Back-splice junctions of KSHV circular RNAs
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ABSTRACT:
PROVIDER: PRJNA694907 | ENA |
REPOSITORIES: ENA
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Project description:Total RNA of KSHV-infected cells were extracted and RT-PCR was performed using viral circRNA specific divergent primers. Amplicons were sequenced with MiSeq.
2021-06-30 | GSE165527 | GEO
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.
2023-04-23 | GSE221102 | GEO
Project description:The purpose was to measure expression changes in human circular RNAs. Total RNA was harvested from KSHV-infected HUVEC and MC116 cells. A portion of the RNA was digested with RNase R to enrich for circular RNAs.
2018-11-20 | GSE120045 | GEO
Project description:RNA sequencing for KSHV circular RNAs
| PRJNA498320 | ENA
Project description:Understanding regulation of KSHV/EBV circular RNAs
| PRJNA694872 | ENA
Project description:Circular RNAs (circRNAs) are a class of ubiquitously expressed, single-stranded, covalently covalently-closed (i.e. circularised) RNA that contain a unique nucleotide sequence created by the ligation of their 5' and 3' ends, called the back-splice junction. Understanding the cellular roles of circRNAs involves, in part, investigating the effects on cell phenotype of increased expression of individual circRNAs. This is frequently done by transfecting cells with plasmid DNA containing cloned exons from which the circRNA is transcribed, flanked by sequences that promote circularisation. We observed that all commonly used plasmids we tested unexpectedly incorporated molecular scars comprising vector sequence vector sequence as a molecular scar into the circRNA back-splice junction upon circularisation. Stepwise redesign of the cloning vector corrected this problem, ensuring bona fide circRNAs are produced with their natural back-splice junction at high efficiency. The fidelity of circRNAs produced from this new construct was validated by RNA sequencing. To increase the utility of this modified resource for expressing circRNA, we developed an expanded set of vectors incorporating this design that enable selection with a variety of antibiotics and fluorescent proteins, a range of promoters varying in promoter strength and plus a complementary set of lentiviral plasmids for difficult-to-transfect cells. These resources provide a versatile toolkit for high-efficiency and scarless overexpression of circular RNAs that fulfil a critical need for the investigation of circRNA function, including the role of the unique back-splice junction.
2023-12-14 | GSE246020 | GEO
Project description:Knockout of circRNAs by base editing back-splice sites of circularized exons
| PRJNA722401 | ENA
Project description:The pervasive expression of circular RNA from protein coding loci is a recently discovered feature of many eukaryotic gene expression programs. Computational methods to discover and quantify circular RNA are essential to the study of the mechanisms of circular RNA biogenesis and potential functional roles they may play. In this paper, we present a new statistical algorithm that increases the sensitivity and specificity of circular RNA detection.by discovering and quantifying circular and linear RNA splicing events at both annotated exon boundaries and in un-annotated regions of the genome Unlike previous approaches which rely on heuristics like read count and homology between exons predicted to be circularized to determine confidence in prediction of circular RNA expression, our algorithm is a statistical approach. We have used this algorithm to discover general induction of circular RNAs in many tissues during human fetal development. We find that some regions of the brain show marked enrichment for genes where circular RNA is the dominant isoform. Beyond this global trend, specific circular RNAs are tissue specifically induced during fetal development, including a circular isoform of NCX1 in the developing fetal heart that, by 20 weeks, is more highly expressed than the linear isoform as well as beta-actin. In addition, while the vast majority of circular RNA production occurs at canonical U2 (major spliceosome) splice sites, we find the first examples of developmentally induced circular RNAs processed by the U12 (minor) spliceosome, and an enriched propensity of U12 donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, our algorithm and its results suggest a potentially significant role for circular RNA in human development. 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kit.
2015-06-25 | E-GEOD-64283 | biostudies-arrayexpress
Project description:Microarray analysis with KSHV infection and enrichment for circular RNAs
| PRJNA491438 | ENA
Project description:RNA sequencing with KSHV infection and enrichment for circular RNAs
| PRJNA489703 | ENA