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Han S, Zhao S, Ren H, Jiao Q, Wu X, Hao X, Liu M, Han L, Han L. Novel lncRNA 803 related to Marek's disease inhibits apoptosis of DF-1 cells. Avian Pathol 2024; 53:229-241. [PMID: 38323582 DOI: 10.1080/03079457.2024.2316817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/02/2024] [Indexed: 02/08/2024]
Abstract
Marek's disease (MD) is a neoplastic disease that significantly affects the poultry industry. Long non-coding RNAs (lncRNAs) are crucial regulatory factors in various biological processes, including tumourigenesis. However, the involvement of novel lncRNAs in the course of MD virus (MDV) infection is still underexplored. Here, we present the first comprehensive characterization of differentially expressed lncRNAs in chicken spleen at different stages of MDV infection. A series of differentially expressed lncRNAs was identified at each stage of MDV infection through screening. Notably, our investigation revealed a novel lncRNA, lncRNA 803, which exhibited significant differential expression at different stages of MDV infection and was likely to be associated with the p53 pathway. Further analyses demonstrated that the overexpression of lncRNA 803 positively regulated the expression of p53 and TP53BP1 in DF-1 cells, leading to the inhibition of apoptosis. This is the first study to focus on the lncRNA expression profiles in chicken spleens during MDV pathogenesis. Our findings highlight the potential role of the p53-related novel lncRNA 803 in MD pathogenesis and provide valuable insights for decoding the molecular mechanism of MD pathogenesis involving non-coding RNA.RESEARCH HIGHLIGHTS Differentially expressed lncRNAs in spleens of chickens infected with Marek's disease virus at different stages were identified for the first time.The effects of novel lncRNA 803 on p53 pathway and apoptosis of DF-1 cells were reported for the first time.
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Affiliation(s)
- Shuo Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Shuang Zhao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Haile Ren
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Qianqian Jiao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Xianjia Wu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Xinrui Hao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Mingchun Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
| | - Liping Han
- Department of Bioscience, Changchun Normal University, Changchun, People's Republic of China
| | - Limei Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, People's Republic of China
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Yin G, Hu J, Huang X, Cai Y, Gao Z, Guo X, Feng X. The Identification and Function of Linc01615 on Influenza Virus Infection and Antiviral Response. Int J Mol Sci 2024; 25:6584. [PMID: 38928290 PMCID: PMC11203770 DOI: 10.3390/ijms25126584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Influenza virus infection poses a great threat to human health globally each year. Non-coding RNAs (ncRNAs) in the human genome have been reported to participate in the replication process of the influenza virus, among which there are still many unknowns about Long Intergenic Non-Coding RNAs (LincRNAs) in the cell cycle of viral infections. Here, we observed an increased expression of Linc01615 in A549 cells upon influenza virus PR8 infection, accompanied by the successful activation of the intracellular immune system. The knockdown of Linc01615 using the shRNAs promoted the proliferation of the influenza A virus, and the intracellular immune system was inhibited, in which the expressions of IFN-β, IL-28A, IL-29, ISG-15, MX1, and MX2 were decreased. Predictions from the catRAPID website suggested a potential interaction between Linc01615 and DHX9. Also, knocking down Linc01615 promoted influenza virus proliferation. The subsequent transcriptome sequencing results indicated a decrease in Linc01615 expression after influenza virus infection when DHX9 was knocked down. Further analysis through cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) in HEK293 cells stably expressing DHX9 confirmed the interaction between DHX9 and Linc01615. We speculate that DHX9 may interact with Linc01615 to partake in influenza virus replication and that Linc01615 helps to activate the intracellular immune system. These findings suggest a deeper connection between DHX9 and Linc01615, which highlights the significant role of Linc01615 in the influenza virus replication process. This research provides valuable insights into understanding influenza virus replication and offers new targets for preventing influenza virus infections.
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Affiliation(s)
- Guihu Yin
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Hu
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangyu Huang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqin Cai
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zichen Gao
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Guo
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiuli Feng
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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He Y, Taylor RL, Bai H, Ashwell CM, Zhao K, Li Y, Sun G, Zhang H, Song J. Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance. Poult Sci 2023; 102:103036. [PMID: 37832188 PMCID: PMC10568563 DOI: 10.1016/j.psj.2023.103036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 10/15/2023] Open
Abstract
Marek's disease virus (MDV), a naturally oncogenic, highly contagious alpha herpesvirus, induces a T cell lymphoma in chickens that causes severe economic loss. Marek's disease (MD) outcome in an individual is attributed to genetic and environmental factors. Further investigation of the host-virus interaction mechanisms that impact MD resistance is needed to achieve greater MD control. This study analyzed genome-wide DNA methylation patterns in 2 highly inbred parental lines 63 and 72 and 5 recombinant congenic strains (RCS) C, L, M, N, and X strains from those parents. Lines 63 and 72, are MD resistant and susceptible, respectively, whereas the RCS have different combinations of 87.5% Line 63 and 12.5% Line 72. Our DNA methylation cluster showed a strong association with MD incidence. Differentially methylated regions (DMRs) between the parental lines and the 5 RCS were captured. MD-resistant and MD-susceptible markers of DNA methylation were identified as transgenerational epigenetic inheritable. In addition, the growth of v-src DNA tumors and antibody response against sheep red blood cells differed among the 2 parental lines and the RCS. Overall, our results provide very solid evidence that DNA methylation patterns are transgenerational epigenetic inheritance (TEI) in chickens and also play a vital role in MD tumorigenesis and other immune responses; the specific methylated regions may be important modulators of general immunity.
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Affiliation(s)
- Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822 USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences West Virginia University, Morgantown, WV 26508 USA
| | - Hao Bai
- Department of Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Christopher M Ashwell
- Division of Animal and Nutritional Sciences West Virginia University, Morgantown, WV 26508 USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, GD 510642, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Huanmin Zhang
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA.
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Marceau A, Wang J, Iqbal V, Jiang J, Liu GE, Ma L. Investigation of lncRNA in Bos taurus Mammary Tissue during Dry and Lactation Periods. Genes (Basel) 2023; 14:1789. [PMID: 37761929 PMCID: PMC10531232 DOI: 10.3390/genes14091789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
This study aims to collect RNA-Seq data from Bos taurus samples representing dry and lactating mammary tissue, identify lncRNA transcripts, and analyze findings for their features and functional annotation. This allows for connections to be drawn between lncRNA and the lactation process. RNA-Seq data from 103 samples of Bos taurus mammary tissue were gathered from publicly available databases (60 dry, 43 lactating). The samples were filtered to reveal 214 dry mammary lncRNA transcripts and 517 lactating mammary lncRNA transcripts. The lncRNAs met common lncRNA characteristics such as shorter length, fewer exons, lower expression levels, and less sequence conservation when compared to the genome. Interestingly, several lncRNAs showed sequence similarity to genes associated with strong hair keratin intermediate filaments. Human breast cancer research has associated strong hair keratin filaments with mammary tissue cellular resilience. The lncRNAs were also associated with several genes/proteins that linked to pregnancy using expression correlation and gene ontology. Such findings indicate that there are crucial relationships between the lncRNAs found in mammary tissue and the development of the tissue, to meet both the animal's needs and our own production needs; these relationships should be further investigated to ensure that we continue to breed the most resilient, efficient dairy cattle.
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Affiliation(s)
- Alexis Marceau
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
| | - Junjian Wang
- Department of Animal Science, North Carlonina State University, Raleigh, NC 27695, USA; (J.W.); (J.J.)
| | - Victoria Iqbal
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
| | - Jicai Jiang
- Department of Animal Science, North Carlonina State University, Raleigh, NC 27695, USA; (J.W.); (J.J.)
| | - George E. Liu
- Animal Genomics and Improvemennt Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA;
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
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Dong JG, Chen MR, Rao D, Zhang N, He S, Na L. Genome-wide analysis of long noncoding RNA profiles in pseudorabies-virus-infected PK15 cells. Arch Virol 2023; 168:240. [PMID: 37668724 DOI: 10.1007/s00705-023-05859-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023]
Abstract
Recently, an increasing number of studies have shown that long noncoding RNAs (lncRNAs) are involved in host metabolism after infection with pseudorabies virus (PRV). In our study, via RNA sequencing analysis, a total of 418 mRNAs, 137 annotated lncRNAs, and 312 new lncRNAs were found to be differentially expressed. These lncRNAs were closely associated with metabolic regulation and immunity-related signalling pathways, including the T-cell receptor signalling pathway, chemokine signalling pathway, mitogen-activated protein kinase (MAPK) signalling pathway, TNF signalling pathway, Ras signalling pathway, calcium signalling pathway, and phosphatidylinositol signalling system. Real-time PCR indicated that several mRNAs and lncRNAs involved in the regulation of the immune effector process, T-cell receptor signalling pathway, TNF signalling pathway, MAPK signalling pathway, and chemokine signalling pathways were significantly expressed. These mRNAs and lncRNAs might play a role in PRV infection.
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Affiliation(s)
- Jian-Guo Dong
- School of Animal Science and Veterinary Medicine, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Ming-Rui Chen
- School of Animal Science and Veterinary Medicine, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Dan Rao
- School of Animal Science and Veterinary Medicine, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Ning Zhang
- Jiangsu Vocational College Agriculture and Forestry, Jurong, 212400, China
- Henan Fengyuan Hepu Agriculture and Animal Husbandry Co. LTD, Zhumadian, 463900, China
| | - Shuhai He
- School of Animal Science and Veterinary Medicine, Xinyang Agriculture and Forestry University, Xinyang, 464000, China.
| | - Lei Na
- College of Animal Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China.
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6
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Tolone M, Sardina MT, Criscione A, Lasagna E, Senczuk G, Rizzuto I, Riggio S, Moscarelli A, Macaluso V, Di Gerlando R, Cassandro M, Portolano B, Mastrangelo S. High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources. Poult Sci 2023; 102:102692. [PMID: 37120867 PMCID: PMC10172703 DOI: 10.1016/j.psj.2023.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.
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Affiliation(s)
- Marco Tolone
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Maria Teresa Sardina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Andrea Criscione
- Department of Agriculture, Food and the Environment, University of Catania, 95131 Catania, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Ilaria Rizzuto
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Silvia Riggio
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Angelo Moscarelli
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Vito Macaluso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Rosalia Di Gerlando
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy.
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Teng M, Zhu ZJ, Yao Y, Nair V, Zhang GP, Luo J. Critical roles of non-coding RNAs in lifecycle and biology of Marek's disease herpesvirus. SCIENCE CHINA. LIFE SCIENCES 2023; 66:251-268. [PMID: 36617590 PMCID: PMC9838510 DOI: 10.1007/s11427-022-2258-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/10/2023]
Abstract
Over the past two decades, numerous non-coding RNAs (ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic alphaherpesvirus, Marek's disease virus (MDV) causes an important immunosuppressive and rapid-onset neoplastic disease of poultry, namely Marek's disease (MD). Vaccinations can efficiently prevent the onset of MD lymphomas and other clinical disease, often heralded as the first successful example of vaccination-based control of cancer. MDV infection is also an excellent model for research into virally-induced tumorigenesis. Recently, great progress has been made in understanding the functions of ncRNAs in MD biology. Herein, we give a review of the discovery and identification of MDV-encoded viral miRNAs, focusing on the genomics, expression profiles, and emerging critical roles of MDV-1 miRNAs as oncogenic miRNAs (oncomiRs) or tumor suppressor genes involved in the induction of MD lymphomas. We also described the involvements of host cellular miRNAs, lincRNAs, and circRNAs participating in MDV life cycle, pathogenesis, and/or tumorigenesis. The prospects, strategies, and new techniques such as the CRISPR/Cas9-based gene editing applicable for further investigation into the ncRNA-mediated regulatory mechanisms in MDV pathogenesis/oncogenesis were also discussed, together with the possibilities of future studies on antiviral therapy and the development of new efficient MD vaccines.
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Affiliation(s)
- Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhi-Jian Zhu
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000, China
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - Venugopal Nair
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey, GU24 0NF, UK
| | - Gai-Ping Zhang
- International Joint Research Center of National Animal Immunology & College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
- Key Laboratory of Animal Disease and Public Safety, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China.
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Dong J, Rao D, Chen M, Zhao P, Huang L. Genome-Wide Analysis of Long Noncoding RNA Profiles in Seneca Valley Virus–Infected PK15 Cells. Front Vet Sci 2022; 9:825150. [PMID: 35310411 PMCID: PMC8927678 DOI: 10.3389/fvets.2022.825150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been demonstrated to play key roles in various biological processes. However, the contributions of lncRNAs to Seneca Valley virus (SVV) infection and host defense remain largely unknown. In this study, differentially expressed lncRNAs and mRNAs in SVV-infected PK15 cells were detected by genome-wide analysis. A total of 14,127 lncRNAs and 63,562 mRNAs were identified, and 1,780 lncRNAs were differentially expressed. The functional prediction of SVV-induced lncRNAs showed high associations with biological regulation and many immunity-related signaling pathways, including the B-cell receptor pathway, RIG-I-like receptor signaling pathway, and NF-kappa B (NF-κB) signaling pathway. We next screened lncRNAs and target genes related to immune response pathways and further demonstrated their differential expression in SVV-infected PK15 cells. Our study investigated the function of lncRNAs involved in SVV infection and provided new insight into the pathogenic mechanisms of SVV.
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Affiliation(s)
- Jianguo Dong
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Dan Rao
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Mingrui Chen
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Pandeng Zhao
- College of Animal Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
- Pandeng Zhao
| | - Li Huang
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, China
- *Correspondence: Li Huang
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9
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Chen Q, Wu C, Yao Z, Cai L, Ni Y, Mao S, Zhao R. Whole transcriptome analysis of RNA expression profiles reveals the potential regulating action of long noncoding RNA in lactating cows fed a high concentrate diet. ACTA ACUST UNITED AC 2021; 7:1315-1328. [PMID: 34786504 PMCID: PMC8567331 DOI: 10.1016/j.aninu.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/07/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Subacute ruminal acidosis (SARA) is a common metabolic disease in the dairy farming industry which is usually caused by an excessive amount of high concentrate diet. SARA not only threatens animal welfare but also leads to economic losses in the farming industry. The liver plays an important role in the distribution of nutritional substances and metabolism; however, a high concentrate diet can cause hepatic metabolic disorders and liver injury. Recently, noncoding RNA has been considered as a critical regulator of hepatic disease, however, its role in the bovine liver is limited. In this study, 12 mid-lactating dairy cows were randomly assigned to a control (CON) group (40% concentrate of dry matter, n = 6) and a SARA group (60% concentrate of dry matter, n = 6). After 21 d of treatment, all cows were sacrificed, and liver tissue samples were collected. Three dairy cows were randomly selected from the CON and SARA groups respectively to perform whole transcriptome analysis. More than 20,000 messenger RNA (mRNA), 10,000 long noncoding RNA (lncRNA), 3,500 circular RNA (circRNA) and 1,000 micro RNA (miRNA) were identified. Furthermore, 43 mRNA, 121 lncRNA and 3 miRNA were differentially expressed, whereas no obvious differentially expressed circRNA were detected between the 2 groups. Gene Ontology (GO) annotation revealed that the differentially expressed genes were mainly enriched in oxidoreductase activity, stress, metabolism, the immune response, cell apoptosis, and cell proliferation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the deferentially expressed genes were highly enriched in the phosphatidylinositol 3 kinase (PI3K)-serine/threonine kinase (AKT) signaling pathway (P < 0.05). According to KEGG pathway analysis, the differentially expressed lncRNA (DElncRNA) target genes were mainly related to proteasomes, peroxisomes, and the hypoxia-inducible factor-1 signaling pathway (P < 0.005). Further bioinformatics and integrative analyses revealed that the lncRNA were strongly correlated with mRNA; therefore, it is reasonable to speculate that lncRNA potentially play important roles in the liver dysfunction induced by SARA. Our study provides a valuable resource for future investigations on the mechanisms of SARA to facilitate an understanding of the importance of lncRNA, and offer functional RNA information.
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Affiliation(s)
- Qu Chen
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Wu
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihao Yao
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
| | - Liuping Cai
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingdong Ni
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruqian Zhao
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, China
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10
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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11
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Chen S, Chen K, Xu J, Li F, Ding J, Ma Z, Li G, Li H. Insights Into mRNA and Long Non-coding RNA Profiling RNA Sequencing in Uterus of Chickens With Pink and Blue Eggshell Colors. Front Vet Sci 2021; 8:736387. [PMID: 34692811 PMCID: PMC8529033 DOI: 10.3389/fvets.2021.736387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
The blue egg is both of biological interest and economic importance for consumers, egg retailers, and scientists. To date, the genetic mechanisms underlying pigment have mainly focused on protein-coding genes. However, the underpinning mechanism of non-coding RNAs on the pigment deposition among different eggshell colors remains unknown. In this study, RNA sequencing was employed to profile the uterine gland transcriptome (lncRNA and mRNA) of 15 Changshun blue eggshell layers, to better understand the genetic mechanisms of deposition of blue eggshell color. Results showed that differentially expressed mRNAs, GO terms, and KEGG pathways among pink-eggshell and blue-eggshell chickens were mainly targeting immune- and transporter-related terms with the SLC family, IgJ, CD family, and MTMR genes. Furthermore, the progesterone-mediated oocyte maturation and cortisol synthesis and secretion pathway with targeted gene PGR and Pbx1 were significantly enriched between blue- and pink-eggshell chickens. Integrating analysis of lncRNA and mRNA profiles predicted 4 and 25 lncRNA–gene pairs by antisense and cis analysis. They were relative to immune, nerve, and lipids and amino acid metabolisms, porphyrin, and chlorophyll metabolism with targeted gene FECH and oxidative phosphorylation and cardiac muscle contraction pathways with targeted gene COX6A1. Within blue-eggshell chickens, the GO terms hindbrain tangential cell migration and phosphatidylinositol monophosphate phosphatase activity with targeted gene Plxna2 and MTRM1 were identified. Integrating analysis of lncRNA and mRNA profiles predicted 8 and 22 lncRNA–gene pairs. Most pathways were mainly enriched on lipid-related metabolisms as found in mRNA sequencing. The lncRNAs did exert similar functions in color formation by modulating pigment disposition and immune- and lipid-related metabolisms. Our results provide a catalog of chicken uterine lncRNAs and genes worthy of further studies to understand their roles in the selection for blue eggshell color layers.
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Affiliation(s)
- Siyu Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Kecheng Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Jiaming Xu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Fangwei Li
- Guizhou Changshun Tiannong Green Shell Laying Hen Industrial Co. Ltd, Chang Shun City, China
| | - Jinlong Ding
- Guizhou Changshun Tiannong Green Shell Laying Hen Industrial Co. Ltd, Chang Shun City, China
| | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Gen Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, China
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12
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Yang K, Dong L, Duan Z, Guo R, Zhou D, Liu Z, Liang W, Liu W, Yuan F, Gao T, Tian Y. Expression profile of long non-coding RNAs in porcine lymphnode response to porcine circovirus type 2 infection. Microb Pathog 2021; 158:105118. [PMID: 34339795 DOI: 10.1016/j.micpath.2021.105118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022]
Abstract
Porcine circovirus type 2 (PCV2) can cause various clinical diseases in pigs, resulting in huge losses for the pig farms all over the world. In order to develop a new strategy to control PCV2, it is essential to understand its mechanisms firstly, especially PCV2 interferes with the host's innate immunity. In the present study, lncRNA and mRNA expression profiles in porcine lymphnode response to PCV2 infection were deeply sequenced and analyzed. 3271 novel lncRNAs were identified in all. 1898 mRNAs and 282 lncRNAs showed differential expression between control and PCV2-infected groups. The bioinformatics analysis including lncRNA-mRNA co-expression network construction, as well as GO and KEGG pathway analysis focused on the DEGs was carried out. The results indicated that lncRNAs might participate in PCV2 infection-induced the pathogenesis of immunosuppression through regulating the host's immune responses, biological regulation, response to stimulus, cellular component organization or biogenesis and metabolism. And these differentially expressed lncRNAs might play important roles in response to PCV2 infection in the host's innate immune system. These findings provided a large-scale survey of dysregulated lncRNAs after PCV2 infection, especially the lncRNAs responded to host's innate immune within the lymphnode. This study will provide a novel insight into the lncRNAs' functions and the possible immunosuppressive mechanism induced by PCV2 infection. However, further research will be required to verify the characteristic function of the dysregulated lncRNAs.
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Affiliation(s)
- Keli Yang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China; Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Wuhan, 430064, Hubei, PR China.
| | - Ling Dong
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhengying Duan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Rui Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Danna Zhou
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Zewen Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Wan Liang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Wei Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Ting Gao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Yongxiang Tian
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China.
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13
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Sun A, Zhu X, Liu Y, Wang R, Yang S, Teng M, Zheng L, Luo J, Zhang G, Zhuang G. Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs during replication of Marek's disease virus in vitro. BMC Genomics 2021; 22:296. [PMID: 33888086 PMCID: PMC8063467 DOI: 10.1186/s12864-021-07619-w] [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] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Background The newly discovered reversible N6-methyladenosine (m6A) modification plays an important regulatory role in gene expression. Long non-coding RNAs (lncRNAs) participate in Marek’s disease virus (MDV) replication but how m6A modifications in lncRNAs are affected during MDV infection is currently unknown. Herein, we profiled the transcriptome-wide m6A modification in lncRNAs in MDV-infected chicken embryo fibroblast (CEF) cells. Results Methylated RNA immunoprecipitation sequencing results revealed that the lncRNA m6A modification is highly conserved with MDV infection increasing the expression of lncRNA m6A modified sites compared to uninfected cell controls. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that lncRNA m6A modifications were highly associated with signaling pathways associated with MDV infection. Conclusions In this study, the alterations seen in transcriptome-wide m6A occurring in lncRNAs following MDV-infection suggest this process plays important regulatory roles during MDV replication. We report for the first time profiling of the alterations in transcriptome-wide m6A modification in lncRNAs of MDV-infected CEF cells.
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Affiliation(s)
- Aijun Sun
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiaojing Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Ying Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Rui Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Shuaikang Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Luping Zheng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.,Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Guoqing Zhuang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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14
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Role of microRNA and long non-coding RNA in Marek's disease tumorigenesis in chicken. Res Vet Sci 2021; 135:134-142. [PMID: 33485054 DOI: 10.1016/j.rvsc.2021.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Marek's disease virus (MDV), the causative agent of Marek's disease (MD), results in highly infectious phymatosis, lymphatic tissue hyperplasia, and neoplasia. MD is associated with high morbidity and mortality rate. Non-coding RNAs (ncRNAs) entails long non-coding RNA (lncRNA) and microRNA (miRNA). Numerous studies have reported that specific miRNAs and lncRNAs participate in multiple cellular processes, such as proliferation, migration, and tumor cell invasion. Specialized miRNAs and lncRNAs militate a similar role in MD tumor oncogenesis. Despite its growing popularity, only a few reviews are available on ncRNA in MDV tumor oncogenes. Herein, we summarized the role of the miRNAs and lncRNAs in MD tumorigenesis. Altogether, we brought forth the research issues, such as MD prevention, screening, regulatory network formation, novel miRNAs, and lncRNAs analysis in MD that needs to be explored further. This review provides a theoretical platform for the further analysis of miRNAs and lncRNAs functions and the prevention and control of MD and malignancies in domestic animals.
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15
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Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System. Life (Basel) 2020; 10:life10080148. [PMID: 32806547 PMCID: PMC7459779 DOI: 10.3390/life10080148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases.
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16
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Tang R, Wang J, Zhou M, Lan Y, Jiang L, Price M, Yue B, Li D, Fan Z. Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages. Anim Genet 2020; 51:731-740. [DOI: 10.1111/age.12990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/04/2020] [Accepted: 07/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Ruixiang Tang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Min Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Lan Jiang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Megan Price
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Diyan Li
- Sichuan Agricultural University Chengdu 611130 China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
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17
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Wang L, Liang W, Wang S, Wang Z, Bai H, Jiang Y, Bi Y, Chen G, Chang G. Circular RNA expression profiling reveals that circ-PLXNA1 functions in duck adipocyte differentiation. PLoS One 2020; 15:e0236069. [PMID: 32692763 PMCID: PMC7373283 DOI: 10.1371/journal.pone.0236069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Adipocytes are derived from pluripotent mesenchymal stem cells through adipogenesis. Pre-adipocyte differentiation in poultry greatly influences fat deposition and meat quality. Circular RNAs (circRNAs) have an important function in cancer and some differentiation processes. Herein, high-throughput transcriptome sequencing was used to detect circRNAs present in cherry valley duck pre-adipocyte and adipocyte differentiation over 3 days. We identified 9,311 circRNAs and 141 differentially expressed circRNAs. Sequencing results were verified through qRT-PCR using seven randomly selected circRNAs, and competing endogenous RNA (ceRNA) networks were exhibited by ten important circRNAs in duck adipocyte differentiation. circRNA plexin A1 (circ-PLXNA1) was detected in duck adipocytes and mainly expressed in adipose, leg muscle and liver. Inhibition of circ-PLXNA1 limited the differentiation of duck adipocyte. There were four corresponding miRNAs for circ-PLXNA1 and 313 target genes for those miRNAs. CeRNA“circ-PLXNA1/miR-214/CTNNB1 axis” was focused and verified by a dual-luciferase reporter experiment. After co-transfection of cells with si-circ-PLXNA1 and miR-214 mimics, the expression level of CTNNB1 was down-regulated, triglyceride content and the adipogenic capacity of preadipocytes decreased. While there were no significant change after si-CTNNB1 transfection. All these results provide further insight into the circRNAs, especially for circ-PLXNA1 in duck adipocyte differentiation.
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Affiliation(s)
- Laidi Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Wenshuang Liang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Shasha Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, China
- * E-mail:
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18
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Yu L, Dong J, Liu Y, Zhang L, Liang P, Wang L, Huang L, Xu Z, Song C. Genome-wide analysis of long noncoding RNA profiles in Vero cells infected with porcine epidemic diarrhea virus. Arch Virol 2020; 165:1969-1977. [PMID: 32529459 DOI: 10.1007/s00705-020-04694-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 05/10/2020] [Indexed: 10/24/2022]
Abstract
Porcine epidemic diarrhea (PED) is an acute enteric disease caused by porcine epidemic diarrhea virus (PEDV). In China, variant PEDV causes severe watery diarrhea, vomiting, and dehydration in piglets, leading to very high morbidity and mortality. However, the pathogenesis of PEDV is still not fully understood. In our study, we analyzed the long noncoding RNA (lncRNA) and mRNA expression profiles of PEDV GDgh16 in infected Vero cells at 60 h postinfection. A total of 61,790 annotated mRNAs, 14,247 annotated lncRNAs and 1290 novel lncRNAs were identified. A total of 227 annotated lncRNAs and 13 novel lncRNAs were significantly and differentially expressed after viral infection. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases were used to identify genes adjacent to the lncRNAs, and it was found that these lncRNAs were enriched in pathways related to immune and antiviral responses. Next, we selected candidate lncRNAs and their predicted target genes for study. RT-qPCR demonstrated that these lncRNAs and genes were differentially expressed after PEDV infection. Our study investigated the function of lncRNAs involved in PEDV infection, providing new insight into the pathogenic mechanisms of PEDV.
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Affiliation(s)
- Linyang Yu
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China
| | - Jianguo Dong
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Yanling Liu
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China
| | - Leyi Zhang
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China
| | - Pengshuai Liang
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China
| | - Lei Wang
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China
| | - Li Huang
- School of Animal Husbandry and Medical Engineering, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Zheng Xu
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China.
| | - Changxu Song
- College of Animal Science and National Engineering Center for Swine Breeding Industry, South China Agriculture University, Guangzhou, 510642, China.
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Long noncoding RNA and mRNA profiling of hypothalamic-pituitary-mammary gland axis in lactating sows under heat stress. Genomics 2020; 112:3668-3676. [PMID: 32360888 DOI: 10.1016/j.ygeno.2020.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 11/23/2022]
Abstract
Heat stress (HS) seriously affects sow lactation performance and Long non-coding RNAs (lncRNAs) play vital roles in the regulation of transcription and post transcription. However, the mechanism of lncRNAs expression affecting lactation performance on the hypothalamus-pituitary-mammary axis of sows is still unclear. In this study, we performed RNA sequencing and bioinformatics analysis of the hypothalamus, pituitary, and mammary gland tissues of lactating sows under HS and thermal comfort. In total, the analysis identified 658, 6021, and 6745 differently expressed (DE) mRNAs, 26, 126, and 169 DE lncRNAs between comparison groups in the hypothalamus, pituitary, and mammary glands, respectively. The hormone genes and most DE mRNAs encoding heat shock protein were differently expressed in the HS group. In addition, 2, 60, and 86 pairs of DE lncRNAs and mRNAs correlation were observed in those tissues, respectively. Some lncRNAs may be involved in the regulation of lactation performance in the HS sows.
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20
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Ma H, Ni A, Ge P, Li Y, Shi L, Wang P, Fan J, Isa AM, Sun Y, Chen J. Analysis of Long Non-Coding RNAs and mRNAs Associated with Lactation in the Crop of Pigeons ( Columba livia). Genes (Basel) 2020; 11:genes11020201. [PMID: 32079139 PMCID: PMC7073620 DOI: 10.3390/genes11020201] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Pigeons have the ability to produce milk and feed their squabs. The genetic mechanisms underlying milk production in the crops of 'lactating' pigeons are not fully understood. In this study, RNA sequencing was employed to profile the transcriptome of lncRNA and mRNA in lactating and non-'lactating' pigeon crops. We identified 7066 known and 17,085 novel lncRNAs. Of these lncRNAs, 6166 were differentially expressed. Among the 15,138 mRNAs detected, 6483 were differentially expressed, including many predominant genes with known functions in the milk production of mammals. A GO annotation analysis revealed that these genes were significantly enriched in 55, 65, and 30 pathways of biological processes, cellular components, and molecular functions, respectively. A KEGG pathway enrichment analysis revealed that 12 pathways (involving 544 genes), including the biosynthesis of amino acids, the propanoate metabolism, the carbon metabolism and the cell cycle, were significantly enriched. The results provide fundamental evidence for the better understanding of lncRNAs' and differentially expressed genes' (DEGs) regulatory role in the molecular pathways governing milk production in pigeon crops. To our knowledge, this is the first genome-wide investigation of the lncRNAs in pigeon crop associated with milk production. This study provided valuable resources for differentially expressed lncRNAs and mRNAs, improving our understanding of the molecular mechanism of pigeon milk production.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jilan Chen
- Correspondence: ; Tel.: +86-10-6281-6005
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21
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He Y, Han B, Ding Y, Zhang H, Chang S, Zhang L, Zhao C, Yang N, Song J. Linc-GALMD1 Regulates Viral Gene Expression in the Chicken. Front Genet 2019; 10:1122. [PMID: 31798630 PMCID: PMC6868033 DOI: 10.3389/fgene.2019.01122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
A rapidly increasing number of reports on dysregulated long intergenic non-coding RNA (lincRNA) expression across numerous types of cancers indicates that aberrant lincRNA expression may be a major contributor to tumorigenesis. Marek’s disease (MD) is a T cell lymphoma of chickens induced by Marek’s disease virus (MDV). Although we have investigated the roles of lincRNAs in bursa tissue of MDV-infected chickens in previous studies, the molecular mechanisms of lincRNA functions in T cells remain poorly understood. In the present study, Linc-GALMD1 was identified from CD4+ T cells and MSB1 cells, and its expression was significantly downregulated in MD-resistant line of birds in response to MDV challenge. Furthermore, loss-of-function experiments indicated that linc-GALMD1 significantly affected the expression of 290 genes in trans. Through integrated analysis of differentially expressed genes (DEGs) induced by MDV and linc-GALMD1, we found that IGLL1 gene expression levels had a positive correlation with the degree of MD infection and could potentially serve as an indicator for clinical diagnosis of MD. Moreover, an interaction between MDV and linc-GALMD1 was also observed. Accordingly, chicken embryonic fibroblast cells were inoculated with MDV with and without the linc-GALMD1 knockdown, and the data showed that linc-GALMD1 could repress MDV gene expression during the course of MDV infection. These findings uncovered a role of linc-GALMD1 as a viral gene regulator and suggested a function of linc-GALMD1 contributing to tumor suppression by coordinating expression of MDV genes and tumor-related genes and regulating immune responses to MDV infection.
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Affiliation(s)
- Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Bo Han
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States.,National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yi Ding
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agricultural Research Service, USDA, East Lansing, MI, United States
| | - Shuang Chang
- Avian Disease and Oncology Laboratory, Agricultural Research Service, USDA, East Lansing, MI, United States.,College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Li Zhang
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunfang Zhao
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
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22
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Ma X, Zhao X, Wang K, Tang X, Guo J, Mi M, Qi Y, Chang L, Huang Y, Tong D. Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection. BMC Genomics 2019; 20:806. [PMID: 31684870 PMCID: PMC6829948 DOI: 10.1186/s12864-019-6156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/09/2019] [Indexed: 12/28/2022] Open
Abstract
Background Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. Results In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). Conclusions The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.
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Affiliation(s)
- Xuelian Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaomin Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Kaili Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoyi Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jianxiong Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mi Mi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yanping Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lingling Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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23
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Chen D, Chen H, Du Y, Zhou D, Geng S, Wang H, Wan J, Xiong C, Zheng Y, Guo R. Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection. INSECTS 2019; 10:insects10080245. [PMID: 31405016 PMCID: PMC6723323 DOI: 10.3390/insects10080245] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.
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Affiliation(s)
- Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Du
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sihai Geng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haipeng Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jieqi Wan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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24
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Ruiz-Orera J, Albà MM. Conserved regions in long non-coding RNAs contain abundant translation and protein-RNA interaction signatures. NAR Genom Bioinform 2019; 1:e2. [PMID: 33575549 PMCID: PMC7671363 DOI: 10.1093/nargab/lqz002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/14/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
The mammalian transcriptome includes thousands of transcripts that do not correspond to annotated protein-coding genes and that are known as long non-coding RNAs (lncRNAs). A handful of lncRNAs have well-characterized regulatory functions but the biological significance of the majority of them is not well understood. LncRNAs that are conserved between mice and humans are likely to be enriched in functional sequences. Here, we investigate the presence of different types of ribosome profiling signatures in lncRNAs and how they relate to sequence conservation. We find that lncRNA-conserved regions contain three times more ORFs with translation evidence than non-conserved ones, and identify nine cases that display significant sequence constraints at the amino acid sequence level. The study also reveals that conserved regions in intergenic lncRNAs are significantly enriched in protein–RNA interaction signatures when compared to non-conserved ones; this includes sites in well-characterized lncRNAs, such as Cyrano, Malat1, Neat1 and Meg3, as well as in tens of lncRNAs of unknown function. This work illustrates how the analysis of ribosome profiling data coupled with evolutionary analysis provides new opportunities to explore the lncRNA functional landscape.
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Affiliation(s)
- Jorge Ruiz-Orera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Dr Aiguader 88, Barcelona 08003, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, Dr Aiguader 88, Barcelona 08003, Spain.,Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona 08010, Spain
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25
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Chu Q, Ding Y, Cai W, Liu L, Zhang H, Song J. Marek's Disease Virus Infection Induced Mitochondria Changes in Chickens. Int J Mol Sci 2019; 20:ijms20133150. [PMID: 31252692 PMCID: PMC6651546 DOI: 10.3390/ijms20133150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are crucial cellular organelles in eukaryotes and participate in many cell processes including immune response, growth development, and tumorigenesis. Marek’s disease (MD), caused by an avian alpha-herpesvirus Marek’s disease virus (MDV), is characterized with lymphomas and immunosuppression. In this research, we hypothesize that mitochondria may play roles in response to MDV infection. To test it, mitochondrial DNA (mtDNA) abundance and gene expression in immune organs were examined in two well-defined and highly inbred lines of chickens, the MD-susceptible line 72 and the MD-resistant line 63. We found that mitochondrial DNA contents decreased significantly at the transformation phase in spleen of the MD-susceptible line 72 birds in contrast to the MD-resistant line 63. The mtDNA-genes and the nucleus-genes relevant to mtDNA maintenance and transcription, however, were significantly up-regulated. Interestingly, we found that POLG2 might play a potential role that led to the imbalance of mtDNA copy number and gene expression alteration. MDV infection induced imbalance of mitochondrial contents and gene expression, demonstrating the indispensability of mitochondria in virus-induced cell transformation and subsequent lymphoma formation, such as MD development in chicken. This is the first report on relationship between virus infection and mitochondria in chicken, which provides important insights into the understanding on pathogenesis and tumorigenesis due to viral infection.
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Affiliation(s)
- Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100094, China
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Yi Ding
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Wentao Cai
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Lei Liu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA
| | - Huanmin Zhang
- USDA, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20740, USA.
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26
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You Z, Zhang Q, Liu C, Song J, Yang N, Lian L. Integrated analysis of lncRNA and mRNA repertoires in Marek's disease infected spleens identifies genes relevant to resistance. BMC Genomics 2019; 20:245. [PMID: 30922224 PMCID: PMC6438004 DOI: 10.1186/s12864-019-5625-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Marek's disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without lesions after MDV infection, and five spleens from noninfected chickens (NS), to explore the underlying mechanism of host resistance in Marek's disease (MD). RESULTS By using a precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed (DE) mRNAs, putative lncRNAs, and known lncRNAs were profiled among three groups. We found that several specific intergroup differentially expressed genes were involved in important biological processes and pathways, including B cell activation and the Wnt signaling pathway; some of these genes were also found to be the hub genes in the co-expression network analyzed by WGCNA. Network analysis depicted both intergenic correlation and correlation between genes and MD traits. Five DE lncRNAs including MSTRG.360.1, MSTRG.6725.1, MSTRG.6754.1, MSTRG.15539.1, and MSTRG.7747.5 strongly correlated with MD-resistant candidate genes, such as IGF-I, CTLA4, HDAC9, SWAP70, CD72, JCHAIN, CXCL12, and CD8B, suggesting that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their target genes. CONCLUSIONS Our results provide both transcriptomic and epigenetic insights on MD resistance and its pathological mechanism. The comprehensive lncRNA and mRNA transcriptomes in MDV-infected chicken spleens were profiled. Co-expression analysis identified integrated lncRNA-mRNA and gene-gene interaction networks, implying that hub genes or lncRNAs exert critical influence on MD resistance and tumorigenesis.
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Affiliation(s)
- Zhen You
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Qinghe Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Changjun Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, 150001 China
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ling Lian
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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27
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Zhang Y, Wang L, Qiu L, Pan R, Bai H, Jiang Y, Wang Z, Bi Y, Chen G, Chang G. Expression patterns of novel circular RNAs in chicken cells after avian leukosis virus subgroup J infection. Gene 2019; 701:72-81. [PMID: 30898701 DOI: 10.1016/j.gene.2019.03.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/02/2019] [Accepted: 03/16/2019] [Indexed: 02/06/2023]
Abstract
Avian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus that causes severe economic losses to the poultry industry worldwide. Circular RNAs (circRNAs) are a class of non-coding RNAs that has been described in various biological systems and pathogenic processes. However, the immune mechanisms in response to circRNAs remain unknown. In this study, high-throughput transcriptome sequencing was used to detect circRNAs present in chicken macrophage (HD11) and chick embryo fibroblast (CEF) cells infected with ALV-J. We identified 7684 circRNAs from diverse genomic locations in CEF and HD11 after ALV-J infection, these RNAs showed complex expression patterns that differed based on the cells type and infection time. In total, 302 differentially expressed (DE) circRNAs and 164 DE circRNAs were identified in CEF and HD11 after ALV-J infection, respectively. CircRNA7419-associated with KDM4C- and circRNA6679 and circRNA6680-associated with TNFAIP6- were involved in the immune response upon ALV-J infection in CEF. Host genes were analyzed through further bioinformatics analysis. The result confirmed that a large number of DE circRNAs corresponded to several immune-associated or tumor-associated terms and pathways, such as Mucin type O-Glycan biosynthesis, MAPK signaling pathway, B cell receptor signaling, and Wnt signaling pathway in CEF, as well as Jak-STAT signaling pathway, apoptosis, and MAPK signaling pathway in HD11. CircRNAs related to the B cell receptor signaling pathway in CEF, and the Jak-STAT signaling pathway in HD11, were selected for circRNA-miRNA interaction network analyses. Our study indicates that circRNAs expression was altered by ALV-J infection in both CEF and HD11, and may play a key role in the progression of ALV-J infection.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Laidi Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Lingling Qiu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Rui Pan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
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28
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Porcine endemic diarrhea virus infection regulates long noncoding RNA expression. Virology 2018; 527:89-97. [PMID: 30471453 PMCID: PMC7112091 DOI: 10.1016/j.virol.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in various life processes. However, the lncRNA expression and potential functions in porcine endemic diarrhea virus (PEDV) infection and host defense are still poorly understood. In this study, we investigated the lncRNA expression profiles during PEDV infection in intestinal porcine epithelial cell-jejunum 2 (IPEC-J2) cell lines by next-generation sequencing and identified 6188 novel lncRNAs. The functional annotation analysis revealed that these lncRNAs might be associated with many immunity-related genes. We next selected candidate lncRNAs related to immune response pathways and further identified their differential expression in PEDV-infected IPEC-J2 cells and newborn piglets. Our results demonstrated that PEDV infection regulated lncRNA expression patterns in both the IPEC-J2 cell line and piglet ileum. These findings provide the first large-scale survey of lncRNAs associated with PEDV infection, specifically the lncRNAs responsible for the activation of the immune system within the ileum.
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29
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Analysis of expression profiles of long noncoding RNAs and mRNAs in brains of mice infected by rabies virus by RNA sequencing. Sci Rep 2018; 8:11858. [PMID: 30089776 PMCID: PMC6082909 DOI: 10.1038/s41598-018-30359-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/20/2018] [Indexed: 02/06/2023] Open
Abstract
Rabies, caused by rabies virus (RABV), is still the deadliest infectious disease. Mechanism of host immune response upon RABV infection is not yet fully understood. Accumulating evidences suggest that long noncoding RNAs (lncRNAs) plays key roles in host antiviral responses. However, expression profile and function of lncRNAs in RABV infection remain unclear. In the present study, expression profile of lncRNAs and mRNAs profiles were investigated in RABV-infected brain tissues of mice by RNA sequencing. A total of 140 lncRNAs and 3,807 mRNAs were differentially expressed in RABV-infected animals. The functional annotation and enrichment analysis using Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that differentially expressed transcripts were predominantly involved in signaling pathways related to host immune response. The expression profiles of the selected lncRNAs in brains of mice during RABV infections were verified by quantitative real time polymerase chain reaction (qRT-PCR). To our knowledge, this is the first report to profile the lncRNA expression in RABV infected mice. Our findings provide insights into understanding the role of lncRNAs in host immune response against RABV infection.
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30
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Cai W, Li C, Liu S, Zhou C, Yin H, Song J, Zhang Q, Zhang S. Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows. Front Genet 2018; 9:281. [PMID: 30105049 PMCID: PMC6077245 DOI: 10.3389/fgene.2018.00281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality.
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Affiliation(s)
- Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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31
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Hu G, Niu F, Humburg BA, Liao K, Bendi S, Callen S, Fox HS, Buch S. Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis. Oncotarget 2018; 9:18648-18663. [PMID: 29719633 PMCID: PMC5915100 DOI: 10.18632/oncotarget.24307] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are long non-coding regulatory RNAs that are longer than 200 nucleotides. One of the major functions of lncRNAs is the regulation of specific gene expression at multiple steps including, recruitment and expression of basal transcription machinery, post-transcriptional modifications and epigenetics [1]. Emerging evidence suggests that lncRNAs also play a critical role in maintaining tissue homeostasis during physiological and pathological conditions, lipid homeostasis, as well as epithelial and smooth muscle cell homeostasis, a topic that has been elegantly reviewed [2-5]. While aberrant expression of lncRNAs has been implicated in several disease conditions, there is paucity of information about their contribution to the etiology of diseases [6]. Several studies have compared the expression of lncRNAs under normal and cancerous conditions and found differential expression of several lncRNAs, suggesting thereby an involvement of lncRNAs in disease processes [7, 8]. Furthermore, the ability of lncRNAs to influence epigenetic changes also underlies their role in disease pathogenesis since epigenetic regulation is known to play a critical role in many human diseases [1]. LncRNAs thus are not only involved in homeostatic functioning but also play a vital role in the progression of many diseases, thereby underscoring their potential as novel therapeutic targets for the alleviation of a variety of human disease conditions.
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Affiliation(s)
- Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Niu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bree A. Humburg
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ke Liao
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sunil Bendi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon Callen
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S. Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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Dynamic Changes in the Splenic Transcriptome of Chickens during the Early Infection and Progress of Marek's Disease. Sci Rep 2017; 7:11648. [PMID: 28912500 PMCID: PMC5599560 DOI: 10.1038/s41598-017-11304-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 08/22/2017] [Indexed: 01/18/2023] Open
Abstract
Gallid alphaherpesvirus 2 (GaHV2) is an oncogenic avian herpesvirus inducing Marek’s disease (MD) and rapid-onset T-cell lymphomas. To reveal molecular events in MD pathogenesis and tumorigenesis, the dynamic splenic transcriptome of GaHV2-infected chickens during early infection and pathogenic phases has been determined utilizing RNA-seq. Based on the significant differentially expressed genes (DEGs), analysis of gene ontology, KEGG pathway and protein-protein interaction network has demonstrated that the molecular events happening during GaHV2 infection are highly relevant to the disease course. In the ‘Cornell Model’ description of MD, innate immune responses and inflammatory responses were established at early cytolytic phase but persisted until lymphoma formation. Humoral immunity in contrast began to play a role firstly in the intestinal system and started at late cytolytic phase. Neurological damage caused by GaHV2 is first seen in early cytolytic phase and is then sustained throughout the following phases over a long time period. During the proliferative phase many pathways associated with transcription and/or translation were significantly enriched, reflecting the cell transformation and lymphoma formation. Our work provides an overall view of host responses to GaHV2 infection and offers a meaningful basis for further studies of MD biology.
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Long intergenic non-coding RNA GALMD3 in chicken Marek's disease. Sci Rep 2017; 7:10294. [PMID: 28860661 PMCID: PMC5579197 DOI: 10.1038/s41598-017-10900-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/16/2017] [Indexed: 12/18/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are transcribed from non-coding DNA sequences. Studies have revealed that aberrant expressions of lincRNAs are associated with various types of cancers and neurological disorders. Marek's disease (MD) is a highly contagious T-cell lymphoid neoplasia of chicken induced by Marek's disease virus (MDV). In this study, we first identified and validated linc-GALMD3 highly expressed in MDV-infected CD4+ T cells by RNA-Seq and qRT-PCR. By RNA-Seq analysis in MDCC-MSB1 cells after loss of function of linc-GALMD3 by shRNA, we found that linc-GALMD3 could positively cis-regulate its downstream gga-miR-223 gene expression. In contrast, it could trans-regulate the 748 differentially expressed genes (FDR < 0.01) that were mainly enriched into mitochondrial structure and cell cycle processes using GO analysis. Of these, the most significantly expressed gene EPYC might cause iris lesion in MD. The other eight genes, NDUFA4, NDUFB6, NDUFV1, NDUFS8, SDHB, UQCRC1, UQCRC2, and COX7A2, actively participated in oxidative phosphorylation in mitochondrial dysfunction and cell death. Most importantly, we found that the MDV replication was repressed when linc-GALMD3 was knocked down in CEF cells. Our results suggested that linc-GALMD3 might be a critical regulator in chicken MD and could be used as a candidate-promising mark for MD prevention, diagnosis, and treatment.
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Hezroni H, Ben-Tov Perry R, Meir Z, Housman G, Lubelsky Y, Ulitsky I. A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes. Genome Biol 2017; 18:162. [PMID: 28854954 PMCID: PMC5577775 DOI: 10.1186/s13059-017-1293-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/31/2017] [Indexed: 12/04/2022] Open
Abstract
Background Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. Results We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. Conclusions We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1293-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Zohar Meir
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Gali Housman
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel.
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Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing in chicken testis with extreme sperm motility. Sci Rep 2017; 7:9055. [PMID: 28831078 PMCID: PMC5567338 DOI: 10.1038/s41598-017-08738-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/18/2017] [Indexed: 01/10/2023] Open
Abstract
Sperm motility is the most important indicator in evaluating roosters' fecundity. However, the genetic mechanisms underlying chicken sperm motility is not yet clear. Long non-coding RNA (lncRNA) play epigenetic roles in reproduction. In this study, RNA sequencing was employed to profile the testis transcriptome (lncRNA and mRNA) of six Beijing-you cocks divergent in sperm motility. In total, 2,597 lncRNAs were identified in the chicken testis, including 1,267 lincRNAs, 975 anti-sense lncRNAs, and 355 intronic lncRNAs. They shared similar features with previous studies. Of these lncRNAs, 124 were differentially expressed. Among 17,690 mRNAs detected in this study, 544 were differentially expressed, including a bunch of genes with known functions on sperm motility. GO annotation analysis revealed these genes were involved in ATP binding, cilium assembly, and oxidation-reduction processes. Integrating analysis of lncRNA and mRNA profiles predicted 10 lncRNA-gene pairs, including 8 co-regulated and 2 inversely-regulated pairs. To the best of our knowledge, this is the first genome-wide investigation of the lncRNAs in the chicken testis associated with sperm motility. Our results provided a catalog of chicken testis lncRNAs and genes worthy of further studies to understand their roles in cocks' reproductive performance regulation.
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Wang YM, Xu HB, Wang MS, Otecko NO, Ye LQ, Wu DD, Zhang YP. Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication. BMC Evol Biol 2017; 17:192. [PMID: 28810830 PMCID: PMC5558714 DOI: 10.1186/s12862-017-1036-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Background Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. Results We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes. Conclusions Our study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1036-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Bo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Newton Otieno Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling-Qun Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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37
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Fan R, Cao C, Zhao X, Shi Q, Zhao J, Xu S. Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase. Oncotarget 2017; 8:52761-52774. [PMID: 28881768 PMCID: PMC5581067 DOI: 10.18632/oncotarget.17187] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/12/2017] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to play a pivotal role in proliferation and differentiation of muscles. However, the study on the roles of lncRNAs in Selenium (Se) deficiency induced muscle injury is still unclear. In this study, deep sequencing was performed to profile lncRNAs and mRNAs of the muscles from the Se deficiency (-Se group) and control (C group) chickens. The results revealed that 38 lncRNAs (23 up-regulated and 15 down-regulated) and 687 mRNAs (285 up-regulated and 402 down-regulated) were significantly dysregulated expressed, and the significantly dysregulated pathway including Phagosome, Cardiac muscle contraction, and Peroxisome Proliferator-Activated Receptor (PPAR) in -Se group. The regulatory relationship between ALDBGALG0000005049 and stearoyl-CoA desaturase (SCD), which involved in PPAR pathway was verified. The results also showed that the decreased expressions of SCD, PPARα, PPARβ and PPARγ, and the increased expressions of interleukin (IL)-1β, IL-6, IL-8, and chemokine (C-C motif) ligand 4 (CCL4) along with silencing of ALDBGALG0000005049 in chicken myoblasts. Moreover, increased expressions of IL-1β, IL-6, IL-8, and CCL4 and inflammatory cell infiltration in microstructure of chicken muscles treated with Se deficiency were observed. This study displayed an overview of aberrantly expressed lncRNAs and mRNAs profiles and PPAR pathway, and revealed that downregulation of ALDBGALG0000005049 caused inflammation by regulating SCD in chicken muscle resulted from Se deficiency.
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Affiliation(s)
- Ruifeng Fan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Changyu Cao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Xia Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Qunxiang Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Jinxin Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P. R. China
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38
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Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver. Sci Rep 2017; 7:6396. [PMID: 28743867 PMCID: PMC5527063 DOI: 10.1038/s41598-017-06634-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
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39
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Li D, Ji Y, Wang F, Wang Y, Wang M, Zhang C, Zhang W, Lu Z, Sun C, Ahmed MF, He N, Jin K, Cheng S, Wang Y, He Y, Song J, Zhang Y, Li B. Regulation of crucial lncRNAs in differentiation of chicken embryonic stem cells to spermatogonia stem cells. Anim Genet 2016; 48:191-204. [PMID: 27862128 DOI: 10.1111/age.12510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2016] [Indexed: 12/15/2022]
Abstract
Regulation of crucial lncRNAs involved in differentiation of chicken embryonic stem cells (ESCs) to spermatogonia stem cells (SSCs) was explored by sequencing the transcriptome of ESCs, primordial germ cells (PGCs) and SSCs with RNA-Seq; analytical bioinformatic methods were used to excavate candidate lncRNAs. We detected expression of candidate lncRNAs in ESCs, PGCs and SSCs and forecasted related target genes. Utilizing wego, david and string, function and protein-protein interactions of target genes were analyzed. Finally, based on string analysis, interaction diagrams and relevant signaling pathways were established. Our results indicate a total of 9657 lncRNAs in ESCs, PGCs and SSCs, with 3549 defined as significantly different. We screened 20 candidate lncRNAs, each demonstrating a greater than eight-fold difference in |logFC| value between groups (ESCs vs. PGCs, ESCs vs. SSCs and PGCs vs. SSCs) or specifically expressed in an individual cell type. qRT-PCR results indicated that expression tendencies of candidate lncRNAs were consistent with RNA-Seq. Fifteen cis and four trans target genes were forecasted. Based on wego and string analyses, we found lnc-SSC1, lnc-SSC5, lnc-SSC2 and lnc-ESC2 negatively regulated target genes SUFU, EPHA3, KLF3, ARL3 and TRIM8, whereas SHH, NOTCH, TGF-β, cAMP/cGMP and JAK/STAT signaling pathways were promoted, causing differentiation of ESCs into SSCs. Our findings represent a preliminary unveiling of lncRNA-associated regulatory mechanisms during differentiation of chicken ESCs into SSCs, filling a research void in male germ cell differentiation related to lncRNA. Our results also provide basic information for improving in vitro induction systems for differentiation of chicken ESCs into SSCs.
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Affiliation(s)
- D Li
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Y Ji
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - F Wang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Y Wang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - M Wang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - C Zhang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - W Zhang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Z Lu
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - C Sun
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - M F Ahmed
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - N He
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - K Jin
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - S Cheng
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Y Wang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Y He
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - J Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Y Zhang
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - B Li
- Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
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Weikard R, Demasius W, Kuehn C. Mining long noncoding RNA in livestock. Anim Genet 2016; 48:3-18. [DOI: 10.1111/age.12493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- R. Weikard
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - W. Demasius
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - C. Kuehn
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
- Faculty of Agricultural and Environmental Sciences; University Rostock; 18059 Rostock Germany
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41
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Ulitsky I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet 2016; 17:601-14. [DOI: 10.1038/nrg.2016.85] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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