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Distinct characteristics of Arabidopsis thaliana circular RNAs

ABSTRACT: Distinct characteristics of Arabidopsis thaliana circular RNAs

PROVIDER: PRJNA515943 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8463991_1.fastq.gz	Fastqsanger.gz
	SRR8463991_2.fastq.gz	Fastqsanger.gz
	SRR8463992_1.fastq.gz	Fastqsanger.gz
	SRR8463992_2.fastq.gz	Fastqsanger.gz
	SRR8463993_1.fastq.gz	Fastqsanger.gz

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Distinct characteristics of Arabidopsis thaliana circular RNAs

Project description:In all living organisms, regulation of gene expression is fundamental for survival and adaptation. Gene expression can be modulated at various steps, including at the level of RNA processing. During the last few years, the importance of alternative splicing of mRNAs in controlling plant development and stress responses were emerged and highlighted its importance. Recently, an other type of alternative splicing has been reported which leads to the generation of circular RNAs (circRNAs), a novel class on endogenous noncoding RNAs. Several functions of circular RNAs have been proven or proposed, including functioning as microRNA or RNA-binding protein decoys, playing regulatory roles in gene expression or affecting transcriptional control via special RNA-RNA interactions. Despite the widening knowledge of circRNAs and their functional aspects in the animal kingdom, relatively little is known about circRNAs in plants. In order to detect and classify circRNAs in Arabidopsis thaliana, we created a workflow that includes generation of Illumina libraries enriched for circRNAs and a comparison of biocomputational tools developed for detecting endogenous circular RNAs in other species. With the power of high-throughput sequencing and evaluation of algorithms, high-fidelity candidates were subjected for an analysis of their functional role in plant development and stress-related responses, especially regarding the role of splicing, including alternative splicing events, splice site preference and strength variances and transcript composition and to comprehend the role of RNA processing in stress response. Here we present an approach combining bioinformatic tools and molecular techniques to investigate the adaptability of detection methods of circRNAs from other species to plant circular RNAs, and based on our high-fidelity results identify and understand the characteristics of circRNAs in Arabidopsis thaliana.

2019-01-24 | GSE125378 | GEO

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Project description:To further investigate the circular RNA gene expression characteristics in SACC cell lines, we utilized the SBC Human (4*180K) ceRNA microarray to identify differential circular RNAs between SACC-83 and SACC-LM cells.

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Investigating the circular RNA gene expression characteristics in salivary adenoid cystic carcinoma (SACC) patients.

Project description:To further investigate the circular RNA gene expression characteristics in SACC patients, we utilized the SBC Human (4*180K) ceRNA microarray to identify differential circular RNAs between SACC tissues and normal SMG tissues from the same patient.

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Circular and fusion RNAs in medulloblastoma development

Project description:The expression of circular RNAs in cerebellar cancer versus medulloblastoma subgroups SHH, WNT, Group3 and Group4 has been interrogated. Fusion RNAs containing exons from distinct genes joined at canonical splice sites were also identified.

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Circular RNAs affect mRNA stability

Project description:Circular RNAs affect mRNA stability

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An improved method for identifying biological circular RNAs

Project description:Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq

2016-07-05 | E-GEOD-83992 | biostudies-arrayexpress

Characteristics of circular extrachromosomal DNA in euglenids

Project description:Characteristics of circular extrachromosomal DNA in euglenids

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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

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