreases) in the levels of specific circRNAs further demonstrating the stability of these molecules in vivo. This unusually high stability suggests that circRNAs can be used as experience markers. Indeed, flies that were treated for ten days at 29°C display high levels of specific temperature-induced circRNAs even six weeks after being returned to standard conditions. Together, our data demonstrates that circRNAs are extremely stable in vivo and that they can be utilized as stress/life experience markers.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE261524 | GEO | 2025/03/04

REPOSITORIES: GEO

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Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [CSaging]

Project description:Circular RNAs are a large class of stable RNAs generated by backsplicing that accumulate with age in neural tissue. To determine the reason for this accumulation, we profiled circRNAs from fly heads at six timepoints during their lifespan. We found that the global levels of circRNAs increase linearly with age and that circRNAs are excellent age-markers. At the individual level, we found that most circRNAs increase their levels with age, and this increase does not correlate with changes on overall transcription, the levels of the mRNA counterparts, changes in intron retention, or splicing of the host gene, demonstrating that the increase is not due to biogenesis. In addition, a sustained stimulus, like transient exposure to higher or lower temperatures, leads to increases (but no decreases) in the levels of specific circRNAs further demonstrating the stability of these molecules in vivo. This unusually high stability suggests that circRNAs can be used as experience markers. Indeed, flies that were treated for ten days at 29°C display high levels of specific temperature-induced circRNAs even six weeks after being returned to standard conditions. Together, our data demonstrates that circRNAs are extremely stable in vivo and that they can be utilized as stress/life experience markers.

2025-03-03 | GSE261460 | GEO

Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [Temp_Stress_circ]

Project description:Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [Temp_Stress_circ]

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Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [CSaging]

Project description:Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [CSaging]

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microRNA levels in patients receiving CRT

Project description:This is a discovery cohort of six patients who received CRT with significant improvement in ejection fraction (EF), and six who received CRT but did not experience improvement. All patients are male, with left bundle branch block and do not have coronary disease (non-ischemic myopathy). Patients are matched for age and ejection fraction (EF)

2016-01-31 | GSE53821 | GEO

Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood

Project description:Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples. Sequencing of blood RNA from five healthy individuals (biological replicates) plus technical replicate of one sample and detection of circRNAs.

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circRNAs microarray analysis in colorectal caner tissues

Project description:Circular RNA (circRNA) is a kind of transcripts characterized by originating from the back-splicing of pre-mRNA. CircRNAs have higher stability than liner transcripts and are more resistant to RNase R due to their loop structure, which makes circRNAs potential diagnostic markers and therapeutic targets for cancer . The biological functions of circRNAs are widely involved in the proliferation, metastasis, apoptosis, and autophagy of various cancers via multiple ways. To further investage the role of circRNA in CRC, a circRNA micoarray was performed.

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Circular RNAs are a large class of animal RNAs with regulatory potency (RNA-Seq)

Project description:Circular RNAs (circRNAs) in animals are an enigmatic class of RNAs with unknown function. To systematically explore circRNAs, we sequenced and computationally analyzed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, with oftentimes tissue/developmental stage specific expression. Sequence analysis suggested important regulatory functions for circRNAs. Indeed, we discovered that human circRNA CDR1as is densely bound by miRNA effector complexes and harbors 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebra fish impaired midbrain development similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, indicating previously unrecognized regulatory potential of coding sequences. 1 Sample

2013-02-28 | E-GEOD-43572 | biostudies-arrayexpress

Cytoplasmic DIS3 degrades circular RNAs independently of the exosome

Project description:Circular RNAs (circRNAs) are frequently generated during splicing. Their physiological roles, however, remain largely elusive. Some specific circRNAs function as microRNA (miRNA) or RNA binding protein (RBP) sponges or encode for proteins and are actively translated. Due to the lack of accessible ends, circRNAs are resistant to exonucleolytic cleavage and thus are more stable than linear RNAs. Nevertheless, circRNAs are most likely turned over by cellular degradation pathways. Here, we used a biochemical purification strategy to find nucleases that could degrade circRNAs. We identified the exosome-associated nuclease DIS3, which contains an endonucleolytic PIN domain and an exonuclease domain. We show that DIS3 can degrade circRNAs independently of the exosome in vitro. Although moderately, RNA-seq reveals that selected circRNAs are stabilized when DIS3 is reduced in vivo. Based on our data, we propose a model, in which cytoplasmic DIS3 contributes to the turnover of circRNAs in human cells.

2025-05-05 | PXD050442 | Pride

Identification of circular RNA hsa_circ_001879 and hsa_circ_004104 as novel biomarkers for coronary artery disease

Project description:The circRNA profiles of 24 CAD patients and 7 controls were performed by microarray. Six classifiers were used to evaluate potential circRNAs biomarkers. The expression levels of candidate circRNAs were further verified by qRT-PCR in large cohorts. Logistic regression analysis and receiver operating characteristic were conducted to assess the diagnostic value. A total of 624 circRNAs and 171 circRNAs were significantly upregulated and downregulated, respectively, in CAD patients relative to controls. A four-circRNA signature was identified using six different classifiers. Among these four circRNAs, hsa_circ_001879 and hsa_circ_004104 were found significantly upregulated in validation cohorts. We offered a transcriptome-wide overview of aberrantly expressed circRNAs in CAD patients, and Hsa_circ_001879 and hsa_circ_004104 were replicated and identified to be significantly upregulated in CAD patients. Our results suggested that hsa_circ_001879 and hsa_circ_004104 might serve as diagnostic biomarkers for CAD.

2021-06-07 | GSE115733 | GEO

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