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The Lesser Known World of RNA Circles

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (15 October 2022) | Viewed by 10871

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Special Issue Editors

Dr. Amaresh Panda

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Guest Editor

Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, Odisha, India
Interests: circular RNAs; backsplicing; RNA-binding proteins; microRNAs; translation; circRNA databases

Dr. Kotb Abdelmohsen

E-Mail Website
Guest Editor

Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
Interests: miRNA; lncRNAs; RBP
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Circular RNAs (circRNAs) represent a heterogeneous class of covalently closed single-stranded RNA molecules. CircRNA was first discovered in plant viroids and eukaryotic cells by electron microscopy more than 40 years ago. For the last four decades, they were mostly considered as non-functional splicing products or intronic lariats. The advent of next-generation sequencing technologies and novel bioinformatic tools led to the discovery of the ubiquitous and abundant expression of circRNAs across eukaryotic organisms. However, it is essential to note that only a handful of circRNAs has been functionally characterized among thousands of circRNAs identified to date. The last few years have seen an increasing number of reports suggesting the association of circRNAs in human development and diseases. In addition, recent studies have established that circRNAs regulate gene expression by modulating the activity of RNA-binding proteins and microRNAs. Some of the circRNAs have been shown to translate into proteins and regulate cellular physiology. However, many of the molecular details of circRNA biogenesis and function remain to be explored.

This Special Issue welcomes research articles, communications, and review articles on, but not limited to, the following topics:

Methods to detect and quantify circRNAs;
Databases and software for circRNA analysis;
Mechanism of circRNA biogenesis;
CircRNA–miRNA–mRNA regulatory axis in cell physiology;
CircRNA acting as sponges for microRNAs and RNA-binding proteins;
Translation of circRNAs;
CircRNA as a diagnostic and therapeutic target.

Dr. Amaresh Panda
Dr. Kotb Abdelmohsen
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

circular RNAs
backsplicing
RNA-binding proteins
microRNAs
translation
circRNA databases

Published Papers (4 papers)

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Research

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15 pages, 3491 KiB

Open AccessArticle

Reconstruction of Full-Length circRNA Sequences Using Chimeric Alignment Information

by Md. Tofazzal Hossain, Jingjing Zhang, Md. Selim Reza, Yin Peng, Shengzhong Feng and Yanjie Wei

Int. J. Mol. Sci. 2022, 23(12), 6776; https://doi.org/10.3390/ijms23126776 - 17 Jun 2022

Cited by 2 | Viewed by 2406

Abstract

Circular RNAs (circRNAs) are RNA molecules formed by joining a downstream 3 splice donor site and an upstream 5 splice acceptor site. Several recent studies have identified circRNAs as potential biomarker for different diseases. A number of methods are available for the identification of circRNAs. The circRNA identification methods cannot provide full-length sequences. Reconstruction of the full-length sequences is crucial for the downstream analyses of circRNA research including differential expression analysis, circRNA-miRNA interaction analysis and other functional studies of the circRNAs. However, a limited number of methods are available in the literature for the reconstruction of full-length circRNA sequences. We developed a new method, circRNA-full, for full-length circRNA sequence reconstruction utilizing chimeric alignment information from the STAR aligner. To evaluate our method, we used full-length circRNA sequences produced by isocirc and ciri-long using long-reads RNA-seq data. Our method achieved better reconstruction rate, precision, sensitivity and F1 score than the existing full-length circRNA sequence reconstruction tool ciri-full for both human and mouse data. Full article

(This article belongs to the Special Issue The Lesser Known World of RNA Circles)

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Review

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16 pages, 904 KiB

Open AccessReview

Circular RNAs as a Diagnostic and Therapeutic Target in Cardiovascular Diseases

by Victor Hugo Antonio Joaquim, Noemy Pinto Pereira, Tiago Fernandes and Edilamar Menezes Oliveira

Int. J. Mol. Sci. 2023, 24(3), 2125; https://doi.org/10.3390/ijms24032125 - 21 Jan 2023

Cited by 8 | Viewed by 2042

Abstract

Circular RNAs (circRNAs) are a family of noncoding RNAs (ncRNAs) that are endogenous and widely distributed in different species, performing several functions, mainly their association with microRNAs (miRNAs) and RNA-binding proteins. CVDs remain the leading cause of death worldwide; therefore, the development of new therapies and strategies, such as gene therapies or nonpharmacological therapies, with low cost, such as physical exercise, to alleviate these diseases is of extreme importance for society. With increasing evidence of ncRNA participating in the progression of CVDs, several studies have reported these RNAs as promising targets for diagnosis and treatment. There are several studies of CVDs and the role of miRNAs and lncRNAs; however, little is known about the new class of RNAs, called circRNAs, and CVDs. In this mini review, we focus on the mechanisms of circRNAs and CVDs. Full article

(This article belongs to the Special Issue The Lesser Known World of RNA Circles)

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11 pages, 669 KiB

Open AccessReview

The Role of Circular RNAs in the Physiology and Pathology of the Mammalian Ovary

by Jinbi Zhang, Caixia Wang, Chao Jia, Yi Zhang, Xinxin Qing, Yuge Zhang, Jingge Liu, Shiyong Xu and Zengxiang Pan

Int. J. Mol. Sci. 2022, 23(23), 15204; https://doi.org/10.3390/ijms232315204 - 02 Dec 2022

Cited by 11 | Viewed by 1708

Abstract

Circular RNAs (circRNAs) are an abundant class of endogenous non-coding RNAs (ncRNAs) generated from exonic, intronic, or untranslated regions of protein-coding genes or intergenic regions. The diverse, stable, and specific expression patterns of circRNAs and their possible functions through cis/trans regulation and protein-coding mechanisms make circRNA a research hotspot in various biological and pathological processes. It also shows practical value as biomarkers, diagnostic indicators, and therapeutic targets. This review summarized the characteristics, classification, biogenesis and elimination, detection and confirmation, and functions of circRNAs. We focused on research advances circRNAs in the mammalian ovary under conditions including ovarian cancer, polycystic ovarian syndrome (PCOS), and maternal aging, as well as during reproductive status, including ovarian follicle development and atresia. The roles of circRNAs in high reproductive traits in domestic animals were also summarized. Finally, we outlined some obstructive factors and prospects to work with circRNA, aiming to provide insights into the functional research interests of circRNAs in the reproduction and gynecology areas. Full article

(This article belongs to the Special Issue The Lesser Known World of RNA Circles)

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22 pages, 2737 KiB

Open AccessReview

Spotlight on Exosomal Non-Coding RNAs in Breast Cancer: An In Silico Analysis to Identify Potential lncRNA/circRNA-miRNA-Target Axis

by Ohanes Ashekyan, Samira Abdallah, Ayman Al Shoukari, Ghada Chamandi, Hayat Choubassy, Abdul Rahman S. Itani, Nisreen Alwan and Rihab Nasr

Int. J. Mol. Sci. 2022, 23(15), 8351; https://doi.org/10.3390/ijms23158351 - 28 Jul 2022

Cited by 10 | Viewed by 4049

Abstract

Breast cancer (BC) has recently become the most common cancer type worldwide, with metastatic disease being the main reason for disease mortality. This has brought about strategies for early detection, especially the utilization of minimally invasive biomarkers found in various bodily fluids. Exosomes have been proposed as novel extracellular vesicles, readily detectable in bodily fluids, secreted from BC-cells or BC-tumor microenvironment cells, and capable of conferring cellular signals over long distances via various cargo molecules. This cargo is composed of different biomolecules, among which are the novel non-coding genome products, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and the recently discovered circular RNA (circRNA), all of which were found to be implicated in BC pathology. In this review, the diverse roles of the ncRNA cargo of BC-derived exosomes will be discussed, shedding light on their primarily oncogenic and additionally tumor suppressor roles at different levels of BC tumor progression, and drug sensitivity/resistance, along with presenting their diagnostic, prognostic, and predictive biomarker potential. Finally, benefiting from the miRNA sponging mechanism of action of lncRNAs and circRNAs, we established an experimentally validated breast cancer exosomal non-coding RNAs-regulated target gene axis from already published exosomal ncRNAs in BC. The resulting genes, pathways, gene ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis could be a starting point to better understand BC and may pave the way for the development of novel diagnostic and prognostic biomarkers and therapeutics. Full article

(This article belongs to the Special Issue The Lesser Known World of RNA Circles)

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