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ncRNA
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circRNAs in Cell and Organ Development
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circRNAs in Cell and Organ Development

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 16320

Special Issue Editor

Dr. Kuei-Yang Hsiao

E-Mail Website
Guest Editor
Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
Interests: noncoding RNA; circRNA; microRNA; hypoxia; colorectal cancer; gynecological cancer; molecular endocrinology; DNA damage response; chemoresistance

Special Issue Information

Dear Colleagues,

Accumulating data have shown that circular RNA (circRNA) play diverse cellular and molecular functions during the pathogenic process of human diseases and developmental stages. CircRNA exert their biological functions at least via regulating gene expression through epigenetic, transcriptional and post-transcriptional mechanisms, modulating protein-protein interaction, and/or serving as templates for translation. To gain more mechanistic insight and/or explore potential translational applications of circRNAs, we are excited to announce this Special Issue of Non-Coding RNA – “circRNAs in Cell and Organ Development”. We are looking for high-quality research papers and review articles which have comprehensive coverage on the roles of circRNA in particular diseases and/or organs. We would like to urge researchers to submit their invaluable studies dissecting physiological or pathological roles of circRNAs in various models of diseases.

Dr. Kuei-Yang Hsiao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • circular RNA
  • microRNA
  • exosomes
  • epigenetics
  • epitranscriptomics
  • biomarkers
  • bioinformatics
  • RNA biology

Published Papers (4 papers)

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Research

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16 pages, 4162 KiB  
Article
Patterns of Differentially Expressed circRNAs in Human Thymocytes
by Pilar López-Nieva, Pablo Fernández-Navarro, María Ángeles Cobos-Fernández, Iria González-Vasconcellos, Raúl Sánchez Pérez, Ángel Aroca, José Fernández-Piqueras and Javier Santos
Non-Coding RNA 2022, 8(2), 26; https://doi.org/10.3390/ncrna8020026 - 30 Mar 2022
Viewed by 2295
Abstract
Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of [...] Read more.
Circular RNAs (circRNAs) are suggested to play a discriminative role between some stages of thymocyte differentiation. However, differential aspects of the stage of mature single-positive thymocytes remain to be explored. The purpose of this study is to investigate the differential expression pattern of circRNAs in three different development stages of human thymocytes, including mature single-positive cells, and perform predictions in silico regarding the ability of specific circRNAs when controlling the expression of genes involved in thymocyte differentiation. We isolate human thymocytes at three different stages of intrathymic differentiation and determine the expression of circRNAs and mRNA by RNASeq. We show that the differential expression pattern of 50 specific circRNAs serves to discriminate between the three human thymocyte populations. Interestingly, the downregulation of RAG2, a gene involved in T-cell differentiation in the thymus, could be simultaneously controlled by the downregulation of two circRNASs (hsa_circ_0031584 and hsa_circ_0019079) through the hypothetical liberation of hsa-miR-609. Our study provides, for the first time, significant insights into the usefulness of circRNAs in discriminating between different stages of thymocyte differentiation and provides new potential circRNA–miRNA–mRNA networks capable of controlling the expression of genes involved in T-cell differentiation in the thymus. Full article
(This article belongs to the Special Issue circRNAs in Cell and Organ Development)
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16 pages, 2020 KiB  
Article
Promoter-Bound Full-Length Intronic Circular RNAs-RNA Polymerase II Complexes Regulate Gene Expression in the Human Parasite Entamoeba histolytica
by Jesús Alberto García-Lerena, Gretter González-Blanco, Odila Saucedo-Cárdenas and Jesús Valdés
Non-Coding RNA 2022, 8(1), 12; https://doi.org/10.3390/ncrna8010012 - 27 Jan 2022
Cited by 5 | Viewed by 2956
Abstract
Ubiquitous eukaryotic non-coding circular RNAs are involved in numerous co- and post-transcriptional regulatory mechanisms. Recently, we reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica, with 3′ss–5′ss ligation points and 5′ss GU-rich elements essential for their biogenesis and their suggested role in [...] Read more.
Ubiquitous eukaryotic non-coding circular RNAs are involved in numerous co- and post-transcriptional regulatory mechanisms. Recently, we reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica, with 3′ss–5′ss ligation points and 5′ss GU-rich elements essential for their biogenesis and their suggested role in transcription regulation. Here, we explored how flicRNAs impact gene expression regulation. Using CLIP assays, followed by qRT-PCR, we identified that the RabX13 control flicRNA and virulence-associated flicRNAs were bound to the HA-tagged RNA Pol II C-terminus domain in E. histolytica transformants. The U2 snRNA was also present in such complexes, indicating that they belonged to transcription initiation/elongation complexes. Correspondingly, inhibition of the second step of splicing using boric acid reduced flicRNA formation and modified the expression of their parental genes and non-related genes. flicRNAs were also recovered from chromatin immunoprecipitation eluates, indicating that the flicRNA-Pol II complex was formed in the promoter of their cognate genes. Finally, two flicRNAs were found to be cytosolic, whose functions remain to be uncovered. Here, we provide novel evidence of the role of flicRNAs in gene expression regulation in cis, apparently in a widespread fashion, as an element bound to the RNA polymerase II transcription initiation complex, in E. histolytica. Full article
(This article belongs to the Special Issue circRNAs in Cell and Organ Development)
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Review

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12 pages, 1458 KiB  
Review
The Functional Roles and Regulation of Circular RNAs during Cellular Stresses
by Yueh-Chun Lee, Wei-Yu Wang, Hui-Hsuan Lin, Yi-Ren Huang, Ya-Chi Lin and Kuei-Yang Hsiao
Non-Coding RNA 2022, 8(3), 38; https://doi.org/10.3390/ncrna8030038 - 27 May 2022
Cited by 3 | Viewed by 2958
Abstract
Circular RNAs (circRNAs) are a novel class of regulatory RNA involved in many biological, physiological and pathological processes by functioning as a molecular sponge, transcriptional/epigenetic/splicing regulator, modulator of protein–protein interactions, and a template for encoding proteins. Cells are constantly dealing with stimuli from [...] Read more.
Circular RNAs (circRNAs) are a novel class of regulatory RNA involved in many biological, physiological and pathological processes by functioning as a molecular sponge, transcriptional/epigenetic/splicing regulator, modulator of protein–protein interactions, and a template for encoding proteins. Cells are constantly dealing with stimuli from the microenvironment, and proper responses rely on both the precise control of gene expression networks and protein–protein interactions at the molecular level. The critical roles of circRNAs in the regulation of these processes have been heavily studied in the past decades. However, how the microenvironmental stimulation controls the circRNA biogenesis, cellular shuttling, translation efficiency and degradation globally and/or individually remains largely uncharacterized. In this review, how the impact of major microenvironmental stresses on the known transcription factors, splicing modulators and epitranscriptomic regulators, and thereby how they may contribute to the regulation of circRNAs, is discussed. These lines of evidence will provide new insight into how the biogenesis and functions of circRNA can be precisely controlled and targeted for treating human diseases. Full article
(This article belongs to the Special Issue circRNAs in Cell and Organ Development)
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20 pages, 1153 KiB  
Review
Emerging Role of Circular RNA–Protein Interactions
by Arundhati Das, Tanvi Sinha, Sharmishtha Shyamal and Amaresh Chandra Panda
Non-Coding RNA 2021, 7(3), 48; https://doi.org/10.3390/ncrna7030048 - 4 Aug 2021
Cited by 51 | Viewed by 7313
Abstract
Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA–protein interaction [...] Read more.
Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA–protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localization, and translation. However, the interaction of RBPs with circRNAs and their implications on circRNA biogenesis and function has been emerging in the last few years. Recent studies suggest that circRNA interaction with target proteins modulates the interaction of the protein with downstream target mRNAs or proteins. This review outlines the emerging mechanisms of circRNA–protein interactions and their functional role in cell physiology. Full article
(This article belongs to the Special Issue circRNAs in Cell and Organ Development)
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