Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2 DOI Creative Commons
Enrico Gaffo, Alessia Buratin, Anna Dal Molin

et al.

Briefings in Bioinformatics, Journal Year: 2021, Volume and Issue: 23(1)

Published: Sept. 13, 2021

Abstract Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by process called back-splicing. CircRNAs emerging as functional involved in the regulation biological processes well disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments characterized low discovery rates performance dependent on analysed data set. We developed CirComPara2 (https://github.com/egaffo/CirComPara2), new automated pipeline quantification, which consistently achieves high recall without losing precision combining multiple detection methods. In our benchmark analysis, outperformed state-of-the-art tools proved to be reliable robust method comprehensive transcriptome characterization.

Language: Английский

The emerging roles of circRNAs in cancer and oncology DOI
Lasse S. Kristensen, Theresa Jakobsen, Henrik Hager

et al.

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

Published: Dec. 15, 2021

Language: Английский

Citations

805
MicroRNAs and complex diseases: from experimental results to computational models DOI
Xing Chen,

Di Xie,

Qi Zhao

et al.

Briefings in Bioinformatics, Journal Year: 2017, Volume and Issue: 20(2), P. 515 - 539

Published: Sept. 15, 2017

Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one the most important components cell, miRNAs play growing role various essential biological processes. For recent few decades, amounts experimental methods computational models have been designed implemented to identify novel miRNA-disease associations. In this review, functions miRNAs, miRNA-target interactions, associations some publicly available miRNA-related databases discussed detail. Specially, considering fact that an increasing number experimentally confirmed, we selected five human diseases crucial disease-related provided corresponding introductions. Identifying has become goal biomedical research, which will accelerate understanding disease pathogenesis molecular level tools design for diagnosis, treatment prevention. Computational means association identification, could select promising pairs validation significantly reduce time cost experiments. Here, reviewed 20 state-of-the-art predicting from different perspectives. Finally, summarized four factors difficulties potential framework constructing powerful predict including feasible research schemas, future directions further development models.

Language: Английский

Citations

584
CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes DOI Creative Commons
Wanying Wu, Peifeng Ji, Fangqing Zhao

et al.

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: April 28, 2020

Abstract Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable mining in-depth information candidate circRNA prioritization. To address this, we integrate transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This contains 1,007,087 highly reliable circRNAs, of which over 81.3% been assembled into full-length sequences. We profile their expression pattern, conservation, and functional annotation. describe a novel multiple conservation score, co-expression, regulatory networks annotation CircAtlas can be accessed at http://circatlas.biols.ac.cn/ .

Language: Английский

Citations

327
Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer DOI Creative Commons
Zhao Zhang, Joo‐Hyung Lee, Hang Ruan

et al.

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Oct. 8, 2019

Enhancer RNA (eRNA) is a type of noncoding transcribed from the enhancer. Although critical roles eRNA in gene transcription control have been increasingly realized, systemic landscape and potential function eRNAs cancer remains largely unexplored. Here, we report integration multi-omics pharmacogenomics data across large-scale patient samples cell lines. We observe cancer-/lineage-specificity eRNAs, which may be driven by tissue-specific TFs. are involved multiple signaling pathways through putatively regulating their target genes, including clinically actionable genes immune checkpoints. They also affect drug response within-pathway or cross-pathway means. characterize oncogenic therapeutic liability one eRNA, NET1e, supporting clinical feasibility eRNA-targeted therapy. identify panel relevant developed user-friendly portal. Our study reveals transcriptional utility cancer.

Language: Английский

Citations

205
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long DOI
Jinyang Zhang,

Lingling Hou,

Zhenqiang Zuo

et al.

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

Published: March 11, 2021

Language: Английский

Citations

157
Functions and clinical significance of circular RNAs in glioma DOI Creative Commons

Jikui Sun,

Banban Li,

Chang Shu

et al.

Molecular Cancer, Journal Year: 2020, Volume and Issue: 19(1)

Published: Feb. 15, 2020

Abstract CircRNAs are a class of single-stranded RNA molecules with covalently closed loop structure and have been characterized by high stability, abundance, conservation, display tissue/developmental stage-specific expression, furthermore, based on the abundance in distinct body fluids or exosomes, circRNAs present novel biomarkers targets for diagnosis prognosis cancers. Recently, regulatory mechanisms biogenesis molecular functions, including miRNAs RBPs sponge, translation as well transcriptional splicing regulation, gradually uncovered, although various aspects remained to be elucidated combination deep-sequence bioinformatics. Accumulating studies indicated that more enriched neuronal tissues partly due specific genes promoting circularization, suggesting dysregulation is closely related diseases nervous system, glioma. In this review, we elaborate biogenesis, databases advances especially involved pathways, highlight its great value diagnostic therapeutic

Language: Английский

Citations

156
Circular RNAs and complex diseases: from experimental results to computational models DOI Creative Commons
Chun-Chun Wang, Chendi Han, Qi Zhao

et al.

Briefings in Bioinformatics, Journal Year: 2021, Volume and Issue: 22(6)

Published: July 5, 2021

Abstract Circular RNAs (circRNAs) are a class of single-stranded, covalently closed RNA molecules with variety biological functions. Studies have shown that circRNAs involved in processes and play an important role the development various complex diseases, so identification circRNA-disease associations would contribute to diagnosis treatment diseases. In this review, we summarize discovery, classifications functions introduce four diseases associated circRNAs. Then, list some significant publicly accessible databases containing comprehensive annotation resources experimentally validated associations. Next, state-of-the-art computational models for predicting novel divide them into two categories, namely network algorithm-based machine learning-based models. Subsequently, several evaluation methods prediction performance these summarized. Finally, analyze advantages disadvantages different types provide suggestions promote association from perspective construction new accumulation circRNA-related data.

Language: Английский

Citations

139
Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets DOI Open Access
Tamizhini Loganathan,

C. George Priya Doss

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

Published: Jan. 10, 2023

Language: Английский

Citations

93
Circular RNA translation: novel protein isoforms and clinical significance DOI
Shuo‐Yang Wen, Javeria Qadir, Burton B. Yang

et al.

Trends in Molecular Medicine, Journal Year: 2022, Volume and Issue: 28(5), P. 405 - 420

Published: April 2, 2022

Language: Английский

Citations

91
circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme DOI Creative Commons
Wanying Wu, Fangqing Zhao, Jinyang Zhang

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D52 - D60

Published: Sept. 22, 2023

Abstract Recent studies have demonstrated the important regulatory role of circRNAs, but an in-depth understanding comprehensive landscape circRNAs across various species still remains unexplored. The current circRNA databases are often species-restricted or based on outdated datasets. To address this challenge, we developed circAtlas 3.0 database, which contains a rich collection 2674 sequencing datasets, curated to delineate within 33 distinct tissues spanning 10 vertebrate species. Notably, represents substantial advancement over its precursor, 2.0, with number cataloged escalating from 1 007 087 3 179 560, 2 527 528 them being reconstructed into full-length isoforms. also introduces several notable enhancements, including: (i) integration both Illumina and Nanopore datasets detect extended lengths; (ii) employment standardized nomenclature scheme for providing information host gene circular exons; (iii) inclusion clinical cancer samples explore biological function context (iv) links other useful resources enable user-friendly analysis target circRNAs. updated provides platform exploring evolution implications is freely available at http://circatlas.biols.ac.cn https://ngdc.cncb.ac.cn/circatlas.

Language: Английский

Citations

45