Characterization of a new class of RNA products from the Pax-5 oncogene: circular RNAs
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ABSTRACT:
PROVIDER: PRJNA779709 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16919532.fastq.gz | Fastqsanger.gz | |||
| SRR16919533.fastq.gz | Fastqsanger.gz | |||
| SRR16919534.fastq.gz | Fastqsanger.gz | |||
| SRR16919535.fastq.gz | Fastqsanger.gz | |||
| SRR16919536.fastq.gz | Fastqsanger.gz |
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Project description:Circular RNAs (circRNAs) represent a relatively new class of RNA products, which are gaining interest due to their involvement in many biological processes and cancer disease. Due to their innate ability to bind and modulate co-interacting proteins and microRNAs (miRs), circRNAs represent an additional layer of complex intracellular signaling and regulatory networks supporting cell biology and cancer phenotypes. In this study, we identify and characterize various circRNA products, which derive from the Pax-5 oncogene (circPax-5) in B lymphocytes. We establish the expression profiles of multiple circPax-5 variants in a collection of previously reported Pax-5 expressing tissues in addition to cell models and clinical samples from B cell cancer lesions. For example, we observe that circPax-5 products are overexpressed (up to 13-fold) in chronic lymphocytic leukemia (CLL) where the majority of these circRNAs consists of a specific circPax-5 isoform containing the sequence of exons 2 to 5 (circPax-5_2-5) of the Pax-5 locus. Given the established role of Pax-5 gene products in cancer biology, we also we set out to assess the impact of circPax-5 in cancer processes using conditional expression of circPax-5_2-5 in B cell lines. Interestingly, we found that circPax-5_2-5 was associated with cancer cell growth rates, which were dependent on B cell differentiation and cancer subtypes. We also characterized mechanistic features of circPax-5 in B cell lines based on common molecular features of circRNAs (ex: miR sequestering and sponging). CircPax-5 complexes from B cells were thus isolated by circRNA precipitations and submitted to deep sequencing analysis to identify co-interacting miRs. In addition to miR sponging profiles, circPax-5 were also studied for potential translation of novel peptides through putative internal ribosome entry sites (IRES). Using a dual IRES-dependent reporter gene assay, we found that circPax-5_2-5 harbors IRES motifs capable of encoding uncharacterized proteins. Altogether, our study introduces a new category of Pax-5 gene products which provide an extension of Pax-5-dependant signaling and function in B lymphocytes. This is particularly important in cancer cells given our observations of elevated circPax-5 levels in specific B cell cancer lesions. Furthermore, the elucidation of new players from the Pax-5 oncogene could provide the mapping of unknown cancer pathways, which could be targeted for therapeutic and/or diagnostic strategies in B cell cancer lesions.
2025-04-01 | GSE188623 | GEO
Project description:The mechanisms behind the evolution of complex genomic amplifications in cancer have remained largely unclear. We here identified a type of amplification, termed as “seismic amplificationâ€Â, that is characterized by multiple rearrangements and discontinuous copy number levels. Seismic amplifications occurred in 9.9% (274/2,756) of cases across 38 cancer types and were associated with massively increased copy numbers and elevated oncogene expression. Reconstruction of the development of seismic amplification revealed a stepwise evolution, starting with a chromothripsis event, followed by formation of circular extrachromosomal DNA that subsequently underwent repetitive rounds of circular recombination. The resulting amplicons persisted as extrachromosomal DNA circles or had reintegrated into the genome in overt tumors. Together, our data indicate that the sequential occurrence of chromothripsis and circular recombination drives oncogene amplification and over-expression in a substantial fraction of human malignancies.
| EGAS00001005424 | EGA
Project description:Oncogenes are commonly amplified on extrachromosomal DNA particles (ecDNA) in cancer, but our understanding of the structure of ecDNA and its impact on gene regulation is limited. We integrated ultrastructural imaging, long range-optical mapping, and computational analysis of whole genome sequencing to demonstrate unequivocally that ecDNA is circular. Pan-cancer analyses reveal that the oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of tumours, linking elevated copy with very high levels of transcription. Quantitative assessment of the chromatin state, including ATAC-seq to map the accessible genome and ATAC-see to examine spatial distribution of open chromatin, reveal that while ecDNA is chromatinized, it lacks higher order compaction typical of chromosomes. In fact, ecDNA contains the most accessible DNA in the tumour genome. Using chromosome conformation capture technologies and CRISPR interference, we reveal the differential organization of active chromatin in cancer that is dictated by the circular shape of ecDNA. Lastly, we develop comprehensive maps that provide new insight into how circular ecDNA structure determines oncogene function, bridging ecDNA biology with modern cancer genomics and epigenetics.
2019-12-31 | GSE131956 | GEO
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
Project description:Alveolar rhabdomyosarcomas (ARMS) are aggressive soft-tissue sarcomas affecting children and young adults. Most ARMS tumors express the PAX3-FKHR or PAX7-FKHR (PAX-FKHR) fusion genes resulting from the t(2;13) or t(1;13) chromosomal translocations, respectively. However, up to 25% of ARMS tumors are fusion negative, making it unclear whether ARMS represent a single disease or multiple clinical and biological entities with a common phenotype. To test to what extent PAX-FKHR determine class and behavior of ARMS, we used oligonucleotide microarray expression profiling on 139 primary rhabdomyosarcoma tumors and an in vitro model. We found that ARMS tumors expressing either PAX-FKHR gene share a common expression profile distinct from fusion-negative ARMS and from the other rhabdomyosarcoma variants. We also observed that PAX-FKHR expression above a minimum level is necessary for the detection of this expression profile. Using an ectopic PAX3-FKHR and PAX7-FKHR expression model, we identified an expression signature regulated by PAX-FKHR that is specific to PAX-FKHR-positive ARMS tumors. Data mining for functional annotations of signature genes suggested a role for PAX-FKHR in regulating ARMS proliferation and differentiation. Cox regression modeling identified a subset of genes within the PAX-FKHR expression signature that segregated ARMS patients into three risk groups with 5-year overall survival estimates of 7%, 48%, and 93%. These prognostic classes were independent of conventional clinical risk factors. Our results show that PAX-FKHR dictate a specific expression signature that helps define the molecular phenotype of PAX-FKHR-positive ARMS tumors and, because it is linked with disease outcome in ARMS patients, determine tumor behavior. NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897589792480:1'
2016-12-22 | GSE92689 | GEO
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. PARCLIP was performed as in Hafner et. al Cell 2010 with HEK293 cell lines stably expressing HIS/FLAG/HA-tagged AGO1 or AGO2. We used 4-thiouridine (4SU) to enhance the crosslink and generated cDNA libraries.
2013-02-28 | E-GEOD-43573 | biostudies-arrayexpress
Project description:modENCODE_submission_3856 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP117(official name : OP117 genotype : unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PAX-1::EGFP fusion protein is expressed in the correct pax-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PAX-1 transcription factor. made_by : Unknown ); Developmental Stage: embryo; Genotype: unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119); Sex: mixed Male and Hermaphrodite population; EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene pax-1; Strain OP117(official name : OP117 genotype : unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PAX-1::EGFP fusion protein is expressed in the correct pax-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PAX-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48722 | biostudies-arrayexpress
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.
2015-10-26 | E-GEOD-73570 | biostudies-arrayexpress
Project description:Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.
2020-12-31 | GSE143957 | GEO
Project description:The use of peripheral blood mononuclear cells (PBMC) for transcriptome analysis has already been proven valuable for assessing disease-associated and drug response related gene signatures. While these proof-of-principle studies have been critically important, the instability of RNA within PBMC prohibits their use in large scale multi-center trials for which samples have to be transported for a prolonged time prior RNA isolation. Therefore, a prerequisite for transcriptome analysis of peripheral blood in clinical trials will be a standardized and valid method to immediately stabilize the RNA profile after blood withdrawal. We demonstrate that the globin mRNA reduction method results in significantly improved data quality of stabilized RNA samples resulting in low intra-group variance and a detection rate of expressed genes similar to PBMC. More important, even small differences in gene expression such as observed between females and males were detected and sufficient to predict gender in whole blood samples. Experiment Overall Design: Whole blood was drawn from 7 female and 7 male subjects into PAXgeneTM blood collection tubes. After isolation of total RNA, a subset of each RNA sample was subjected to a globin reduction protocol (GRP) Microarray analysis was performed from PAX and GRP samples using Affymetrix U133A arrays. Experiment Overall Design: Gene expression profiles of females and males were compared in the PAX and the GRP group.
2008-06-12 | E-GEOD-2888 | biostudies-arrayexpress