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Di Agostino S, Riccioli A, De Cesaris P, Fontemaggi G, Blandino G, Filippini A, Fazi F. Circular RNAs in Embryogenesis and Cell Differentiation With a Focus on Cancer Development. Front Cell Dev Biol 2020; 8:389. [PMID: 32528957 PMCID: PMC7266935 DOI: 10.3389/fcell.2020.00389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
In the recent years thousands of non-coding RNAs have been identified, also thanks to highthroughput sequencing technologies. Among them, circular RNAs (circRNAs) are a well-represented class characterized by the high sequence conservation and cell type specific expression in eukaryotes. They are covalently closed loops formed through back-splicing. Recently, circRNAs were shown to regulate a variety of cellular processes functioning as miRNA sponges, RBP binding molecules, transcriptional regulators, scaffold for protein translation, as well as immune regulators. A growing number of studies are showing that deregulated expression of circRNAs plays important and decisive actions during the development of several human diseases, including cancer. The research on their biogenesis and on the various molecular mechanisms in which they are involved is going very fast, however, there are still few studies that address their involvement in embryogenesis and eukaryotic development. This review has the intent to describe the most recent progress in the study of the biogenesis and molecular activities of circRNAs providing insightful information in the field of embryogenesis and cell differentiation. In addition, we describe the latest research on circRNAs as novel promising biomarkers in diverse types of tumors.
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Affiliation(s)
- Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Anna Riccioli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Paola De Cesaris
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Antonio Filippini
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy.,Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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52
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Gòdia M, Castelló A, Rocco M, Cabrera B, Rodríguez-Gil JE, Balasch S, Lewis C, Sánchez A, Clop A. Identification of circular RNAs in porcine sperm and evaluation of their relation to sperm motility. Sci Rep 2020; 10:7985. [PMID: 32409652 PMCID: PMC7224279 DOI: 10.1038/s41598-020-64711-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 12/16/2022] Open
Abstract
Circular RNAs (circRNAs) are emerging as a novel class of noncoding RNAs which potential role as gene regulators is quickly gaining interest. circRNAs have been studied in different tissues and cell types across several animal species. However, a thorough characterization of the circRNAome in ejaculated sperm remains unexplored. In this study, we profiled the sperm circRNA catalogue using 40 porcine ejaculates. A complex population of 1,598 circRNAs was shared in at least 30 of the 40 samples. Generally speaking, the predicted circRNAs presented low abundances and were tissue-specific. Around 80% of the circRNAs identified in the boar sperm were reported as novel. Results from abundance correlation between circRNAs and miRNAs together with the prediction of microRNA (miRNA) target sites in circRNAs suggested that circRNAs may act as miRNA sponges. Moreover, we found significant correlations between the abundance of 148 exonic circRNAs and sperm motility parameters. Two of these correlations, involving ssc_circ_1458 and ssc_circ_1321, were confirmed by RT-qPCR using 36 additional samples with extreme and opposite sperm motility values. Our study provides a thorough characterization of circRNAs in sperm and suggests that circRNAs hold potential as noninvasive biomarkers for sperm quality and male fertility.
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Affiliation(s)
- Marta Gòdia
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Anna Castelló
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,Unit of Animal Science, Department of Animal and Food Science, Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Martina Rocco
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,Unit of Animal Reproduction, Department of Animal Medicine and Surgery, Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Betlem Cabrera
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,Unit of Animal Science, Department of Animal and Food Science, Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Joan Enric Rodríguez-Gil
- Unit of Animal Reproduction, Department of Animal Medicine and Surgery, Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Sam Balasch
- Grup Gepork S.A., Barcelona, Catalonia, Spain
| | - Craig Lewis
- PIC Europe, Sant Cugat del Vallés, Catalonia, Spain
| | - Armand Sánchez
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain.,Unit of Animal Science, Department of Animal and Food Science, Autonomous University of Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Alex Clop
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Barcelona, Catalonia, Spain. .,Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Catalonia, Spain.
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53
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Cai Y, Lei X, Chen Z, Mo Z. The roles of cirRNA in the development of germ cells. Acta Histochem 2020; 122:151506. [PMID: 32008790 DOI: 10.1016/j.acthis.2020.151506] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
Circular RNA (CircRNA), a type of endogenous non-coding RNAs (ncRNAs), is generally generated from precursor mRNA (pre-mRNA) by canonical splicing and head-to-tail back splicing. The structure without a polyA tail renders circRNA highly insensitive to ribonuclease. Simultaneously, the distribution of circRNAs is tissue and developmental stage-specific. There are five potential biological functions of circRNAs: 1) promote transcription of their parental genes; 2) function as a miRNA sponge; 3) RNA binding protein (RBP) sponge; 4) encode protein; 5) act as an mRNA trap. Recently, circRNA has attracted attention because studies have shown that circRNAs are associated with follicular development, ovarian senescence, spermatogenesis, and germ cell development process, suggesting that circRNAs may function in germ cells regulation. The investigation of circRNAs in germ cells will provide an excellent opportunity to understand its potential molecular basis, and potentially improving reproduction status in human. In this article, the relationship between circRNA and germ cell development will be discussed.
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Affiliation(s)
- Yaqin Cai
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; Institute of Basic Medical Sciences, Center for Diabetic Systems Medicine (Guangxi Key Laboratory of Excellence), Guilin Medical University, Guangxi, Guilin, 541100, China
| | - Xiaocan Lei
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhuo Chen
- Hunan Province Innovative Training Base for Medical Postgraduates, University of South China and Yueyang Women & Children's Medical Center, Institute of Reproductive Medicine, Yueyang, Hunan, 416000, China
| | - Zhongcheng Mo
- Institute of Basic Medical Sciences, Center for Diabetic Systems Medicine (Guangxi Key Laboratory of Excellence), Guilin Medical University, Guangxi, Guilin, 541100, China; Hunan Province Innovative Training Base for Medical Postgraduates, University of South China and Yueyang Women & Children's Medical Center, Institute of Reproductive Medicine, Yueyang, Hunan, 416000, China.
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54
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Chioccarelli T, Pierantoni R, Manfrevola F, Porreca V, Fasano S, Chianese R, Cobellis G. Histone Post-Translational Modifications and CircRNAs in Mouse and Human Spermatozoa: Potential Epigenetic Marks to Assess Human Sperm Quality. J Clin Med 2020; 9:jcm9030640. [PMID: 32121034 PMCID: PMC7141194 DOI: 10.3390/jcm9030640] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 12/14/2022] Open
Abstract
Spermatozoa (SPZ) are motile cells, characterized by a cargo of epigenetic information including histone post-translational modifications (histone PTMs) and non-coding RNAs. Specific histone PTMs are present in developing germ cells, with a key role in spermatogenic events such as self-renewal and commitment of spermatogonia (SPG), meiotic recombination, nuclear condensation in spermatids (SPT). Nuclear condensation is related to chromatin remodeling events and requires a massive histone-to-protamine exchange. After this event a small percentage of chromatin is condensed by histones and SPZ contain nucleoprotamines and a small fraction of nucleohistone chromatin carrying a landascape of histone PTMs. Circular RNAs (circRNAs), a new class of non-coding RNAs, characterized by a nonlinear back-spliced junction, able to play as microRNA (miRNA) sponges, protein scaffolds and translation templates, have been recently characterized in both human and mouse SPZ. Since their abundance in eukaryote tissues, it is challenging to deepen their biological function, especially in the field of reproduction. Here we review the critical role of histone PTMs in male germ cells and the profile of circRNAs in mouse and human SPZ. Furthermore, we discuss their suggested role as novel epigenetic biomarkers to assess sperm quality and improve artificial insemination procedure.
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55
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Xiong S, Li Y, Xiang Y, Peng N, Shen C, Cai Y, Song D, Zhang P, Wang X, Zeng X, Zhang X. Dysregulation of lncRNA and circRNA Expression in Mouse Testes after Exposure to Triptolide. Curr Drug Metab 2020; 20:665-673. [PMID: 31362668 PMCID: PMC7062010 DOI: 10.2174/1389200220666190729130020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Triptolide has been shown to exert various pharmacological effects on systemic autoimmune diseases and cancers. However, its severe toxicity, especially reproductive toxicity, prevents its widespread clinical use for people with fertility needs. Noncoding RNAs including lncRNAs and circRNAs are novel regulatory molecules that mediate a wide variety of physiological activities; they are crucial for spermatogenesis and their dysregulation might cause male infertility. However, whether they are involved in triptolide-induced reproductive toxicity is completely unknown. METHODS After exposure of mice to triptolide, the total RNAs were used to investigate lncRNA/circRNA/mRNA expression profiles by strand-specific RNA sequencing at the transcriptome level to help uncover RNA-related mechanisms in triptolide-induced toxicity. RESULTS Triptolide significantly decreased testicular weight, damaged testis and sperm morphology, and reduced sperm motility and density. Remarkable deformities in sperm head and tail were also found in triptolide-exposed mice. At the transcriptome level, the triptolide-treated mice exhibited aberrant expression profiles of lncRNAs/circRNAs/mRNAs. Gene Ontology and pathway analyses revealed that the functions of the differentially expressed lncRNA targets, circRNA cognate genes, and mRNAs were closely linked to many processes involved in spermatogenesis. In addition, some lncRNAs/circRNAs were greatly upregulated or inducibly expressed, implying their potential value as candidate markers for triptolide-induced male reproductive toxicity. CONCLUSION This study provides a preliminary database of triptolide-induced transcriptome, promotes understanding of the reproductive toxicity of triptolide, and highlights the need for research on increasing the medical efficacy of triptolide and decreasing its toxicity.
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Affiliation(s)
- Suping Xiong
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yanting Li
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yang Xiang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Na Peng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Chunmiao Shen
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yanqiu Cai
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Dandan Song
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Peng Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Xiaolong Wang
- Traditional Chinese Medicine Department, Jilin Women and Children Health Hospital, Changchun, China
| | - Xuihui Zeng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Xiaoning Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China.,Medical School, Institute of Reproductive Medicine, Nantong University, Nantong, China
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56
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The Epigenetics of the Endocannabinoid System. Int J Mol Sci 2020; 21:ijms21031113. [PMID: 32046164 PMCID: PMC7037698 DOI: 10.3390/ijms21031113] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
The endocannabinoid system (ES) is a cell-signalling system widely distributed in biological tissues that includes endogenous ligands, receptors, and biosynthetic and hydrolysing machineries. The impairment of the ES has been associated to several pathological conditions like behavioural, neurological, or metabolic disorders and infertility, suggesting that the modulation of this system may be critical for the maintenance of health status and disease treatment. Lifestyle and environmental factors can exert long-term effects on gene expression without any change in the nucleotide sequence of DNA, affecting health maintenance and influencing both disease load and resistance. This potentially reversible "epigenetic" modulation of gene expression occurs through the chemical modification of DNA and histone protein tails or the specific production of regulatory non-coding RNA (ncRNA). Recent findings demonstrate the epigenetic modulation of the ES in biological tissues; in the same way, endocannabinoids, phytocannabinoids, and cannabinoid receptor agonists and antagonists induce widespread or gene-specific epigenetic changes with the possibility of trans-generational epigenetic inheritance in the offspring explained by the transmission of deregulated epigenetic marks in the gametes. Therefore, this review provides an update on the epigenetics of the ES, with particular attention on the emerging role in reproduction and fertility.
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57
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Bo H, Liu Z, Tang R, Gong G, Wang X, Zhang H, Zhu F, Zhou D, Zhu W, Tan Y, Fan L. Testicular biopsies microarray analysis reveals circRNAs are involved in the pathogenesis of non-obstructive azoospermia. Aging (Albany NY) 2020; 12:2610-2625. [PMID: 32029690 PMCID: PMC7041731 DOI: 10.18632/aging.102765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/12/2020] [Indexed: 01/05/2023]
Abstract
Circular RNAs (circRNAs) have been reported to be involved in many diseases. But there is no report on circRNAs in non-obstructive azoospermia (NOA). The purpose of this paper is to explore the circular RNA expression profile and potential functions of circRNAs in NOA patients. We first preformed circRNA expression profiling analysis using a circRNA microarray in testicular samples from NOA and obstructive azoospermia (OA) patients. CircRNAs were validated by qRT-PCR. Bioinformatics analysis were used to construct the ceRNA network. GO and KEGG enrichment analysis were performed by using DAVID. Microarray analysis identified 82 differentially expressed circRNAs in NOA specimens. The differential expression of hsa_circRNA_402130, hsa_circRNA_072697, hsa_circRNA_030050, hsa_circRNA_100812 and hsa_circRNA_406168 was confirmed by qRT-PCR. Enrichment analysis revealed the association of hsa_circRNA_402130 and hsa_circRNA_072697 with multiple signaling pathways. The data indicated that circRNAs were significantly dysregulated in NOA specimens and might involve in the pathogenesis of NOA.
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Affiliation(s)
- Hao Bo
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Zhizhong Liu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Hunan Cancer Hospital and The Affliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ruiling Tang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Guanghui Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Xingming Wang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Han Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Fang Zhu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Dai Zhou
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Wenbing Zhu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Liqing Fan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
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58
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Manfrevola F, Chioccarelli T, Cobellis G, Fasano S, Ferraro B, Sellitto C, Marella G, Pierantoni R, Chianese R. CircRNA Role and circRNA-Dependent Network (ceRNET) in Asthenozoospermia. Front Endocrinol (Lausanne) 2020; 11:395. [PMID: 32754116 PMCID: PMC7366322 DOI: 10.3389/fendo.2020.00395] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
The role of circRNA in reproduction is under investigation. CircRNAs are expressed in human testis, spermatozoa (SPZ), and seminal plasma. Their involvement in embryo development has also been suggested. Asthenozoospermia, a common cause of male infertility, is characterized by reduced or absent sperm motility in fresh ejaculate. While abnormal mitochondrial function, altered sperm tail, and genomic causes have been deeply investigated, the epigenetic signature of asthenozoospermic derived SPZ still remains unexplored. CircRNAs may take part in the repertoire of differentially expressed molecules in infertile men. Considering this background, we carried out a circRNA microarray, identifying a total of 9,138 transcripts, 22% of them novel based and 83.5% with an exonic structure. Using KEGG analysis, we evaluated the circRNA contribution in pathways related to mitochondrial function and sperm motility. In order to discriminate circRNAs with a differential expression in SPZ with differential morphological parameters, we separated sperm cells by Percoll gradient and analyzed their differential circRNA payload. A bioinformatic approach was then utilized to build a circRNA/miRNA/mRNA network. With the aim to demonstrate a dynamic contribution of circRNAs to the sperm epigenetic signature, we verified their modulation as a consequence of an oral amino acid supplementation, efficacious in improving SPZ motility.
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Affiliation(s)
- Francesco Manfrevola
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Teresa Chioccarelli
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Gilda Cobellis
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Fasano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Bruno Ferraro
- UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise, Caserta, Italy
| | - Carolina Sellitto
- UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise, Caserta, Italy
| | - Giovanni Marella
- UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise, Caserta, Italy
| | - Riccardo Pierantoni
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
| | - Rosanna Chianese
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania Luigi Vanvitelli, Naples, Italy
- *Correspondence: Rosanna Chianese
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Song H, Wang L, Chen D, Li F. The Function of Pre-mRNA Alternative Splicing in Mammal Spermatogenesis. Int J Biol Sci 2020; 16:38-48. [PMID: 31892844 PMCID: PMC6930371 DOI: 10.7150/ijbs.34422] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Alternative pre-mRNA splicing plays important roles in co-transcriptional and post-transcriptional regulation of gene expression functioned during many developmental processes, such as spermatogenesis. The studies focusing on alternative splicing on spermatogenesis supported the notion that the development of testis is regulated by a higher level of alternative splicing than other tissues. Here, we aim to review the mechanisms underlying alternative splicing, particularly the splicing variants functioned in the process of spermatogenesis and the male infertility. There are five points regarding the alternative splicing including ⅰ) a brief introduction of alternative pre-mRNA splicing; ⅱ) the alternative splicing events in spermatogenesis-associated genes enriched in different stages of spermatogenesis; ⅲ) the mechanisms of alternative splicing regulation, such as splicing factors and m6A demethylation; ⅳ) the splice site recognition and alternative splicing, including the production and degradation of abnormal transcripts caused by gene variations and nonsense-mediated mRNA decay, respectively; ⅴ) abnormal alternative splicing correlated with male infertility. Taking together, this review highlights the impacts of alternative splicing and splicing variants in mammal spermatogenesis and provides new insights of the potential application of the alternative splicing into the therapy of male infertility.
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Affiliation(s)
- Huibin Song
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ling Wang
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dake Chen
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Fenge Li
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, PR China
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60
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Ge P, Zhang J, Zhou L, Lv MQ, Li YX, Wang J, Zhou DX. CircRNA expression profile and functional analysis in testicular tissue of patients with non-obstructive azoospermia. Reprod Biol Endocrinol 2019; 17:100. [PMID: 31775841 PMCID: PMC6880412 DOI: 10.1186/s12958-019-0541-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Non-obstructive azoospermia (NOA) is a multifactorial disorder whose molecular basis remains largely unknown. Circular RNAs (CircRNAs), a novel class of endogenous RNAs, have been recognized to play important roles in many biological processes. However, little is known about the expression patterns and functions of circRNAs in human testes involved in NOA. METHODS In this study, the testicular circRNA expression profile were explored in NOA patients and the controls by high-throughput circRNA microarray. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm the microarray data. Bioinformatics analyses including the circRNA/miRNA/mRNA interaction network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to predict the functions of differentially expressed circRNAs. RESULTS A total of 368 differentially down-regulated and 526 up-regulated circRNAs were detected in NOA patients. These findings have been verified by qRT-PCR on 6 selected circRNAs. Among these differentially expressed circRNAs, the hsa_circRNA_0023313 was obviously up-regulated in testicular tissue of NOA patients. The most likely potential target miRNA for hsa_circRNA_0023313 include hsa-miR-520d-3p, hsa-miR-373-3p, hsa-miR-372-3p, hsa-miR-302c-3p and hsa-miR-130b-5p. Function analysis indicated that hsa_circRNA_0023313 was ubiquitin-protein transferase activity and chromatin binding. KEGG analysis revealed that the top five pathways related to hsa_circRNA_0023313 were endocytosis, meiosis, FoxO signaling pathway, ubiquitin mediated proteolysis and AMPK signaling pathway. CONCLUSIONS This is the first report that the testicular circRNA expression profile is altered in NOA patients indicating circRNAs might play important roles in regulating spermatogenesis and be potential biomarkers for the diagnosis and treatment of NOA.
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Affiliation(s)
- Pan Ge
- Department of Pathology, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
- Research Center of Reproductive Medicine, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jian Zhang
- Department of Pathology, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Liang Zhou
- Reproductive Center Medicine, Maternal and child care Hospital of Shaanxi Province, Xi'an, 710063, China
| | - Mo-Qi Lv
- Department of Pathology, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
- Research Center of Reproductive Medicine, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yi-Xin Li
- Department of Pathology, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
- Research Center of Reproductive Medicine, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jin Wang
- Obstetrics and Gynecology Department, Xi'an Angel Women's & children's Hospital, Xi'an, 710077, China.
- Obstetrics and Gynecology Department, Maternal and child care Hospital of Shaanxi Province, Xi'an, 710063, China.
| | - Dang-Xia Zhou
- Department of Pathology, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China.
- Research Center of Reproductive Medicine, Medical School, Xi'an Jiaotong University, Xi'an, 710061, China.
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Liu L, Li T, Li F, Zhao X, Zhang R, Liu J, Zhang W, Lu J, Zhang X, Ma X. The influence of l-carnitine on the expression of miRNAs in asthenospermia spermatozoa and the network regulation of the associated molecules. Andrologia 2019; 52:e13478. [PMID: 31749176 DOI: 10.1111/and.13478] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/19/2019] [Indexed: 12/12/2022] Open
Abstract
l-carnitine is a natural compound that is indispensable for energy metabolism in mammals. The efficiency and safety of l-carnitine in improving sperm activity, enhancing epididymal function and treating male infertility has been widely acknowledged by clinicians. CircRNAs can regulate gene expression at the transcriptional or post-transcriptional level by serving as a molecular sponge of miRNAs with miRNA response elements. However, the detailed mechanism linking miRNA, circRNA and asthenospermia remains unclear. The present study demonstrated that hsa-miR-27b-3p, hsa-miR-151a-5p and hsa-miR-206 play an important role in the effects of l-carnitine treatment of the spermatozoa in asthenospermia patients. Furthermore, the target mRNAs of hsa-miR-206 were analysed by GO and KEGG. The results show that the target mRNAs of hsa-miR-206 may change the activity of ATP synthase and participate in the cAMP signalling pathway and the calcium signalling pathway, which may play an important role in sperm motility.
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Affiliation(s)
- Lin Liu
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China.,Lanzhou University, Lanzhou, China
| | - Tao Li
- Lanzhou University, Lanzhou, China
| | | | - Xiaodong Zhao
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Rui Zhang
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Jing Liu
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Wei Zhang
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Jianqi Lu
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Xuehong Zhang
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
| | - Xiaoling Ma
- The Reproductive Medicine Special Hospital of the 1st hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Reproductive Medicine and Embryo of Gansu, Lanzhou, China
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62
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Cai H, Li Y, Li H, Niringiyumukiza JD, Zhang M, Chen L, Chen G, Xiang W. Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging. Aging (Albany NY) 2019; 10:2511-2534. [PMID: 30260796 PMCID: PMC6188495 DOI: 10.18632/aging.101565] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/14/2018] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) have recently been shown to exert effects on multiple pathological processes by acting as miRNA sponges. However, the roles of circRNAs in ovarian senescence are largely unknown. The objective of this study was to identify the circRNAs involved in ovarian aging and predict their potential biological functions. We first performed RNA-sequencing to generate ovarian circRNA expression profiles from young (n = 3) and aging (n = 3) groups. In total, 48,220 circRNAs were identified, of which 194 circRNAs were significantly up-regulated and 207 circRNAs were down-regulated during aging (fold change > 2, P < 0.05). Bioinformatics analysis demonstrated that the metabolic process, regulated secretory pathway, oxidation-reduction process, steroid hormone biosynthesis, and insulin secretion pathways, which may be associated with ovarian aging, were significantly enriched (P < 0.05). The biological characteristics of ovary-derived circRNA, such as back-splicing, RNase R resistance, stability, and alternative splicing, were further validated. Bioinformatics predicted that most of the circRNAs harboured miRNA binding sites, of which circDDX10-miR-1301-3p/miR-4660-SIRT3 axis may be involved in the regulation of ovarian function. Our study indicates that circRNAs are aberrantly expressed in the aging ovary and may play potential roles in the development of ovarian senescence.
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Affiliation(s)
- Hongcai Cai
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yamin Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Huimin Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jean Damascene Niringiyumukiza
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mengdi Zhang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Wenpei Xiang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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La Y, Tang J, Di R, Wang X, Liu Q, Zhang L, Zhang X, Zhang J, Hu W, Chu M. Differential Expression of Circular RNAs in Polytocous and Monotocous Uterus during the Reproductive Cycle of Sheep. Animals (Basel) 2019; 9:ani9100797. [PMID: 31615050 PMCID: PMC6827132 DOI: 10.3390/ani9100797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/20/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The uterus is an important reproductive organ that provides nutrition and place for embryonic development. In this study, we identified circular RNAs by deep sequencing and analyzed their expression in the uteri of polytocous and monotocous sheep (FecB++) during follicular and luteal phases. Gene Ontology (GO) and KEGG enrichment analyses revealed that the source genes of these differential circular RNAs (circRNAs) were mainly enriched in reproductive hormone- and energy metabolism-related pathways. These results provide information on the molecular mechanisms of sheep prolificacy. Abstract CircRNA plays important roles in cell proliferation, differentiation, autophagy and apoptosis during development. However, there are few reports on circRNAs related to livestock reproduction. In this study, we identified circRNAs by deep sequencing and analyzed their expression in the uteri of polytocous and monotocous sheep (FecB++) during follicular and luteal phases. There were 147 and 364 circRNAs with differential expression in the follicular and luteal phases, respectively. GO and KEGG enrichment analysis was performed for the host genes of the circRNAs to predict the functions of differentially expressed circRNAs. These source genes were mainly involved in the estrogen signaling pathway, TGFβ signaling pathway, GnRH signaling pathway, oxytocin signaling pathway, pentose phosphate pathway, and starch and sucrose metabolism related to reproduction and energy metabolism. CircRNA expression patterns were validated by RT-qPCR. Our findings provide a solid foundation for the identification and characterization of key important circRNAs involved in reproduction.
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Affiliation(s)
- Yongfu La
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jishun Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China.
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China.
| | - Wenping Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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64
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Cao Z, Gao D, Xu T, Zhang L, Tong X, Zhang D, Wang Y, Ning W, Qi X, Ma Y, Ji K, Yu T, Li Y, Zhang Y. Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation. Aging (Albany NY) 2019; 11:8015-8034. [PMID: 31562810 PMCID: PMC6781969 DOI: 10.18632/aging.102315] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/21/2019] [Indexed: 12/13/2022]
Abstract
Thousands of circular RNAs (circRNAs) have been recently discovered in cumulus cells and oocytes from several species. However, the expression and function of circRNA during porcine oocyte meiotic maturation have been never examined. Here, we separately identified 7,067 and 637 circRNAs in both cumulus cells and oocytes via deep sequencing and bioinformatic analysis. Further analysis revealed that a faction of circRNAs is differentially expressed (DE) in a developmental stage-specific manner. The host genes of DE circRNAs are markedly enriched to multiple signaling pathways associated with cumulus cell function and oocyte maturation. Additionally, most DE circRNAs harbor several miRNA targets, suggesting that these DE circRNAs potentially act as miRNA sponge. Importantly, we found that maternal circARMC4 knockdown by siRNA microinjection caused a severely impaired chromosome alignment, and significantly inhibited first polar body extrusion and early embryo development. Taken together, these results demonstrate for the first time that circRNAs are abundantly and dynamically expressed in a developmental stage-specific manner in cumulus cells and oocytes, and maternally expressed circARMC4 is essential for porcine oocyte meiotic maturation and early embryo development.
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Affiliation(s)
- Zubing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Di Gao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tengteng Xu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Ling Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xu Tong
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yiqing Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Wei Ning
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xin Qi
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yangyang Ma
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Kaiyuan Ji
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tong Yu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yunsheng Li
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yunhai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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65
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Yuan W, Peng S, Wang J, Wei C, Ye Z, Wang Y, Wang M, Xu H, Jiang S, Sun D, Dai C, Jiang L, Li X. Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer. PeerJ 2019; 7:e7602. [PMID: 31579577 PMCID: PMC6754974 DOI: 10.7717/peerj.7602] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Wenliang Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.,School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Jingyu Wang
- Department of Pathology, The First Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Zhen Ye
- College of Engineering, Lishui University, Lishui, China
| | - Ye Wang
- College of Engineering, Lishui University, Lishui, China
| | - Meiliang Wang
- College of Engineering, Lishui University, Lishui, China
| | - Hao Xu
- College of Engineering, Lishui University, Lishui, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Chaoxu Dai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiaobo Li
- College of Engineering, Lishui University, Lishui, China
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Guo T, Zhang J, Yao W, Du X, Li Q, Huang L, Ma M, Li Q, Liu H, Pan Z. CircINHA resists granulosa cell apoptosis by upregulating CTGF as a ceRNA of miR-10a-5p in pig ovarian follicles. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194420. [PMID: 31476383 DOI: 10.1016/j.bbagrm.2019.194420] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 12/11/2022]
Abstract
Mammalian ovarian follicular atresia is a complex and fine-regulated biological process with active involvement of connective tissue growth factor (CTGF). The emergence of studies of endogenous non-coding RNAs has raised a new aspect for exploration of the regulatory mechanisms involved in follicular atresia. Here, we aimed to illustrate a circRNA involved in the CTGF regulatory pathway during the apoptosis and follicular atresia of pig granulosa cells (GCs). We first detected a decreased expression pattern of CTGF during follicular atresia using IHC, FISH and qRT-PCR and confirmed the anti-apoptosis effect of CTGF in GCs in vitro by CTGF siRNA knockdown. Then, we used a dual luciferase activity assay to demonstrate CTGF as a direct functional target of miR-10a-5p, which was upregulated in atresic follicles and promoted the apoptosis of GCs in vitro. The negative effect of miR-10a-5p on GC viability was confirmed by cell cycle assays, cell proliferation/apoptosis assays and the WB detection of marker proteins. More importantly, we identified a novel circRNA, termed circINHA, that was downregulated during atresia in ovarian follicles, and we confirmed a direct interaction between miR-10a-5p and circINHA. Finally, we demonstrated that circINHA promoted GCs proliferation and inhibited GCs apoptosis via CTGF as a competing endogenous RNA (ceRNA) that directly bound to miR-10a-5p. Taken together, this study provides evidence for the circINHA/miR-10a-5p/CTGF regulatory pathway in follicular GC apoptosis and provides novel insights into the role of circRNAs in the modulation of ovarian physiological functions.
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Affiliation(s)
- Tianya Guo
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Jinbi Zhang
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Wang Yao
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Xing Du
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - QiQi Li
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Long Huang
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Menglan Ma
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agriculture University, 210095, China; National Experimental Teaching Demonstration Center of Animal Science, China.
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Lu C, Sun X, Li N, Wang W, Kuang D, Tong P, Han Y, Dai J. CircRNAs in the tree shrew ( Tupaia belangeri) brain during postnatal development and aging. Aging (Albany NY) 2019; 10:833-852. [PMID: 29723158 PMCID: PMC5940110 DOI: 10.18632/aging.101437] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/23/2018] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs) are a novel type of non-coding RNA expressed across different species and tissues. At present, little is known about the expression and function of circRNAs in the tree shrew brain. In this study, we used RNA-seq to identify 35,007 circRNAs in hippocampus and cerebellum samples from infant (aged 47-52 days), young (aged 15-18 months), and old (aged 78-86 months) tree shrews. We observed no significant changes in the total circRNA expression profiles in different brain regions over time. However, circRNA tended to be downregulated in the cerebellum over time. Real-time RT-PCR analysis verified the presence of circRNAs. KEGG analysis indicated the occurrence of ubiquitin-mediated proteolysis, the MAPK signaling pathway, phosphatidylinositol signaling system, long-term depression, the rap1 signaling pathway, and long-term potentiation in both brain regions. We also observed that 29,087 (83.1%) tree shrew circRNAs shared homology with human circRNAs. The competing endogenous RNA networks suggested novel_circRNA_007362 potential functions as a 24-miRNAs sponge to regulate UBE4B expression. Thus, we obtained comprehensive circRNA expression profiles in the tree shrew brain during postnatal development and aging, which might help to elucidate the functions of circRNAs during brain aging and in age-related diseases.
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Affiliation(s)
- CaiXia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - XiaoMei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - WenGuang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - DeXuan Kuang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China
| | - PinFen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China
| | - YuanYuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China
| | - JieJie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
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Abstract
Having been debated for many years, the presence and role of spermatozoal RNAs is resolving, and their contribution to development is now appreciated. Data from different species continue show that sperm contain a complex suite of coding and noncoding RNAs that play a role in an individual's life course. Mature sperm RNAs provide a retrospective of spermatogenesis, with their presence and abundance reflecting sperm maturation, fertility potential, and the paternal contribution to the developmental path the offspring may follow.Sperm RNAs delivered upon fertilization provide some of the initial contacts with the oocyte, directly confront the maternal with the paternal contribution as a prelude to genome consolidation. Following syngamy, early embryo development may in part be modulated by paternal RNAs that can include epidydimal passengers. This provides a direct path to relay an experience and then initiate a paternal response to the environment to the oocyte and beyond. Their epigenetic impact is likely felt prior to embryonic genome activation when the population of sperm delivered transcripts markedly changes. Here, we review the insights gained from sperm RNAs over the years, the subtypes, and the caveats of the RNAs described. We discuss the role of sperm RNAs in fertilization and embryo development, and their possible mechanism(s) influencing offspring phenotype. Approaches to meet the future challenges as the study of sperm RNAs continues, include, elucidating the potential mechanisms underlying how paternal allostatic load, the constant adaptation of health to external conditions, may be relayed by sperm RNAs to affect future generations.
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Affiliation(s)
- Marta Gòdia
- Animal Genomics Group, Center for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Cerdanyola del Vallès (Barcelona), Catalonia, Spain
| | - Grace Swanson
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA.,C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan, USA
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Chen X, Shi W, Chen C. Differential circular RNAs expression in ovary during oviposition in honey bees. Genomics 2019; 111:598-606. [DOI: 10.1016/j.ygeno.2018.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/10/2018] [Accepted: 03/19/2018] [Indexed: 02/02/2023]
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Ragusa M, Barbagallo D, Chioccarelli T, Manfrevola F, Cobellis G, Di Pietro C, Brex D, Battaglia R, Fasano S, Ferraro B, Sellitto C, Ambrosino C, Roberto L, Purrello M, Pierantoni R, Chianese R. CircNAPEPLD is expressed in human and murine spermatozoa and physically interacts with oocyte miRNAs. RNA Biol 2019; 16:1237-1248. [PMID: 31135264 DOI: 10.1080/15476286.2019.1624469] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) have a critical role in the control of gene expression. Their function in spermatozoa (SPZ) is unknown to date. Twenty-eight genes, involved in SPZ/testicular and epididymal physiology, were given in circBase database to find which of them may generate circular transcripts. We focused on circNAPEPLDiso1, one of the circular RNA isoforms of NAPEPLD transcript, because expressed in human and murine SPZ. In order to functionally characterize circNAPEPLDiso1 as potential microRNA (miRNA) sponge, we performed circNAPEPLDiso1-miR-CATCH and then profiled the expression of 754 miRNAs, by using TaqMan® Low Density Arrays. Among them, miRNAs 146a-5p, 203a-3p, 302c-3p, 766-3p and 1260a (some of them previously shown to be expressed in the oocyte), resulted enriched in circNAPEPLDiso1-miR-CATCHed cell lysate: the network of interactions generated from their validated targets was centred on a core of genes involved in the control of cell cycle. Moreover, computational analysis of circNAPEPLDiso1 sequence also showed its potential translation in a short form of NAPEPLD protein. Interestingly, the expression analysis in murine-unfertilized oocytes revealed low and high levels of circNAPEPLDiso1 and circNAPEPLDiso2, respectively. After fertilization, circNAPEPLDiso1 expression significantly increased, instead circNAPEPLDiso2 expression appeared constant. Based on these data, we suggest that SPZ-derived circNAPEPLDiso1 physically interacts with miRNAs primarily involved in the control of cell cycle; we hypothesize that it may represent a paternal cytoplasmic contribution to the zygote and function as a miRNA decoy inside the fertilized oocytes to regulate the first stages of embryo development. This role is proposed here for the first time.
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Affiliation(s)
- Marco Ragusa
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy.,b Oasi Research Institute - IRCCS , Troina , Italy
| | - Davide Barbagallo
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy
| | - Teresa Chioccarelli
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
| | - Francesco Manfrevola
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
| | - Gilda Cobellis
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
| | - Cinzia Di Pietro
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy
| | - Duilia Brex
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy
| | - Rosalia Battaglia
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy
| | - Silvia Fasano
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
| | - Bruno Ferraro
- d UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise , Caserta , Italy
| | - Carolina Sellitto
- d UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise , Caserta , Italy
| | - Concetta Ambrosino
- e Dipartimento di Scienze e Tecnologie, Università del Sannio , Benevento , Italy
| | - Luca Roberto
- f IRGS, Biogem , Ariano Irpino, Avellino , Italy
| | - Michele Purrello
- a Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania , Catania , Italy
| | - Riccardo Pierantoni
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
| | - Rosanna Chianese
- c Dipartimento di Medicina Sperimentale, sez "F. Bottazzi", Università della Campania "Luigi Vanvitelli" , Napoli , Italy
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Robic A, Faraut T, Djebali S, Weikard R, Feve K, Maman S, Kuehn C. Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs. RNA Biol 2019; 16:1190-1204. [PMID: 31120323 DOI: 10.1080/15476286.2019.1621621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone.
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Affiliation(s)
- Annie Robic
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Thomas Faraut
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Sarah Djebali
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Rosemarie Weikard
- b Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Katia Feve
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Sarah Maman
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France.,c Sigenae group, GenPhySE, INRA Auzeville , Castanet Tolosan , France
| | - Christa Kuehn
- b Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany.,d Faculty of Agricultural and Environmental Sciences, University of Rostock , Rostock , Germany
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72
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Meng X, Peng H, Ding Y, Zhang L, Yang J, Han X. A transcriptomic regulatory network among miRNAs, piRNAs, circRNAs, lncRNAs and mRNAs regulates microcystin-leucine arginine (MC-LR)-induced male reproductive toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 667:563-577. [PMID: 30833255 DOI: 10.1016/j.scitotenv.2019.02.393] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Microcystin-leucine arginine (MC-LR) which is produced by cyanobacteria is a potent toxin for the reproductive system. Our previous work has demonstrated that both acute and chronic reproductive toxicity engendered by MC-LR can result in the decline of sperm quality and damage of testicular structures in male mice. The present study was designed to investigate the impact of chronic low-dose exposure to MC-LR on the regulation of RNA networks including mRNA, microRNA (miRNA), piwi-associated RNA (piRNA), covalently closed circular RNA (circRNA) and long non-coding RNA (lncRNA) in testicular tissues. By high-throughput sequencing analysis, 1091 mRNAs, 21 miRNAs, 644 piRNAs, 278 circRNAs and 324 lncRNAs were identified to be significantly altered in testicular tissues treated with MC-LR. We performed gene ontology (GO) analysis to ascertain the biological functions of differentially expressed genes. Among the altered 21 miRNAs and 644 piRNAs, the miRNA chr13_8977, which is a newly discovered species, and the piRNA mmu_piR_027558 were dramatically down-regulated after exposure to MC-LR. Consistently, both mRNA levels and protein expression levels of their predicted targets were increased significantly when chr13_8977 and mmu_piR_027558 were each down-regulated. Testicular structures, germ cell apoptosis and sperm quality were also affected by the altered expression of chr13_8977 and mmu_piR_027558 severally. We further investigated the differential expression of circRNAs and lncRNAs and their biological functions in testicular tissues following treatment with chronic low-dose exposure to MC-LR. We also constructed a competing endogenous RNA (ceRNA) network to predict the functions of the altered expressed RNAs using MiRanda. Our study suggested a crucial role for the potential network regulation of miRNAs, piRNAs, circRNAs, lncRNAs and mRNAs impacting the cytotoxicity of MC-LR in testicular tissues, which provides new perspectives in the development of diagnosis and treatment strategies for MC-LR-induced male reproductive toxicity.
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Affiliation(s)
- Xiannan Meng
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Haoran Peng
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yuanzhen Ding
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Ling Zhang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Jingping Yang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, China.
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73
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Li HM, Ma XL, Li HG. Intriguing circles: Conflicts and controversies in circular RNA research. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1538. [PMID: 31034768 DOI: 10.1002/wrna.1538] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA circles without a 5' cap or 3' tail. Since the landmark discovery of ciRS-7/CDR1as functioning as a miR-7 sponge in 2013, circRNAs have become a hot topic in RNA research. CircRNAs have been found to play active roles in cancer, cardiovascular diseases, neurological disorders, and many other diseases. They can function as microRNA (miRNA) sponges, protein scaffolds, and even translation templates. However, as circRNA research expands, many divergent views have emerged. For example, are most circRNAs competent in serving as miRNA sponges? What kinds of circRNAs are most likely to sponge miRNAs? Apart from sponging miRNAs, what could the functions of most circRNAs be? What are the features of circRNAs that are translatable? Many researchers have claimed that circRNAs are abundant, stable, conserved, and specific molecules, which hold great potential in serving as biomarkers. However, circRNA abundance is variable and some circRNAs are abundant while others are not. In addition, their stability and conservation may vary under different circumstances. Furthermore, it is unclear whether circRNA biogenesis is more likely to be regulated by RNA binding proteins or transcription factors. All of these are open questions that remain to be answered by researchers in this field. Discussing and investigating these questions will advance the understanding of this class of novel molecules and may propel inspiring new ideas for future studies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Hui-Min Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xiu-Lan Ma
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Hong-Gang Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
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74
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Li HM, Dai YW, Yu JY, Duan P, Ma XL, Dong WW, Li N, Li HG. Comprehensive circRNA/miRNA/mRNA analysis reveals circRNAs protect against toxicity induced by BPA in GC-2 cells. Epigenomics 2019; 11:935-949. [PMID: 31020848 DOI: 10.2217/epi-2018-0217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify the circRNAs expression pattern and roles in bisphenol A (BPA) induced germ cell apoptosis. Materials & methods: We performed circRNA/miRNA/mRNA-Seq in 120 μM BPA treated and nontreated GC-2 cells. Bioinformatic analysis, qPCR, apoptosis assays, luciferase report were done in the function analysis. Results: A large number of apoptosis related circRNAs/miRNAs/mRNAs were differentially expressed with competing endogenous RNA network constructed. Interestingly, most investigated upregulated circRNAs, including circDcbld2, circMapk1, circMpp6 and circTbc1d20 showed protective effects in antagonizing BPA toxicity, with the effects individually and synergistically observed. CircMapk1 may take its role by sponging miR-214-3p. Conclusion: circRNAs can play protective roles via sponging miRNAs in toxicity. Some circRNAs may serve as novel targets for BPA toxicity intervention or as biomarkers.
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Affiliation(s)
- Hui-Min Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Yu-Wan Dai
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Jiang-Yu Yu
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Peng Duan
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Xiu-Lan Ma
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Wei-Wei Dong
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Na Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China
| | - Hong-Gang Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, PR China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, PR China
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75
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Yang W, Liu Y, Gao R, Xiu Z, Sun T. Knockdown of cZNF292 suppressed hypoxic human hepatoma SMMC7721 cell proliferation, vasculogenic mimicry, and radioresistance. Cell Signal 2019; 60:122-135. [PMID: 31028816 DOI: 10.1016/j.cellsig.2019.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 02/08/2023]
Abstract
Hypoxia is a classic feature of the tumor microenvironment, and has been established as a key epigenetic factor modulating the outcome of radiotherapy. Circular RNAs (circRNAs) are novel RNA molecules with covalently closed circular structures and are highly expressed in eukaryotic transcriptomes. Although previous analysis have shown that circRNA ZNF292 (cZNF292) was hypoxia-responsive and exhibited a proangiogenic function in vitro, the molecular mechanism of cZNF292's biological function is still unclear and deserves further exploration. In this study, we investigated the effect of cZNF292 on the vasculogenic mimicry (VM) and radiosensitivity of hypoxic hepatoma SMMC7721 cells and its mechanism. Our data indicated that cZNF292 could be induced by hypoxia in a time-dependent manner in hepatoma cells independent of hypoxia inducible factor (HIF)-1α. Knockdown of cZNF292 increased SRY (sex determining region Y)-box 9 (SOX9) nuclear translocation, subsequently reduced Wnt/β-catenin pathway activity, leading to suppression of hypoxic hepatoma cell proliferation, VM, and radioresistance in vitro and in vivo. Our results delineated a novel mechanism of cZNF292 in enhancing hypoxic tumor cell radiosensitivity, which might provide valuable targets for radiation therapy for hepatoma.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China.
| | - Yingying Liu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China; Isotopic Laboratory of Nuclear Medicine, Xi'an Central Hospital, Xi'an, Shaanxi, China
| | - Ruoling Gao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Zenghe Xiu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, Jiangsu, China
| | - Ting Sun
- Neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; Division of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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76
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Han DX, Wang CJ, Sun XL, Liu JB, Jiang H, Gao Y, Chen CZ, Yuan B, Zhang JB. Identification of circular RNAs in the immature and mature rat anterior pituitary. J Endocrinol 2019; 240:393-402. [PMID: 30657740 DOI: 10.1530/joe-18-0540] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022]
Abstract
Circular RNAs (circRNAs) are a new class of RNA that have a stable structure characterized by covalently closed circular molecules and are involved in invasive pituitary adenomas and recurrent clinically nonfunctioning pituitary adenomas. However, information on circRNAs in the normal pituitary, especially in rats, is limited. In this study, we identified 4123 circRNAs in the immature (D15) and mature (D120) rat anterior pituitary using the Illumina platform, and 32 differentially expressed circRNAs were found. A total of 150 Gene Ontology terms were significantly enriched, and 16 KEGG pathways were found to contain differentially expressed genes. Moreover, we randomly selected eight highly expressed circRNAs and detected their relative expression levels in the mature and immature rat pituitary by qPCR. In addition, we predicted 90 interactions between 53 circRNAs and 57 miRNAs using miRanda. Notably, circ_0000964 and circ_0001303 are potential miRNA sponges that may regulate the Fshb gene. The expression profile of circRNAs in the immature and mature rat anterior pituitary may provide more information about the roles of circRNAs in the development and reproduction in mammals.
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Affiliation(s)
- Dong-Xu Han
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Chang-Jiang Wang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Xu-Lei Sun
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Jian-Bo Liu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Hao Jiang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yan Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Cheng-Zhen Chen
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Jia-Bao Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, People's Republic of China
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77
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Liu KS, Pan F, Mao XD, Liu C, Chen YJ. Biological functions of circular RNAs and their roles in occurrence of reproduction and gynecological diseases. Am J Transl Res 2019; 11:1-15. [PMID: 30787966 PMCID: PMC6357300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Circular RNAs (circRNAs) are a large class of non coding endogenous RNAs in eukaryotic that are formed through 3'-5' ligation of a single RNA molecule. According to the different sources of the sequences, circRNA can be divided into three types: exon circRNA (ecRNA), intron circRNA (ciRNA), and exon-intron circRNA. Accumulating studies have shown that circRNAs are abundant, diverse, stable, and cell or tissue specific expression, etc. CircRNA plays a regulating role in gene expression, and an essential role in the process of biological development, such as miRNA sponges, endogenous RNAs and biomarkers, as well as critical role in the diagnosis of diseases. Studies have verified the interplay between circRNAs and the development of embryos, sperms, ovarian epithelial tumors, endometrial cancer and preeclampsia, suggesting the potential of circRNAs to become biomarkers or therapeutical targets for human diseases. In this paper, we reviewed the researches on circRNAs' characteristics, databases of circRNA, high-throughput sequencing of circRNA, and effect on reproductive and gynecological diseases.
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Affiliation(s)
- Kang-Sheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Feng Pan
- Department of Andrology and Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Xiao-Dong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Ya-Jun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
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78
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Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing. Int J Legal Med 2019; 133:699-710. [DOI: 10.1007/s00414-018-1986-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023]
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79
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Chioccarelli T, Manfrevola F, Ferraro B, Sellitto C, Cobellis G, Migliaccio M, Fasano S, Pierantoni R, Chianese R. Expression Patterns of Circular RNAs in High Quality and Poor Quality Human Spermatozoa. Front Endocrinol (Lausanne) 2019; 10:435. [PMID: 31338066 PMCID: PMC6626923 DOI: 10.3389/fendo.2019.00435] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are expressed in human testis and seminal plasma. Until today, there is missing information about a possible payload of circRNAs in human spermatozoa (SPZ). With this in mind, we carried out a circRNA microarray identifying a total of 10.726 transcripts, 28% novel based and 84.6% with exonic structure; their potential contribution in molecular pathways was evaluated by KEGG analysis. Whether circRNAs may be related to SPZ quality was speculated evaluating two different populations of SPZ (A SPZ = good quality, B SPZ = low quality), separated on the basis of morphology and motility parameters, by Percoll gradient. Thus, 148 differentially expressed (DE)-circRNAs were identified and the expression of selected specific SPZ-derived circRNAs was evaluated in SPZ head/tail-enriched preparations, to check the preservation of these molecules during SPZ maturation and their transfer into oocyte during fertilization. Lastly, circRNA/miRNA/mRNA network was built by bioinformatics approach.
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Affiliation(s)
- Teresa Chioccarelli
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Francesco Manfrevola
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Bruno Ferraro
- UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise, Caserta, Italy
| | - Carolina Sellitto
- UOSD di Fisiopatologia della Riproduzione, Presidio Ospedaliero di Marcianise, Caserta, Italy
| | - Gilda Cobellis
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marina Migliaccio
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Silvia Fasano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Riccardo Pierantoni
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
- *Correspondence: Riccardo Pierantoni
| | - Rosanna Chianese
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
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80
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Xie F, Zhao Y, Wang S, Ma J, Wang X, Qian L. Identification, characterization, and functional investigation of circular RNAs in subventricular zone of adult rat brain. J Cell Biochem 2018; 120:3428-3437. [DOI: 10.1002/jcb.27614] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Fang Xie
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
| | - Yun Zhao
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
| | - Shi‐Da Wang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
| | - Jing Ma
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
| | - Xue Wang
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
| | - Ling‐Jia Qian
- Institute of Military Cognitive and Brain Sciences, Academy of Military Medical Sciences Beijing China
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81
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Ghorbani A, Izadpanah K, Peters JR, Dietzgen RG, Mitter N. Detection and profiling of circular RNAs in uninfected and maize Iranian mosaic virus-infected maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:402-409. [PMID: 30080628 DOI: 10.1016/j.plantsci.2018.06.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 05/10/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed non-coding RNAs that are usually derived from exonic regions of genes, but can also arise from intronic and intergenic regions. Studies of circRNAs in humans, animals and several plant species have shown an altered population of circRNAs in response to abiotic and biotic stress. Recently it was shown that circRNAs also occur in maize, but it is unknown if maize circRNAs are responsive to stress. Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. In this study, we used data from RNA-Seq of MIMV-infected maize and uninfected controls to identify differentially expressed circRNAs. Such circRNAs were confirmed by two-dimensional polyacrylamide gel electrophoresis, northern blot, RT-qPCR and sequencing. A total of 1443 circRNAs were identified in MIMV-infected maize and 1165 circRNAs in uninfected maize. Two hundred and one circRNAs were in common between MIMV-infected and uninfected samples. Of these, 155 circRNAs were up-regulated and 5 down-regulated in MIMV infected plants, compared to the uninfected control. This study for the first time identified and profiled circRNA expression in maize in response to virus infection. Moreover, we predict that 33 circRNAs may bind 23 maize miRNAs, possibly affecting plant metabolism and development. Our data suggest a role for circRNAs in plant cell regulation and response to biotic stress such as virus infection, and give new insights into the complexity of plant-microbe interactions.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, QLD, Australia.
| | | | - Jonathan R Peters
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, QLD, Australia
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, QLD, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, QLD, Australia
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82
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Zhou J, Ge Y, Hu Y, Rong D, Fu K, Wang H, Cao H, Tang W. Circular RNAs as novel rising stars with huge potentials in development and disease. Cancer Biomark 2018; 22:597-610. [PMID: 29914009 DOI: 10.3233/cbm-181296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jian Zhou
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuyuan Ge
- Department of Neurosurgery, Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Hu
- Department of General Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dawei Rong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kai Fu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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83
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Bie B, Wang Y, Li L, Fang H, Liu L, Sun J. Noncoding RNAs: Potential players in the self-renewal of mammalian spermatogonial stem cells. Mol Reprod Dev 2018; 85:720-728. [PMID: 29969526 DOI: 10.1002/mrd.23041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/30/2018] [Indexed: 12/11/2022]
Abstract
Spermatogonial stem cells (SSCs), a unique population of male germ cells with self-renewal ability, are the foundation for maintenance of spermatogenesis throughout the life of the male. Although many regulatory molecules essential for SSC self-renewal have been identified, the fundamental mechanism underlying how SSCs acquire and maintain their self-renewal activity remains largely to be elucidated. In recent years, many types of noncoding RNAs (ncRNAs) have been suggested to regulate the SSC self-renewal through multiple ways, indicating ncRNAs play crucial roles in SSC self-renewal. In this paper, we mainly focus on four types of ncRNAs including microRNA, long ncRNA, piwi-interacting RNA, as well as circular RNAs, and reviewed their potential roles in SSC self-renewal that discovered recently to help us gain a better understanding of molecular mechanisms by which ncRNAs perform their function in regulating SSC self-renewal.
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Affiliation(s)
- Beibei Bie
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Ya Wang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Liang Li
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Huanle Fang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Libing Liu
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Jin Sun
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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84
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Gao Y, Wu M, Fan Y, Li S, Lai Z, Huang Y, Lan X, Lei C, Chen H, Dang R. Identification and characterization of circular RNAs in Qinchuan cattle testis. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180413. [PMID: 30109096 PMCID: PMC6083711 DOI: 10.1098/rsos.180413;180413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/21/2018] [Indexed: 05/27/2023]
Abstract
Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ruihua Dang
- Author for correspondence: Ruihua Dang e-mail:
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85
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Gao Y, Wu M, Fan Y, Li S, Lai Z, Huang Y, Lan X, Lei C, Chen H, Dang R. Identification and characterization of circular RNAs in Qinchuan cattle testis. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180413. [PMID: 30109096 PMCID: PMC6083711 DOI: 10.1098/rsos.180413] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ruihua Dang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
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86
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Zeng RF, Zhou JJ, Hu CG, Zhang JZ. Transcriptome-wide identification and functional prediction of novel and flowering-related circular RNAs from trifoliate orange (Poncirus trifoliata L. Raf.). PLANTA 2018; 247:1191-1202. [PMID: 29417269 DOI: 10.1007/s00425-018-2857-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
A total of 558 potential circular RNAs (circRNAs) were identified in citrus, and these were analyzed and compared. One hundred seventy-six differentially expressed circRNAs were identified in two genotypes of trifoliate orange. Circular RNAs (circRNAs) play diverse roles in transcriptional control and microRNA (miRNA) function. However, little information is known about circRNAs in citrus. To identify citrus circRNAs and investigate their functional roles, high-throughput sequencing of precocious trifoliate orange (an early-flowering trifoliate orange mutant, Poncirus trifoliata L. Raf.) and its wild type was performed. A total of 558 potential circRNAs were identified by bioinformatic analysis, and 86.02% of these were sense-overlapping circRNAs. Their sequence features, alternative circularization, and other characteristics were investigated in this study. Compared with the wild type, 176 circRNAs were identified as differentially expressed circRNAs, 61 were significantly up-regulated and 115 were down-regulated in precocious trifoliate orange, indicating that they may play an important role in the early flowering process. Alternative circularization and differential expression of some circRNAs were verified by Sanger sequencing and real-time polymerase chain reaction. The functions of differentially expressed circRNAs and their host genes were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We found that many differentially expressed circRNAs had abundant miRNA binding sites: 29 circRNAs were found to act as the 16 miRNA targets. Overall, these results will help to reveal the biological functions of circRNAs in growth and development of citrus.
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Affiliation(s)
- Ren-Fang Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing-Jing Zhou
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
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87
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Stoll L, Sobel J, Rodriguez-Trejo A, Guay C, Lee K, Venø MT, Kjems J, Laybutt DR, Regazzi R. Circular RNAs as novel regulators of β-cell functions in normal and disease conditions. Mol Metab 2018; 9:69-83. [PMID: 29396373 PMCID: PMC5870096 DOI: 10.1016/j.molmet.2018.01.010] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE There is strong evidence for an involvement of different classes of non-coding RNAs, including microRNAs and long non-coding RNAs, in the regulation of β-cell activities and in diabetes development. Circular RNAs were recently discovered to constitute a substantial fraction of the mammalian transcriptome but the contribution of these non-coding RNAs in physiological and disease processes remains largely unknown. The goal of this study was to identify the circular RNAs expressed in pancreatic islets and to elucidate their possible role in the control of β-cells functions. METHODS We used a microarray approach to identify circular RNAs expressed in human islets and searched their orthologues in RNA sequencing data from mouse islets. We then measured the level of four selected circular RNAs in the islets of different Type 1 and Type 2 diabetes models and analyzed the role of these circular transcripts in the regulation of insulin secretion, β-cell proliferation, and apoptosis. RESULTS We identified thousands of circular RNAs expressed in human pancreatic islets, 497 of which were conserved in mouse islets. The level of two of these circular transcripts, circHIPK3 and ciRS-7/CDR1as, was found to be reduced in the islets of diabetic db/db mice. Mimicking this decrease in the islets of wild type animals resulted in impaired insulin secretion, reduced β-cell proliferation, and survival. ciRS-7/CDR1as has been previously proposed to function by blocking miR-7. Transcriptomic analysis revealed that circHIPK3 acts by sequestering a group of microRNAs, including miR-124-3p and miR-338-3p, and by regulating the expression of key β-cell genes, such as Slc2a2, Akt1, and Mtpn. CONCLUSIONS Our findings point to circular RNAs as novel regulators of β-cell activities and suggest an involvement of this novel class of non-coding RNAs in β-cell dysfunction under diabetic conditions.
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Affiliation(s)
- Lisa Stoll
- Department of Fundamental Neurosciences, University of Lausanne, Switzerland
| | - Jonathan Sobel
- Department of Fundamental Neurosciences, University of Lausanne, Switzerland
| | | | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Switzerland
| | - Kailun Lee
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Morten Trillingsgaard Venø
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - D Ross Laybutt
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Switzerland.
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88
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Quan G, Li J. Circular RNAs: biogenesis, expression and their potential roles in reproduction. J Ovarian Res 2018; 11:9. [PMID: 29343298 PMCID: PMC5773157 DOI: 10.1186/s13048-018-0381-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/12/2018] [Indexed: 12/18/2022] Open
Abstract
Unlike other non-coding RNAs (ncRNAs), circular RNA (circRNA) is generally presented as a covalently linked circle lacking both a 5' cap and a 3' tail. circRNAs were thought to be spliced intermediates, byproducts, or products of abnormal RNA splicing events. However, the high-throughput sequencing technology coupled with bioinformatics has recently uncovered thousands of endogenous circRNAs in cells of many different species. These circRNAs show various features, such as abundant expression, evolutionary conservation, cell- or tissue-specific expression, and a higher resistance to degradation caused by exonuclease or ribonuclease (RNase), suggesting their potentially biological significance. However, the function of these circRNAs, their mechanism of action, and the regulation of their biogenesis and degradation remains largely unclear. The current research and findings of circRNA in the context of reproduction will be reviewed. Additionally, the perspectives of circRNAs in the field will be discussed.
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Affiliation(s)
- Guobo Quan
- Yunnan Animal Science and Veterinary Institute, Jindian, Panlong county, Kunming, Yunnan province 650224 China
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Building #70, Guelph, ON N1G 2W1 Canada
| | - Julang Li
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Building #70, Guelph, ON N1G 2W1 Canada
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong province China
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89
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Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes (Basel) 2017; 8:genes8120366. [PMID: 29206165 PMCID: PMC5748684 DOI: 10.3390/genes8120366] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 11/16/2022] Open
Abstract
Non-coding ribonucleic acid (RNA) has without a doubt captured the interest of biomedical researchers. The ability to screen the entire human genome with high-throughput sequencing technology has greatly enhanced the identification, annotation and prediction of the functionality of non-coding RNAs. In this review, we discuss the current landscape of non-coding RNA research and quantitative analysis. Non-coding RNA will be categorized into two major groups by size: long non-coding RNAs and small RNAs. In long non-coding RNA, we discuss regular long non-coding RNA, pseudogenes and circular RNA. In small RNA, we discuss miRNA, transfer RNA, piwi-interacting RNA, small nucleolar RNA, small nuclear RNA, Y RNA, single recognition particle RNA, and 7SK RNA. We elaborate on the origin, detection method, and potential association with disease, putative functional mechanisms, and public resources for these non-coding RNAs. We aim to provide readers with a complete overview of non-coding RNAs and incite additional interest in non-coding RNA research.
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Affiliation(s)
- Jing Wang
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, TN 37232, USA.
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University, Medical Center, Nashville, TN 37232, USA.
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Yan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87102, USA.
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90
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Tao H, Xiong Q, Zhang F, Zhang N, Liu Y, Suo X, Li X, Yang Q, Chen M. Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus). Genomics 2017; 110:S0888-7543(17)30129-5. [PMID: 29107014 DOI: 10.1016/j.ygeno.2017.10.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 01/01/2023]
Abstract
Circular RNAs (circRNAs) are a new class of non-coding RNAs in animals and are a novel target of non-coding RNA (ncRNA) regulation. The mechanism and function of circRNAs have been reported in some species and tissues. However, there is little available information on the functions of circRNAs in the goat reproductive system. In the present study, we deeply sequenced and analyzed circRNAs through bioinformatics to reveal the expression profiles, and predicted 13,950 circRNAs in the pre-ovulatory ovarian follicles of goats for the first time. Thirty-seven circRNAs were differentially expressed in the Boer goat compared with the Macheng black goat. The chi_circ_0008219 was involved in a vast circRNA-miRNA-mRNA co-expression network. Via a luciferase activity assay, chi_circ_0008219 is observed to sponge to 3 ovarian follicle-related miRNAs. These findings demonstrate that circRNAs have potential effects in the ovarian follicles of ewes and may represent a promising new research field in ovarian follicular development.
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Affiliation(s)
- Hu Tao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Qi Xiong
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Feng Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Nian Zhang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yang Liu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiaojun Suo
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiaofeng Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Qianping Yang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mingxin Chen
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei, Academy of Agricultural Sciences, Wuhan 430064, China.
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