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      Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens

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          Abstract

          Avian leukosis virus subgroup (ALV-J) is an oncogenic neoplasm-inducing retrovirus that causes significant economic losses in the poultry industry. Recent studies have demonstrated circular RNAs (circRNAs) are implicated in pathogenic processes; however, no research has indicated circRNAs are involved in resistance to disease. In this study, over 1800 circRNAs were detected by circRNA sequencing of liver tissues from ALV-J-resistant ( n = 3) and ALV-J-susceptible chickens ( n = 3). 32 differentially expressed circRNAs were selected for analyzing including 12 upregulated in ALV-J-resistant chickens and 20 upregulated in ALV-J-susceptible chickens, besides, the top five microRNAs (miRNAs) for 12 upregulated circRNAs in ALV-J-resistant chickens were analyzed. Gene ontology and KEGG pathway analyses were performed for miRNA target genes, the predicted genes were mainly involved in immune pathways. This study provides the first evidence that circRNA alterations are involved in resistance to ALV-J-induced tumor formation. We propose circRNAs may help to mediate tumor induction and development in chickens.

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          Ago HITS-CLIP decodes miRNA-mRNA interaction maps

          Sung Wook Chi, Julie B. Zang, Aldo Mele … (2009)
          Summary MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. However, since miRNA activity requires base pairing with only 6-8 nucleotides of mRNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native Argonaute (Ago) protein-RNA complexes in mouse brain. This produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
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            MicroRNA Targets in Drosophila

            Anton Enright, Bino John, Ulrike Gaul … (2003)
            Additional data files Additional data file 1, 2, 3 and 4. Supplementary Material Additional data file 1 Additional data file 1 Click here for additional data file Additional data file 2 Additional data file 2 Click here for additional data file Additional data file 3 Additional data file 3 Click here for additional data file Additional data file 4 Additional data file 4 Click here for additional data file
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              Real-time PCR in virology.

              I. M. Mackay (2002)
              The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Oncotarget
                Journal ID (iso-abbrev): Oncotarget
                Journal ID (publisher-id): Oncotarget
                Journal ID (publisher-id): ImpactJ
                Title: Oncotarget
                Publisher: Impact Journals LLC
                ISSN (Electronic): 1949-2553
                Publication date Collection: 23 May 2017
                Publication date (Electronic): 22 March 2017
                Volume: 8
                Issue: 21
                Pages: 34961-34970
                Affiliations
                1 College of Animal Science, South China Agricultural University, Guangzhou, 510642, P.R. China
                2 Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, 510642, P.R. China
                3 College of Science and Engineering, Jinan University, Guangzhou, 510632, P.R. China
                4 USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
                5 Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangdong, Guangzhou, 510642, P.R. China
                6 South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, P.R. China
                Author notes
                Correspondence to: Qingmei Xie, qmx@ 123456scau.edu.cn
                Article
                Publisher ID: 16442
                DOI: 10.18632/oncotarget.16442
                PMC ID: 5471026
                PubMed ID: 28415618
                SO-VID: b79ea36f-35c8-4d83-a2ce-5032f6c10999
                Copyright © Copyright: © 2017 Zhang et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 25 November 2016
                Date accepted : 8 March 2017
                Categories
                Subject: Research Paper

                ScienceOpen disciplines: Oncology & Radiotherapy
                Keywords: circular rna,alv-j-resistant chickens,circular-seq,tumor
                Data availability:
                ScienceOpen disciplines: Oncology & Radiotherapy
                Keywords: circular rna, alv-j-resistant chickens, circular-seq, tumor

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