Genome-Wide Identification of Circular RNAs in Fungal Parasite Nosema ceranae

Abstract Background As a novel class of non-coding RNAs, circular RNAs (circRNAs) are key regulators of the development and progression of different cancers. However, little is known about the function and biological mechanism of circLMTK2, also named hsa_circ_0001725, in gastric cancer (GC) tumourigenesis. Methods circLMTK2 was identified in ten paired cancer specimens and adjacent normal tissues by RNA sequencing and genome-wide bioinformatic analysis and verified by quantitative real-time PCR (qRT-PCR). Knockdown or exogenous expression of circLMTK2 combined with in vitro and in vivo assays were performed to prove the functional significance of circLMTK2. The molecular mechanism of circLMTK2 was demonstrated by searching the CircNet database and confirmed by RNA in vivo precipitation assays, western blotting, luciferase assays and rescue experiments. Results circLMTK2 was frequently upregulated in GC tissues, and high circLMTK2 expression was associated with poor prognosis, lymph node metastasis and poor TNM stage in GC patients. Functionally, circLMTK2 overexpression promoted GC cell proliferation and tumourigenicity in vitro and in vivo. Furthermore, ectopic circLMTK2 expression enhanced GC cell migration and invasion in vitro and tumour metastasis in vivo. In addition, we demonstrated that circLMTK2 could sponge miR-150-5p, thus indirectly regulating the c-Myc expression and contributing to GC tumourigenesis. Conclusion Our findings demonstrate that circLMTK2 functions as a tumour promoter in GC through the miR-150-5p/c-Myc axis and could thus be a prognostic predictor and therapeutic target for GC.

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Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

Cell Reports ◽

10.1016/j.celrep.2014.10.062 ◽

2014 ◽

Vol 9 (5) ◽

pp. 1966-1980 ◽

Cited By ~ 459

Author(s):

Jakub O. Westholm ◽

Pedro Miura ◽

Sara Olson ◽

Sol Shenker ◽

Brian Joseph ◽

...

Keyword(s):

Circular Rnas ◽

Genome Wide Analysis ◽

Genome Wide ◽

Age Dependent

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Whole transcriptome data of uninfected and Nosema ceranae-infected midguts of eastern honeybee workers

10.1101/2020.03.13.990697 ◽

2020 ◽

Author(s):

Huazhi Chen ◽

Dingding Zhou ◽

Yu Du ◽

Cuiling Xiong ◽

Yanzhen Zheng ◽

...

Keyword(s):

Apis Cerana ◽

Gc Content ◽

Nosema Ceranae ◽

Post Inoculation ◽

List Type ◽

Valuable Resource ◽

Fungal Parasite ◽

Differential Expression Pattern ◽

Non Coding Rnas ◽

Whole Transcriptome

ABSTRACTApis cerana cerana is a subspecies of eastern honeybee, Apis cerana. Nosema ceranae is a widespread fungal parasite of honeybee, causing heavy losses for beekeeping industry all over the world. In this article, total RNA of normal midguts (AcCK1, AcCK2) and N. ceranae-infected midguts of A. c. cerana workers at 7 d and 10 d post inoculation (AcT1, AcT2) were respectively isolated followed by strand-specific cDNA library construction and next-generation RNA sequencing. In tolal, 56270223688, 44860946964, 78991623806, and 92712308296 raw reads were derived from AcCK1, AcCK2, AcT1 and AcT2, respectively. Following strict quality control, 54495191388, 43570608753, 76708161525, and 89467858351 clean reads were obtained, with Q30 value of 95.80%, 95.99%, 96.07% and 96.04%, and GC content of 44.20%, 43.44%, 44.83% and 43.63%, respectively. The raw data were submitted to the NCBI Sequence Read Archive database and connected to BioProject PRJNA562784. These data offers a valuable resource for deep investigation of mechanisms underlying eastern honeybee responding to N. ceranae infection and host-fungal parasite interaction during microsporidiosis.Value of the DataCurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response of A. c. cerana worker to N. ceranae infection.The accessible data can be used to investigate differential expression pattern and regulatory network of non-coding RNAs in A. c. cerana workers’ midguts responding to N. ceranae challenge.This data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranae interaction.

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Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets

10.20944/preprints201911.0202.v1 ◽

2019 ◽

Author(s):

Minzhe Zhang ◽

Tao Wang ◽

Guanghua Xiao ◽

Yang Xie

Keyword(s):

Large Scale ◽

Rna Binding ◽

Rna Binding Proteins ◽

Read Length ◽

Circular Rnas ◽

Binding Partners ◽

Genome Wide ◽

Wide Scale ◽

And Function ◽

Short Read Length

Circular RNAs are a special type of RNAs which recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes but are relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of CLIP-Seq experiments, RBP-circRNA interactions could also be identified through specialized analysis of CLIP-Seq datasets. However, many technical difficulties are involved in this process, such as the usually short read length of CLIP-Seq reads. In this study, we created a pipeline called Clirc specialized for profiling circRNAs in CLIP-Seq data and analyzing the characteristics of RBP- circRNAs interactions. In conclusion, this is one of the first few studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets to our knowledge, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs. Clirc software is available at https://github.com/Minzhe/Clirc

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A CLEAR pipeline for direct comparison of circular and linear RNA expression

10.1101/668657 ◽

2019 ◽

Author(s):

Xu-Kai Ma ◽

Meng-Ran Wang ◽

Chu-Xiao Liu ◽

Rui Dong ◽

Gordon G. Carmichael ◽

...

Keyword(s):

Ribosomal Rna ◽

Circular Rnas ◽

Rna Expression ◽

Computational Pipeline ◽

Rna Seq ◽

Link Type ◽

Genome Wide ◽

A Genome

ABSTRACTSequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with sequences from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, but a direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging. This is because quantification of BSJ fragments differs from that of linear RNA expression that uses normalized RNA-seq fragments mapped to the whole gene bodies. Here, we have developed a computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq (CLEAR, https://github.com/YangLab/CLEAR). A new quantitation parameter, FPB (fragments per billion mapped bases), is applied to evaluate circular and linear RNA expression individually by fragments mapped to circRNA-specific BSJ sites or to linear RNA-specific splicing junction (SJ) sites. Then, circular and linear RNA expression are directly compared by dividing FPBcirc by FPBlinear to generate a CIRCscore, which indicates the relative circRNA expression using linear RNA expression as the background. Highly-expressed circRNAs with low cognate linear RNA expression background can be identified for further investigation.

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circVAR database: genome-wide archive of genetic variants for human circular RNAs

10.21203/rs.3.rs-48904/v2 ◽

2020 ◽

Author(s):

Min Zhao ◽

Hong Qu

Keyword(s):

Genetic Variants ◽

Complex Traits ◽

Large Scale ◽

Rna Binding ◽

Rna Binding Proteins ◽

Association Studies ◽

Chromosome 17 ◽

Circular Rnas ◽

Genome Wide Association Studies ◽

Genome Wide

Abstract Background: Circular RNAs (circRNAs) play important roles in regulating gene expression through binding miRNAs and RNA binding proteins. Genetic variation of circRNAs may affect complex traits/diseases by changing their binding efficiency to target miRNAs and proteins. There is a growing demand for investigations of the functions of genetic changes using large-scale experimental evidence. However, there is no online genetic resource for circRNA genes. Results: We performed extensive genetic annotation of 295,526 circRNAs integrated from circBase, circNet and circRNAdb. All pre-computed genetic variants were presented at our online resource, circVAR, with data browsing and search functionality. We explored the chromosome-based distribution of circRNAs and their associated variants. We found that, based on mapping to the 1000 Genomes and ClinVAR databases, chromosome 17 has a relatively large number of circRNAs and associated common and health-related genetic variants. Following the annotation of genome wide association studies (GWAS)-based circRNA variants, we found many non-coding variants within circRNAs, suggesting novel mechanisms for common diseases reported from GWAS studies. For cancer-based somatic variants, we found that chromosome 7 has many highly complex mutations that have been overlooked in previous research. Conclusion: We used the circVAR database to collect SNPs and small insertions and deletions (INDELs) in putative circRNA regions and to identify their potential phenotypic information. To provide a reusable resource for the circRNA research community, we have published all the pre-computed genetic data concerning circRNAs and associated genes together with data query and browsing functions at http://soft.bioinfo-minzhao.org/circvar .

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Nanopore-based genome-wide DNA methylation sequencing data of Nosema ceranae-inoculated and un-inoculated eastern honeybee workers' midguts

10.1101/2021.11.23.469791 ◽

2021 ◽

Author(s):

Jun Ke Yu ◽

Da Fu Chen ◽

Rui Guo

Keyword(s):

Dna Methylation ◽

Host Response ◽

Reference Genome ◽

Apis Cerana ◽

Vital Role ◽

Nosema Ceranae ◽

Post Inoculation ◽

Sequencing Data ◽

Average Quality ◽

Genome Wide

Apis cerana cerana is an excellent subspecies of Apis cerana, playing a vital role in pollination for wild flowers and crops as well as ecological balance. Nosema ceranae, an emergent fungal parasite infecting various bee species, originates from eastern honeybee. In this article, midguts of N. ceranae-inoculated A. c. cerana workers at 7 days post inoculation (dpi) and 10 dpi (AcT1 and AcT2) and un-inoculated workers' midguts (AcCK1, AcCK2) were subjected to Nanopore-based genome-wide DNA methylation sequencing. Totally, 1773258, 2151476, 1927874 and 2109961 clean reads were generated from AcCK1, AcCK2, AcT1, and AcT2 groups, with the N50 lengths of 7548, 7936, 7678, and 7291 and the average quality value of 8.97, 8.95, 9.24, and 8.98, respectively. Among these, 93.85%, 94.49%, 88.69%, and 81.27% clean reads could be mapped to the reference genome of A. c. cerana. In the aforementioned four groups, 2149685, 2614513, 1637018 and 2726985 CHG sites were identified; the numbers of CHH sites were 9581990, 11801082, 7178559, and 12342423, whereas those of CpG sites were 14325356, 15703508, 14856284 and 13956849, respectively. Additionally, there were 36114, 118867, 30249, and 82984 6mA methylation sites respectively discovered. These data can be used for identifying differential 5mC methylation and 6mA methylation engaged in response of eastern honeybee workers to N. ceranae infestation, and for investigating the 5mC or 6mA methylation-mediated mechanism underlying host response.

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