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Zucko D, Hayir A, Grinde K, Boris-Lawrie K. Circular RNA Profiles in Viremia and ART Suppression Predict Competing circRNA–miRNA–mRNA Networks Exclusive to HIV-1 Viremic Patients. Viruses 2022; 14:v14040683. [PMID: 35458413 PMCID: PMC9027527 DOI: 10.3390/v14040683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 02/01/2023] Open
Abstract
Since the onset of the HIV-1/AIDS epidemic in 1981, 75 million people have been infected with the virus, and the disease remains a public health crisis worldwide. Circular RNAs (circRNAs) are derived from excised exons and introns during backsplicing, a form of alternative splicing. The relevance of unconventional, non-capped, and non-poly(A) transcripts to transcriptomics studies remains to be routinely investigated. Knowledge gaps to be filled are the interface between host-encoded circRNAs and viral replication in chronically progressed patients and upon treatment with antiviral drugs. We implemented a bioinformatic pipeline and repurpose publicly archived RNA sequence reads from the blood of 19 HIV-1-positive patients that previously compared transcriptomes during viremia and viremia suppression by antiretroviral therapy (ART). The in silico analysis identified viremic patients’ circRNA that became undetectable after ART. The circRNAs originated from a subset of host genes enriched in the HDAC biological pathway. These circRNAs and parental mRNAs held in common a small collection of miRNA response elements (MREs), some of which were present in HIV-1 mRNAs. The function of the MRE-containing target mRNA enriched the RNA polymerase II GO pathway. To visualize the interplay between individual circRNA–miRNA–target mRNA, important for HIV-1 and potentially other diseases, an Interactive Circos tool was developed to efficiently parse the intricately competing endogenous network of circRNA–miRNA–mRNA interactions originating from seven circRNA singled out in viremic versus non-viremic patients. The combined downregulation of the identified circRNAs warrants investigation as a novel antiviral targeting strategy.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
| | - Abdullgadir Hayir
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kelsey Grinde
- Department of Mathematics, Statistics and Computer Science, Macalester College, Saint Paul, MN 55105, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (D.Z.); (A.H.)
- Correspondence:
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Li X, Gao F, Fan Y, Xie S, Li C, Meng L, Li L, Zhang S, Wei H. A novel identified circ-ANKHD1 targets the miR-27a-3p/SFRP1 signaling pathway and modulates the apoptosis of granulosa cells. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:57459-57469. [PMID: 34091845 DOI: 10.1007/s11356-021-14699-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
The specific expression profile and function of circular RNAs (circRNAs) in mammalian ovarian follicles, especially during the atresia process, are unclear. In this study, we verified and explored the expression and function of circ-ANKHD1 in granulosa cells. Our results showed that abundance of circ-ANKHD1 was significantly lower in the granulosa cells than that of ANKHD1. The expression of ANKHD1 was highest in the granulosa cells from follicles with a diameter of 5-6 mm and lowest in that with a diameter of 3-4 mm. Furthermore, the expression level of circ-ANKHD1 in the ovarian tissue of 1-day-old piglets was significantly higher than that of 17-month-old multiparous sows. The luciferase reporter assay showed the potential interaction between circ-ANKHD1 and miR-27a-3p/miR-142-5p. Furthermore, circ-ANKHD1 overexpression up-regulated SFRP1 expression, while miR-27a-3p overexpression suppressed SFRP1 expression in granulosa cells. Circ-ANKHD1 overexpression significantly decreased the cell apoptotic rates of the granulosa cells and repressed the cell population at G0/G1 and S phases but increased cell population at G2/M phase. Finally, circ-ANKHD1 overexpression increased the mRNA expression levels of Bcl-2 and cyclin D1 in the granulosa cells, while there are no effects on the mRNA expression levels of caspase-3, p53, Bax, and proliferating cell nuclear antigen. In conclusion, our study for the first time identified a novel circRNA, circ-ANKHD1 that may be associated with the biological functions of granulosa cells. Circ-ANKHD1 may promote the granulosa cell proliferation, but attenuate apoptosis, and these effects may be associated with modulation of miR-27a-3p/SFRP1.
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Affiliation(s)
- Xiaoyan Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Fenglei Gao
- Department of Tropical Agriculture and Forestry, College of Guangdong Agriculture Industry Business Polytechnic, Guangzhou, 510507, Guangdong, China
| | - Yushan Fan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shefeng Xie
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Chengde Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Li Meng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Li Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shouquan Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hengxi Wei
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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Ding W, Shi Y, Zhang H. Circular RNA circNEURL4 inhibits cell proliferation and invasion of papillary thyroid carcinoma by sponging miR-1278 and regulating LATS1 expression. Am J Transl Res 2021; 13:5911-5927. [PMID: 34306334 PMCID: PMC8290797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 12/14/2020] [Indexed: 06/13/2023]
Abstract
Circular RNAs (circRNA) are found to be closely associated with cancers as their possibility as "sponges" to miRNAs, thus liberating the downstream target mRNA. However, deep research is still needed to study the function of circRNA in papillary thyroid carcinoma (PTC). Here, we sought to explore new circRNA which could play an important role in the development of PTC. We filtered candidate circRNAs based on microarray data from public database and verified the result using qRT-PCR. We performed CCK8 assay, colony formation assay, apoptosis assay, transwell assays, and xenograft experiments to explore the function of selected circRNA on PTC. We predicted the miRNA targets of the circRNA and the target gene of miRNA through bioinformatic analysis and validated the target by mutant experiments. And by the use of overexpression experiments, knockdown experiments, and the functional assays mentioned above, we figured out the pathway behind the selected circRNA. Based on our data, we found that circNEURL4 was significantly decreased in the PTC samples and lower expression of circNEURL4 was closely associated with a poor prognosis of patients with PTC. Then, we proved that circNEURL4 could inhibit cell proliferation and invasion of PTC in vivo and in vitro. Furthermore, we demonstrated that circNEURL4 may binding to miR-1278 and thus indirectly improving the expression of LATS1. Our findings revealed that circNEURL4 may probably serve as a diagnostic marker to predict PTC patients' prognosis and a possible therapeutic target to PTC via miR-1278/LATS1 axis.
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Affiliation(s)
- Wei Ding
- Department of Thyroid Surgery, The Second Hospital of Jilin University Changchun, Jilin Province, China
| | - Ying Shi
- Department of Thyroid Surgery, The Second Hospital of Jilin University Changchun, Jilin Province, China
| | - Hong Zhang
- Department of Thyroid Surgery, The Second Hospital of Jilin University Changchun, Jilin Province, China
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Robic A, Cerutti C, Kühn C, Faraut T. Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. Front Genet 2021; 12:665153. [PMID: 34040640 PMCID: PMC8141914 DOI: 10.3389/fgene.2021.665153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.
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Affiliation(s)
- Annie Robic
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Chloé Cerutti
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Christa Kühn
- Institute Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Thomas Faraut
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
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Ng AYE, Pek JW. Circular sisRNA identification and characterisation. Methods 2021; 196:138-146. [PMID: 33838268 DOI: 10.1016/j.ymeth.2021.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 01/22/2023] Open
Abstract
Stable Intronic Sequence RNA (sisRNA) is a relatively new class of non-coding RNA. Found in many organisms, these sisRNA produced from their host genes are generally involved in regulatory roles, controlling gene expression at multiple levels through active involvement in regulatory feedback loops. Large scale identification of sisRNA via genome-wide RNA sequencing has been difficult, largely in part due to its low abundance. Done on its own, RNA sequencing often yields a large mass of information that is ironically uninformative; the potential sisRNA reads being masked by other highly abundant RNA species like ribosomal RNA and messenger RNA. In this review, we present a practical workflow for the enrichment of circular sisRNA through the use of transcriptionally quiescent systems, rRNA-depletion, and RNase R treatment prior to deep sequencing. This workflow allows circular sisRNA to be reliably detected. We also present various methods to experimentally validate the circularity and stability of the circular sisRNA identified, as well as a few methods for further functional characterisation.
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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miRNA Regulatory Functions in Farm Animal Diseases, and Biomarker Potentials for Effective Therapies. Int J Mol Sci 2021; 22:ijms22063080. [PMID: 33802936 PMCID: PMC8002598 DOI: 10.3390/ijms22063080] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs that regulate gene expression post-transcriptionally by targeting either the 3′ untranslated or coding regions of genes. They have been reported to play key roles in a wide range of biological processes. The recent remarkable developments of transcriptomics technologies, especially next-generation sequencing technologies and advanced bioinformatics tools, allow more in-depth exploration of messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), including miRNAs. These technologies have offered great opportunities for a deeper exploration of miRNA involvement in farm animal diseases, as well as livestock productivity and welfare. In this review, we provide an overview of the current knowledge of miRNA roles in major farm animal diseases with a particular focus on diseases of economic importance. In addition, we discuss the steps and future perspectives of using miRNAs as biomarkers and molecular therapy for livestock disease management as well as the challenges and opportunities for understanding the regulatory mechanisms of miRNAs related to disease pathogenesis.
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Gu Q, Liu H, Ma J, Yuan J, Li X, Qiao L. A Narrative Review of Circular RNAs in Brain Development and Diseases of Preterm Infants. Front Pediatr 2021; 9:706012. [PMID: 34621711 PMCID: PMC8490812 DOI: 10.3389/fped.2021.706012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
Circular RNAs (circRNAs) generated by back-splicing are the vital class of non-coding RNAs (ncRNAs). Circular RNAs are highly abundant and stable in eukaryotes, and many of them are evolutionarily conserved. They are blessed with higher expression in mammalian brains and could take part in the regulation of physiological and pathophysiological processes. In addition, premature birth is important in neurodevelopmental diseases. Brain damage in preterm infants may represent the main cause of long-term neurodevelopmental disorders in surviving babies. Until recently, more and more researches have been evidenced that circRNAs are involved in the pathogenesis of encephalopathy of premature. We aim at explaining neuroinflammation promoting the brain damage. In this review, we summarize the current findings of circRNAs properties, expression, and functions, as well as their significances in the neurodevelopmental impairments, white matter damage (WMD) and hypoxic-ischemic encephalopathy (HIE). So we think that circRNAs have a direct impact on neurodevelopment and brain injury, and will be a powerful tool in the repair of the injured immature brain. Even though their exact roles and mechanisms of gene regulation remain elusive, circRNAs have potential applications as diagnostic biomarkers for brain damage and the target for neuroprotective intervention.
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Affiliation(s)
- Qianying Gu
- School of Medicine, Southeast University, Nanjing, China.,Department of Pediatrics, Zhongda Hospital, Southeast University, Nanjing, China
| | - Heng Liu
- Department of Pediatrics, Zhongda Hospital, Southeast University, Nanjing, China
| | - Jingjing Ma
- School of Medicine, Southeast University, Nanjing, China.,Department of Pediatrics, Zhongda Hospital, Southeast University, Nanjing, China
| | - Jiaming Yuan
- Department of Pediatrics, Tianchang People's Hospital, Anhui, China
| | - Xinger Li
- Department of Biobank, Zhongda Hospital, Southeast University, Nanjing, China
| | - Lixing Qiao
- School of Medicine, Southeast University, Nanjing, China.,Department of Pediatrics, Zhongda Hospital, Southeast University, Nanjing, China
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