The emerging roles of circRNAs in cancer and oncology

Nature Reviews Clinical Oncology, Journal Year: 2021, Volume and Issue: 19(3), P. 188 - 206

Published: Dec. 15, 2021

Language: Английский

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Biogenesis and Regulatory Roles of Circular RNAs

Annual Review of Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 38(1), P. 263 - 289

Published: May 25, 2022

Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well the processing of cellular housekeeping noncoding and precursor messenger RNAs. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes subjected to backsplicing, leading widespread expression a specific type (circRNAs) in eukaryotic cells. Here, we discuss experimental strategies used discover characterize diverse circRNAs at both genome individual gene scales. We further highlight current understanding how are generated mature transcripts function. Some act impact regulation by serving decoys or competitors for microRNAs proteins. Others form extensive networks ribonucleoprotein complexes encode functional peptides translated response certain stresses. Overall, emerged an important class RNAmolecules physiological processes, including early development, immune responses, neurogenesis, tumorigenesis.

Language: Английский

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Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(7), P. 836 - 845

Published: March 11, 2021

Language: Английский

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The potential of using blood circular RNA as liquid biopsy biomarker for human diseases

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(12), P. 911 - 946

Published: Nov. 1, 2020

Abstract Circular RNA (circRNA) is a novel class of single-stranded RNAs with closed loop structure. The majority circRNAs are formed by back-splicing process in pre-mRNA splicing. Their expression dynamically regulated and shows spatiotemporal patterns among cell types, tissues developmental stages. CircRNAs have important biological functions many physiological processes, their aberrant implicated human diseases. Due to high stability, becoming promising biomarkers diseases, such as cardiovascular autoimmune diseases cancers. In this review, we focus on the translational potential using blood liquid biopsy for We highlight abundant expression, essential significant correlations various components peripheral blood, including whole cells extracellular vesicles. addition, summarize current knowledge circRNA disease diagnosis or prognosis.

Language: Английский

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catRAPIDomics v2.0: going deeper and wider in the prediction of protein–RNA interactions

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(W1), P. W72 - W79

Published: April 29, 2021

Prediction of protein-RNA interactions is important to understand post-transcriptional events taking place in the cell. Here we introduce catRAPID omics v2.0, an update our web server dedicated computation interaction propensities at transcriptome- and RNA-binding proteome-level 8 model organisms. The accepts multiple input protein or RNA sequences computes their scores on updated precompiled libraries. Additionally, it now possible predict between a custom set set. Considerable effort has been put into generation new database motifs that are searched within predicted targets proteins. In this update, sequence fragmentation scheme fragment module included, which allows handle long linear RNAs analyse circular RNAs. For top-scoring pairs, shows binding sites both reports whether conserved orthologous pairs. v2.0 powerful tool for characterization classification RNA-protein freely available http://service.tartaglialab.com/page/catrapid_omics2_group along with documentation tutorial.

Language: Английский

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Going circular: history, present, and future of circRNAs in cancer

Oncogene, Journal Year: 2023, Volume and Issue: 42(38), P. 2783 - 2800

Published: Aug. 16, 2023

Abstract To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional that shown to regulate gene expression transcriptionally post-transcriptionally exhibit distinct tissue- development-specific patterns associated with a variety normal disease conditions, including cancer pathogenesis. Over the past years, due their intrinsic stability resistance ribonucleases, particular attention has drawn use as reliable diagnostic prognostic biomarkers in diagnosis, treatment, prevention. However, there some critical caveats utility clinic. Their circular shape limits annotation complete functional elucidation is lacking. This makes detection biomedical application still challenging. Herein, we review current knowledge circRNA biogenesis function, involvement tumorigenesis potential cancer-targeted therapy.

Language: Английский

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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets

Functional & Integrative Genomics, Journal Year: 2023, Volume and Issue: 23(1)

Published: Jan. 10, 2023

Language: Английский

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circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c‐Myc Translation

Advanced Science, Journal Year: 2022, Volume and Issue: 9(8)

Published: Jan. 24, 2022

Previous studies have identified the regulatory roles of circular RNAs (circRNAs) in human cancers. However, molecular mechanisms circRNAs hepatocellular carcinoma (HCC) remain largely unknown. This study screens expression profile HCC and identifies circVAMP3 as a significantly downregulated circRNA tissues. patients with low present poor prognosis. negatively regulates proliferation metastasis cells vitro vivo by driving phase separation CAPRIN1 promoting stress granule formation cells, which can downregulate protein level Myc proto-oncogene inhibiting c-Myc translation. Furthermore, is widely expressed many tissues related Therefore, potential prognostic indicator for may serve therapeutic target treatment.

Language: Английский

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A guide to naming eukaryotic circular RNAs

Nature Cell Biology, Journal Year: 2023, Volume and Issue: 25(1), P. 1 - 5

Published: Jan. 1, 2023

Language: Английский

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RNA-seq data science: From raw data to effective interpretation

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: March 13, 2023

RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due large part to the continuous efforts of bioinformatics community develop accurate scalable computational tools analyze enormous amounts transcriptomic data that it produces. RNA-seq analysis enables genes their corresponding transcripts be probed for a variety purposes, such as detecting novel exons or whole transcripts, assessing expression alternative studying splicing structure. It can challenge, however, obtain meaningful biological signals from raw because scale well inherent limitations different technologies, amplification bias biases library preparation . The need overcome these technical challenges pushed rapid development tools, which have evolved diversified accordance with technological advancements, leading current myriad tools. These combined diverse skill sets biomedical researchers, help unlock full potential RNA-seq. purpose this review explain basic concepts define discipline-specific jargon.

Language: Английский

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