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SeekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

ABSTRACT: seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

PROVIDER: PRJNA472991 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7215564.fastq.gz	Fastqsanger.gz
	SRR7215565.fastq.gz	Fastqsanger.gz

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seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

Project description:Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT.

2021-02-02 | GSE114896 | GEO

seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data.

Project description:Over the past two decades, researchers have discovered a special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs (circRNAs) have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of current studies has been on the tissue-specific circRNAs that exist only in one tissue but not in other tissues or on the disease-specific circRNAs that exist in certain disease conditions, such as cancer, but not under normal conditions. This approach was conducted in the relative absence of methods that analyze a group of common circRNAs that exist in both conditions, but are more abundant in one condition relative to another (differentially expressed). Studies of differentially expressed circRNAs (DECs) between two conditions would serve as a significant first step in filling this void. Here, we introduce a novel computational tool, seekCRIT (seek for differentially expressed CircRNAs In Transcriptome), that identifies the DECs between two conditions from high-throughput sequencing data. Using rat retina RNA-seq data from ischemic and normal conditions, we show that over 74% of identifiable circRNAs are expressed in both conditions and over 40 circRNAs are differentially expressed between two conditions. We also obtain a high qPCR validation rate of 90% for DECs with a FDR of < 5%. Our results demonstrate that seekCRIT is a novel and efficient approach to detect DECs using rRNA depleted RNA-seq data. seekCRIT is freely downloadable at https://github.com/UofLBioinformatics/seekCRIT. The source code is licensed under the MIT License. seekCRIT is developed and tested on Linux CentOS-7.

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Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells

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The differentially expressed circular RNAs in the hippocampus of Nrf2-knockout mice

Project description:The differentially expressed circular RNAs in the hippocampus of Nrf2-knockout mice

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Detecting differentially expressed circular RNAs from multiple quantification methods using a generalized linear mixed model.

Project description:Finding differentially expressed circular RNAs (circRNAs) is instrumental to understanding the molecular basis of phenotypic variation between conditions linked to circRNA-involving mechanisms. To date, several methods have been developed to identify circRNAs, and combining multiple tools is becoming an established approach to improve the detection rate and robustness of results in circRNA studies. However, when using a consensus strategy, it is unclear how circRNA expression estimates should be considered and integrated into downstream analysis, such as differential expression assessment. This work presents a novel solution to test circRNA differential expression using quantifications of multiple algorithms simultaneously. Our approach analyzes multiple tools' circRNA abundance count data within a single framework by leveraging generalized linear mixed models (GLMM), which account for the sample correlation structure within and between the quantification tools. We compared the GLMM approach with three widely used differential expression models, showing its higher sensitivity in detecting and efficiently ranking significant differentially expressed circRNAs. Our strategy is the first to consider combined estimates of multiple circRNA quantification methods, and we propose it as a powerful model to improve circRNA differential expression analysis.

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Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs

Project description:Conversely to canonical splicing, back-splicing covalently ligates the upstream 3' splice site (SS) with downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely-identified in eukaryotes and have regulatory functions in gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA-seq of various sex-specific Drosophila samples including head, body and gonads from both genders, and identified more than ten thousand of circular RNAs, in which hundreds are sex-differentially expressed and back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene which only functionally spliced in females, promotes back-splicing of many female-differentially expressed circRNAs in the male S2 cells, while expression of a SXL mutant did not. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through a PAR-CLIP approach and revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing of those circRNAs, whereas SXL-binding on the circRNA exons inhibits the back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specifc circRNAs, as well as in the initiation of Drosophila sex-determination cascade through canoncial forward-splicing.

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Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs

Project description:Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs

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