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Zhuang A, Tan Y, Liu Y, Yang C, Kiriazis H, Grigolon K, Walker S, Bond ST, McMullen JR, Calkin AC, Drew BG. Deletion of the muscle enriched lncRNA Oip5os1 induces atrial dysfunction in male mice with diabetes. Physiol Rep 2023; 11:e15869. [PMID: 38054572 PMCID: PMC10698826 DOI: 10.14814/phy2.15869] [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: 10/05/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023] Open
Abstract
Long ncRNAs (lncRNAs) have been shown to play a biological and physiological role in various tissues including the heart. We and others have previously established that the lncRNA Oip5os1 (1700020I14Rik, OIP5-AS1, Cyrano) is enriched in striated muscles, and its deletion in mice leads to defects in both skeletal and cardiac muscle function. In the present study, we investigated the impact of global Oip5os1 deletion on cardiac function in the setting of streptozotocin (STZ)-induced diabetes. Specifically, we studied male WT and KO mice with or without diabetes for 24 weeks, and phenotyped animals for metabolic and cardiac endpoints. Independent of genotype, diabetes was associated with left ventricular diastolic dysfunction based on a fall in E'/A' ratio. Deletion of Oip5os1 in a setting of diabetes had no significant impact on ventricular function or ventricular weight, but was associated with left atrial dysfunction (reduced fractional shortening) and myopathy which was associated with anesthesia intolerance and premature death in the majority of KO mice tested during cardiac functional assessment. This atrial phenotype was not observed in WT diabetic mice. The most striking molecular difference was a reduction in the metabolic regulator ERRalpha in the atria of KO mice compared with WT mice. There was also a trend for a reduction in Serca2a. These findings highlight Oip5os1 as a gene of interest in aspects of atrial function in the setting of diabetes, highlighting an additional functional role for this lncRNA in cardiac pathological settings.
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Affiliation(s)
- Aowen Zhuang
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
| | - Yanie Tan
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Yingying Liu
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
| | - Christine Yang
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
| | - Helen Kiriazis
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Kyah Grigolon
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
| | - Shannen Walker
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Simon T. Bond
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Julie R. McMullen
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Anna C. Calkin
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Brian G. Drew
- Baker Heart & Diabetes InstituteMelbourneVictoriaAustralia
- Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneVictoriaAustralia
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Liu B, San L, Guo H, Zhu K, Zhang N, Yang J, Liu B, Hou J, Zhang D. Transcriptomic Analysis Reveals Functional Interaction of mRNA-lncRNA-miRNA in Trachinotus ovatus Infected by Cryptocaryon irritans. Int J Mol Sci 2023; 24:15886. [PMID: 37958869 PMCID: PMC10648848 DOI: 10.3390/ijms242115886] [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: 08/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The skin of Trachinotus ovatus is a crucial component of the mucosal immune system and serves as the primary site of infection by Cryptocaryon irritans. In order to investigate the significant role of skin in C. irritans infection, a comprehensive transcriptome analysis was conducted on skin tissues from the infection group, infection-adjacent group, and infection group compared with the infection-adjacent group (ATT_vs_PER, ADJ_vs_PER, ATT_vs_ADJ). This study identified differentially expressed long non-coding RNAs (DE lncRNAs), microRNAs (DE miRNAs), and differentially expressed genes (DEGs). The prediction of lncRNA target genes was accomplished by utilizing positional relationship (co-location) and expression correlation (co-expression) with protein-coding genes. Subsequently, functional enrichment analysis was conducted on the target genes of differentially expressed lncRNAs, revealing their involvement in signaling pathways such as tight junction, MAPK, and cell adhesion molecules. This study describes the regulatory network of lncRNA-miRNA-mRNA in T. ovatus skin tissue infected with C. irritans. Functional prediction analysis showed that differentially expressed lncRNA and miRNA may regulate the expression of immune genes such as interleukin-8 (il8) to resist the infection of C. irritans. Conducting additional research on these non-coding RNAs will facilitate a deeper understanding of their immune regulatory function in T. ovatus during C. irritans infection. The study of non-coding RNA in this study laid a foundation for revealing the molecular mechanism of the immune system of T. ovatus to respond to the infection of C. irritans. It provided a choice for the molecular breeding of Trachinotus ovatus against C. irritans.
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Affiliation(s)
- Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Lize San
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jingwen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Bo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
| | - Jilun Hou
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Dianchang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (B.L.); (B.L.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572000, China
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3
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Zheng W, Chen Y, Wang Y, Chen S, Xu XW. Genome-Wide Identification and Involvement in Response to Biotic and Abiotic Stresses of lncRNAs in Turbot ( Scophthalmus maximus). Int J Mol Sci 2023; 24:15870. [PMID: 37958851 PMCID: PMC10648414 DOI: 10.3390/ijms242115870] [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: 10/07/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in a variety of biological processes, including stress response. However, the number, characteristics and stress-related expression of lncRNAs in turbot are still largely unknown. In this study, a total of 12,999 lncRNAs were identified at the genome-wide level of turbot for the first time using 24 RNA-seq datasets. Sequence characteristic analyses of transcripts showed that lncRNA transcripts were shorter in average length, lower in average GC content and in average expression level as compared to the coding genes. Expression pattern analyses of lncRNAs in 12 distinct tissues showed that lncRNAs, especially lincRNA, exhibited stronger tissue-specific expression than coding genes. Moreover, 612, 1351, 1060, 875, 420 and 1689 differentially expressed (DE) lncRNAs under Vibrio anguillarum, Enteromyxum scophthalmi, and Megalocytivirus infection and heat, oxygen, and salinity stress conditions were identified, respectively. Among them, 151 and 62 lncRNAs showed differential expression under various abiotic and biotic stresses, respectively, and 11 lncRNAs differentially expressed under both abiotic and biotic stresses were selected as comprehensive stress-responsive lncRNA candidates. Furthermore, expression pattern analysis and qPCR validation both verified the comprehensive stress-responsive functions of these 11 lncRNAs. In addition, 497 significantly co-expressed target genes (correlation coefficient (R) > 0.7 and q-value < 0.05) for these 11 comprehensive stress-responsive lncRNA candidates were identified. Finally, GO and KEGG enrichment analyses indicated that these target genes were enriched mainly in molecular function, such as cytokine activity and active transmembrane transporter activity, in biological processes, such as response to stimulus and immune response, and in pathways, such as protein families: signaling and cellular processes, transporters and metabolism. These findings not only provide valuable reference resources for further research on the molecular basis and function of lncRNAs in turbot but also help to accelerate the progress of molecularly selective breeding of stress-resistant turbot strains or varieties.
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Affiliation(s)
- Weiwei Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
| | - Yadong Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Yaning Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Xi-wen Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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Zhu N, Hu L, Hu W, Li Q, Mao H, Wang M, Ke Z, Qi L, Wang J. Comparative Transcriptome Profiling of mRNA and lncRNA of Mouse Spleens Inoculated with the Group ACYW135 Meningococcal Polysaccharide Vaccine. Vaccines (Basel) 2023; 11:1295. [PMID: 37631863 PMCID: PMC10458039 DOI: 10.3390/vaccines11081295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The Group ACYW135 meningococcal polysaccharide vaccine (MPV-ACYW135) is a classical common vaccine used to prevent Neisseria meningitidis serogroups A, C, Y, and W135, but studies on the vaccine at the transcriptional level are still limited. In the present study, mRNAs and lncRNAs related to immunity were screened from the spleens of mice inoculated with MPV-ACYW135 and compared with the control group to identify differentially expressed mRNAs and lncRNAs in the immune response. The result revealed 34375 lncRNAs and 41321 mRNAs, including 405 differentially expressed (DE) lncRNAs and 52 DE mRNAs between the MPV group and the control group. Results of GO and KEGG enrichment analysis turned out that the main pathways related to the immunity of target genes of those DE mRNAs and DE lncRNAs were largely associated with positive regulation of T cell activation, CD8-positive immunoglobulin production in mucosal tissue, alpha-beta T cell proliferation, negative regulation of CD4-positive, and negative regulation of interleukin-17 production, suggesting that the antigens of MPV-ACYW135 capsular polysaccharide might activate T cell related immune reaction in the vaccine inoculation. In addition, it was noted that Bach2 (BTB and CNC homolog 2), the target gene of lncRNA MSTRG.17645, was involved in the regulation of immune response in MPV-ACYW135 vaccination. This study provided a preliminary catalog of both mRNAs and lncRNAs associated with the proliferation and differentiation of body immune cells, which was worthy of further research to enhance the understanding of the biological immune process regulated by MPV-ACYW135.
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Affiliation(s)
- Nan Zhu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Liping Hu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Wenlong Hu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Qiang Li
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
| | - Zhijian Ke
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China; (N.Z.); (L.H.); (W.H.); (Q.L.); (M.W.); (Z.K.); (L.Q.)
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5
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Fan YX, Andoh V, Chen L. Multi-omics study and ncRNA regulation of anti-BmNPV in silkworms, Bombyx mori: an update. Front Microbiol 2023; 14:1123448. [PMID: 37275131 PMCID: PMC10232802 DOI: 10.3389/fmicb.2023.1123448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Bombyx mori silkworm is an important economic insect which has a significant contribution to the improvement of the economy. Bombyx mori nucleopolyhedrovirus (BmNPV) is a vitally significant purulent virus that impedes the sustainable and stable development of the silkworm industry, resulting in substantial economic losses. In recent years, with the development of biotechnology, transcriptomics, proteomics, metabolomics, and the related techniques have been used to select BmNPV-resistant genes, proteins, and metabolites. The regulatory networks between viruses and hosts have been gradually clarified with the discovery of ncRNAs, such as miRNA, lncRNA, and circRNA in cells. Thus, this paper aims to highlight the results of current multi-omics and ncRNA studies on BmNPV resistance in the silkworm, providing some references for resistant strategies in the silkworm to BmNPV.
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Zhu N, Zhang F, Zhou H, Ma W, Mao H, Wang M, Ke Z, Wang J, Qi L. Mechanisms of Immune-Related Long Non-Coding RNAs in Spleens of Mice Vaccinated with 23-Valent Pneumococcal Polysaccharide Vaccine (PPV23). Vaccines (Basel) 2023; 11:vaccines11030529. [PMID: 36992112 DOI: 10.3390/vaccines11030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/05/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The 23-valent pneumococcal vaccine (PPV23) is a classical common vaccine used to prevent pneumococcal disease. In past decades, it was thought that vaccination with this vaccine induces humoral immunity, thereby reducing the disease associated with infection with 23 common serotypes of Streptococcus pneumoniae (Sp). However, for this polysaccharide vaccine, the mechanism of immune response at the transcriptional level has not been fully studied. To identify the lncRNAs (long noncoding RNAs) and mRNAs in spleens related to immunity after PPV23 vaccination in mice, high-throughput RNA sequencing of spleens between a PPV23 treatment group and a control group were performed and evaluated in this study. The RNA-seq results identified a total of 41,321 mRNAs and 34,375 lncRNAs, including 55 significantly differentially expressed (DE) mRNAs and 389 DE lncRNAs (p < 0.05) between the two groups. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to T-cell costimulation, positive regulation of alpha–beta T-cell differentiation, the CD86 biosynthetic process, and the PI3K-Akt signaling pathway, indicating that the polysaccharide component antigens of PPV23 might activate a cellular immune response during the PPV23 immunization process. Moreover, we found that Trim35 (tripartite motif containing 35), a target gene of lncRNA MSTRG.9127, was involved in regulating immunity. Our study provides a catalog of lncRNAs and mRNAs associated with immune cells’ proliferation and differentiation, and they deserve further study to deepen the understanding of the biological processes in the regulation of PPV23 during humoral immunity and cellular immunity.
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Affiliation(s)
- Nan Zhu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Fan Zhang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Huan Zhou
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Wei Ma
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Zhijian Ke
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
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Mao H, Chen L, Bao R, Weng S, Wang M, Xu N, Qi L, Wang J. Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone. Front Vet Sci 2022; 8:838703. [PMID: 35281430 PMCID: PMC8908959 DOI: 10.3389/fvets.2021.838703] [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: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Reproductive efficiency is of significant importance in pork production for it has a great impact on economic success. Ovulation rate is an early component of reproduction efficiency of pigs, and it contributes to the upper limit of litter size. In this study, we used the newly developed recombinant pig follicle stimulating hormone (rpFSH) instead of traditional PMSG to increase ovulation rate of pigs in order to achieve higher litter size, for it was better at stimulating ovulation, and showed more cheaper and greener. However, relatively little is known about the underlying genetic bases and molecular mechanisms. Consequently, an experiment was carried out in ovaries of replacement gilts to screen the key genes and lncRNAs that affect the fecundity of pigs by RNA-seq technology. Twenty gilts were divided into two groups, including 10 rpFSH treatment pigs and 10 control animals. After slaughtering and collecting the phenotypic data, ovaries of five pigs in each group were selected for RNA-seq. Total RNA was extracted to construct the library and then sequence on an Illumina Hiseq 4000 system. A comprehensive analysis of mRNAs and long non-coding RNAs (lncRNAs) from 10 samples was performed with bioinformatics. The phenotypic data showed that rpFSH treatment groups had the higher (P < 0.01) ovarian weight and more mature follicles. The RNA-seq results showed that a total of 43,499 mRNAs and 21,703 lncRNAs were identified, including 21,300 novel lncRNAs and 403 known lncRNAs, of which 585 mRNAs and 398 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the two groups of rpFSH treatment group and controlled group. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to prolactin receptor activity, mitophagy by induced vacuole formation, and meiotic spindle. Moreover, we found that NR5A2 (nuclear receptor subfamily 5, group A, member 2), a target gene of lncRNA MSTRG.3902.1, was involved in regulating follicular development, ovulation, and estrogen production. Our study provided a catalog of lncRNAs and mRNAs associated with ovulation of rpFSH treatment, and they deserve further study to deepen the understanding of biological processes in the regulation of ovaries of rpFSH treatment pigs.
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Affiliation(s)
- Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Lu Chen
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Rupo Bao
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Shiqiao Weng
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Ningying Xu
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- *Correspondence: Lili Qi
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- Jinbo Wang
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8
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Gandhi S, Witten A, De Majo F, Gilbers M, Maessen J, Schotten U, de Windt LJ, Stoll M. Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology. Genomics 2021; 113:3782-3792. [PMID: 34506887 DOI: 10.1016/j.ygeno.2021.09.002] [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: 04/28/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 12/14/2022]
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. A deeper characterization of regional transcription patterns within different heart chambers may aid to improve our understanding of the molecular mechanisms involved in myocardial function and further, our ability to develop novel therapeutic strategies. Here, we used RNA sequencing to determine differentially expressed protein coding (PC) and long non-coding (lncRNA) transcripts within the heart chambers across seven vertebrate species and identified evolutionarily conserved chamber specific genes, lncRNAs and pathways. We investigated lncRNA homologs based on sequence, secondary structure, synteny and expressional conservation and found most lncRNAs to be conserved by synteny. Regional co-expression patterns of transcripts are modulated by multiple factors, including genomic overlap, strandedness and transcript biotype. Finally, we provide a community resource designated EvoACTG, which informs researchers on the conserved yet intertwined nature of the coding and non-coding cardiac transcriptome across popular model organisms in CVD research.
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Affiliation(s)
- Shrey Gandhi
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Anika Witten
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany
| | - Federica De Majo
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Martijn Gilbers
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Jos Maessen
- Department of Cardiothoracic Surgery, CARIM School for Cardiovascular Diseases, Maastricht University Medical Centre+, Maastricht, the Netherlands
| | - Ulrich Schotten
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - Leon J de Windt
- Department of Molecular Genetics, Maastricht University, Maastricht, the Netherlands
| | - Monika Stoll
- Institute of Human Genetics, Division of Genetic Epidemiology, University of Muenster, Muenster, Germany; Department of Biochemistry, Genetic Epidemiology and Statistical Genetics, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands.
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Zhou C, He T, Chen L. LncRNA CASC19 accelerates chondrocytes apoptosis and proinflammatory cytokine production to exacerbate osteoarthritis development through regulating the miR-152-3p/DDX6 axis. J Orthop Surg Res 2021; 16:399. [PMID: 34158095 PMCID: PMC8218455 DOI: 10.1186/s13018-021-02543-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/08/2021] [Indexed: 01/02/2023] Open
Abstract
Background Osteoarthritis (OA) is one kind of degenerative joint disease that happens in articular cartilage and other joint tissues. Long non-coding RNAs (lncRNAs) have been reported to serve as pivotal regulators in many diseases, including OA. However, the role and relevant regulatory mechanisms of CASC19 in OA remain unknown. Methods The expression levels of CASC19, miR-152-3p, and DDX6 were identified by reverse-transcription polymerase chain reaction (RT-qPCR). Cell viability and apoptosis were determined by Cell Counting Kit-8 (CCK-8) and flow cytometry assays, respectively. The relationship between miR-152-3p and CASC19 or DDX6 was predicted by bioinformatics tools and verified by the dual-luciferase reporter assay. Results CASC19 was verified to exhibit higher expression in OA tissues and cells. Moreover, inhibition of CASC19 weakened proinflammatory cytokine (IL-6, IL-8, and TNF-α) production and cell apoptosis but facilitated cell viability. Experiments of the ceRNA mechanism elucidated that miR-152-3p was a sponge for CASC19, and miR-152-3p targeted DDX6, suggesting that CASC19 sponged miR-152-3p to release DDX6. Finally, results from rescue assays proved that the impacts of CASC19 silencing on chondrocytes apoptosis and proinflammatory cytokine production could be reversed by DDX6 overexpression. Conclusions It was concluded that lncRNA CASC19 accelerated chondrocytes apoptosis and proinflammatory cytokine production to exacerbate osteoarthritis development through regulating the miR-152-3p/DDX6 axis. These findings may offer an effective biological target for OA treatment.
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Affiliation(s)
- Chang Zhou
- Department of Orthopedics, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, People's Republic of China
| | - Tianda He
- Department of Osteoarthritis, The Third Affiliated Hospital of Soochow University, Changzhou, 213000, People's Republic of China
| | - Liji Chen
- Department of Encephalopathy, Changzhou Hospital of Traditional Chinese Medicine, No. 25 Heping North Road, Changzhou, 213000, People's Republic of China.
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10
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Zhuang A, Calkin AC, Lau S, Kiriazis H, Donner DG, Liu Y, Bond ST, Moody SC, Gould EA, Colgan TD, Carmona SR, Inouye M, de Aguiar Vallim TQ, Tarling EJ, Quaife-Ryan GA, Hudson JE, Porrello ER, Gregorevic P, Gao XM, Du XJ, McMullen JR, Drew BG. Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner. iScience 2021; 24:102537. [PMID: 34142046 PMCID: PMC8184514 DOI: 10.1016/j.isci.2021.102537] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/28/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to influence numerous biological processes, being strongly implicated in the maintenance and physiological function of various tissues including the heart. The lncRNA OIP5-AS1 (1700020I14Rik/Cyrano) has been studied in several settings; however its role in cardiac pathologies remains mostly uncharacterized. Using a series of in vitro and ex vivo methods, we demonstrate that OIP5-AS1 is regulated during cardiac development in rodent and human models and in disease settings in mice. Using CRISPR, we engineered a global OIP5-AS1 knockout (KO) mouse and demonstrated that female KO mice develop exacerbated heart failure following cardiac pressure overload (transverse aortic constriction [TAC]) but male mice do not. RNA-sequencing of wild-type and KO hearts suggest that OIP5-AS1 regulates pathways that impact mitochondrial function. Thus, these findings highlight OIP5-AS1 as a gene of interest in sex-specific differences in mitochondrial function and development of heart failure. The lncRNA OIP5-AS1 is enriched in striated muscles in mice and humans. OIP5-AS1 is regulated during heart development and in models of heart disease. Global deletion of OIP5-AS1 exacerbates heart failure specifically in female mice. Transcriptomics analysis suggests that loss OIP5-AS1 alters mitochondrial function.
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Affiliation(s)
- Aowen Zhuang
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Anna C. Calkin
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Shannen Lau
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Helen Kiriazis
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Daniel G. Donner
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Yingying Liu
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Simon T. Bond
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Sarah C. Moody
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | | | | | | | - Michael Inouye
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | | | - Elizabeth J. Tarling
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | | | - Enzo R. Porrello
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul Gregorevic
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiao-Ming Gao
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Xiao-Jun Du
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Julie R. McMullen
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Corresponding author
| | - Brian G. Drew
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Corresponding author
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11
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Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel) 2021; 11:1118. [PMID: 33919662 PMCID: PMC8069800 DOI: 10.3390/ani11041118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Shivasmi Sharma
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Smit Patel
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Prachi Mehta
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam;
| | - Subhash Rajpurohit
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad, Telangana 500072, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
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12
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Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
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Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
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13
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Mao H, Xu X, Cao H, Dong X, Zou X, Xu N, Yin Z. Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons ( Columba livia). Front Genet 2021; 12:571325. [PMID: 33833772 PMCID: PMC8021926 DOI: 10.3389/fgene.2021.571325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022] Open
Abstract
Egg production performance is one of the most important economic traits in pigeon industry. However, little is known regarding how egg production performance is regulated by long non-coding RNAs (lncRNAs) in pigeons. To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study. A total of 34,346 mRNAs and 24,601 lncRNAs were identified, including 14,525 known lncRNAs and 10,076 novel lncRNAs, of which 811 mRNAs and 148 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the groups of high and low egg production performance. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to cell differentiation, ATP binding and methylation. Moreover, we found that FOXK2, a target gene of lncRNA MSTRG.7894.4, was involved in regulating estrogen receptors. Our study provided a catalog of lncRNAs and mRNAs associated with egg production performance, and they deserve further study to deepen the understanding of biological processes in the ovaries of pigeons.
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Affiliation(s)
- Haiguang Mao
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, Zhejiang, China
| | - Xiuli Xu
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haiyue Cao
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyang Dong
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Zou
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ningying Xu
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhaozheng Yin
- Animal Science College, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Constanty F, Shkumatava A. lncRNAs in development and differentiation: from sequence motifs to functional characterization. Development 2021; 148:148/1/dev182741. [PMID: 33441380 DOI: 10.1242/dev.182741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of long noncoding RNAs (lncRNAs) with characterized developmental and cellular functions continues to increase, but our understanding of the molecular mechanisms underlying lncRNA functions, and how they are dictated by RNA sequences, remains limited. Relatively short, conserved sequence motifs embedded in lncRNA transcripts are often important determinants of lncRNA localization, stability and interactions. Identifying such RNA motifs remains challenging due to the substantial length of lncRNA transcripts and the rapid evolutionary turnover of lncRNA sequences. Nevertheless, the recent discovery of specific RNA elements, together with their experimental interrogation, has enabled the first step in classifying heterogeneous lncRNAs into sub-groups with similar molecular mechanisms and functions. In this Review, we focus on lncRNAs with roles in development, cell differentiation and normal physiology in vertebrates, and we discuss the sequence elements defining their functions. We also summarize progress on the discovery of regulatory RNA sequence elements, as well as their molecular functions and interaction partners.
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Affiliation(s)
- Florian Constanty
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
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15
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Jiang G, Su Z, Liang X, Huang Y, Lan Z, Jiang X. Long non-coding RNAs in prostate tumorigenesis and therapy (Review). Mol Clin Oncol 2020; 13:76. [PMID: 33005410 DOI: 10.3892/mco.2020.2146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed malignancy. Although there have been many advances in PCa diagnosis and therapy, the concrete mechanism remains unknown. Long non-coding RNAs (lncRNAs) are novel biomarkers associated with PCa, and their dysregulated expression is closely associated with risk stratification, diagnosis and carcinogenesis. Accumulating evidence has suggested that lncRNAs play important roles in prostate tumorigenesis through relevant pathways, such as androgen receptor interaction and PI3K/Akt. The present review systematically summarized the potential clinical utility of lncRNAs and provided a novel guide for their function in PCa.
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Affiliation(s)
- Ganggang Jiang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China.,Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Zhengming Su
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China.,Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Xue Liang
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Yiqiao Huang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Ziquan Lan
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Xianhan Jiang
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China.,Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
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16
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Jones AN, Pisignano G, Pavelitz T, White J, Kinisu M, Forino N, Albin D, Varani G. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA (NEW YORK, N.Y.) 2020; 26:1234-1246. [PMID: 32457084 PMCID: PMC7430676 DOI: 10.1261/rna.076117.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
The wide prevalence and regulated expression of long noncoding RNAs (lncRNAs) highlight their functional roles, but the molecular basis for their activities and structure-function relationships remains to be investigated, with few exceptions. Among the relatively few lncRNAs conserved over significant evolutionary distances is the long intergenic noncoding RNA (lincRNA) Cyrano (orthologous to human OIP5-AS1), which contains a region of 300 highly conserved nucleotides within tetrapods, which in turn contains a functional stretch of 26 nt of deep conservation. This region binds to and facilitates the degradation of the microRNA miR-7, a short ncRNA with multiple cellular functions, including modulation of oncogenic expression. We probed the secondary structure of Cyrano in vitro and in cells using chemical and enzymatic probing, and validated the results using comparative sequence analysis. At the center of the functional core of Cyrano is a cloverleaf structure maintained over the >400 million years of divergent evolution that separates fish and primates. This strikingly conserved motif provides interaction sites for several RNA-binding proteins and masks a conserved recognition site for miR-7. Conservation in this region strongly suggests that the function of Cyrano depends on the formation of this RNA structure, which could modulate the rate and efficiency of degradation of miR-7.
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Affiliation(s)
- Alisha N Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Giuseppina Pisignano
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH-6500, Switzerland
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Jessica White
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Martin Kinisu
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Nicholas Forino
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Dreycey Albin
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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17
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He J, Leng C, Pan J, Li A, Zhang H, Cong F, Wang H. Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells. Pathogens 2020; 9:pathogens9060479. [PMID: 32560439 PMCID: PMC7350310 DOI: 10.3390/pathogens9060479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) can cause severe disease in infected pigs, resulting in massive economic loss for the swine industry. Transcriptomic and proteomic approaches have been widely employed to identify the underlying molecular mechanisms of the PCV2 infection. Numerous differentially expressed mRNAs, miRNAs, and proteins, together with their associated signaling pathways, have been identified during PCV2 infection, paving the way for analysis of their biological functions. Long noncoding RNAs (lncRNAs) are important regulators of multiple biological processes. However, little is known regarding their role in the PCV2 infection. Hence, in our study, RNA-seq was performed by infecting PK-15 cells with PCV2. Analysis of the differentially expressed genes (DEGs) suggested that the cytoskeleton, apoptosis, cell division, and protein phosphorylation were significantly disturbed. Then, using stringent parameters, six lncRNAs were identified. Additionally, potential targets of the lncRNAs were predicted using both cis- and trans-prediction methods. Interestingly, we found that the HOXB (Homeobox B) gene cluster was probably the target of the lncRNA LOC106505099. Enrichment analysis of the target genes showed that numerous developmental processes were altered during PCV2 infection. Therefore, our study revealed that lncRNAs might affect porcine embryonic development through the regulation of the HOXB genes.
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Affiliation(s)
- Jin He
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Chaoliang Leng
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Wolong District, Nanyang 473061, China;
| | - Jiazhen Pan
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Aoqi Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Hua Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
| | - Feng Cong
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510640, China;
| | - Huanan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (J.H.); (J.P.); (A.L.); (H.Z.)
- Correspondence:
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18
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Jia Y, Shi L, Yun F, Liu X, Chen Y, Wang M, Chen C, Ren Y, Bao Y, Wang L. Transcriptome sequencing profiles reveal lncRNAs may involve in breast cancer (ER/PR positive type) by interaction with RAS associated genes. Pathol Res Pract 2019; 215:152405. [PMID: 30981459 DOI: 10.1016/j.prp.2019.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/18/2019] [Accepted: 03/31/2019] [Indexed: 01/22/2023]
Abstract
To reveal novel lncRNAs and explore how could lncRNA affect the ER/PR positive type breast cancer, 16 different lncRNA transcriptomes (8 breast cancer tissues and 8 normal breast tissues) were successfully sequenced. In total, 8,954 high quality lncRNAs, including 5,516 lncRNAs reported in the previous studies and 3,438 novel lncRNAs, were annotated. The highest expressed lncRNAs were MALAT1, SCARNA10, RP11-206M11.7 and NEAT1, and the highest expressing mRNAs were RPL19, SCGB2A2, FTL and TMSB4 × . Of the 615 differentially expressed lncRNAs, 323 showed up regulated (P < 0.05) expression patterns in breast cancer, and 292 showed down regulated expression patterns. Of the 8,954 genes, 5,516 genes were upregulated in breast cancer, and 3,438 were downregulated. In total, the targets of 238 lncRNAs were confirmed by two lncRNA target prediction programs. Within these genes, Ras responsive element binding protein 1, Ras association domain family member 6, Ras association domain family member 8, Ras protein specific guanine nucleotide releasing factor 1and other 10 different Ras associated different expressed genes were predicted as targets of lncRNAs. These different expressed lncRNAs which could regulate the Ras gene families and ECM pathway may be another mechanism why the expression pattern of Ras genes changed in breast cancer. All these cancer-related genes (Ras genes) were annotated as targets of lncRNAs in the breast cancer transcriptome may provide us with a new way to understand the occurrence and development of breast cancer.
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Affiliation(s)
- Yongfeng Jia
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China; Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Lin Shi
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Fen Yun
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Xia Liu
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yongxia Chen
- Tumor Molecular Diagnostic Laboratory, The Inner Mongolia Cancer Hospital, Hohhot, Inner Mongolia, China
| | - Minjie Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Chen Chen
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yanni Ren
- Department of Pathology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yulong Bao
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China.
| | - Li Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China.
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Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C. Comparative analysis of long non-coding RNAs in Atlantic and Coho salmon reveals divergent transcriptome responses associated with immunity and tissue repair during sea lice infestation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:36-50. [PMID: 29803715 DOI: 10.1016/j.dci.2018.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/19/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
The increasing capacity of transcriptomic analysis by high throughput sequencing has highlighted the presence of a large proportion of transcripts that do not encode proteins. In particular, long non-coding RNAs (lncRNAs) are sequences with low coding potential and conservation among species. Moreover, cumulative evidence has revealed important roles in post-transcriptional gene modulation in several taxa. In fish, the role of lncRNAs has been scarcely studied and even less so during the immune response against sea lice. In the present study we mined for lncRNAs in Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynkus kisutch), which are affected by the sea louse Caligus rogercresseyi, evaluating the degree of sequence conservation between these two fish species and their putative roles during the infection process. Herein, Atlantic and Coho salmon were infected with 35 lice/fish and evaluated after 7 and 14 days post-infestation (dpi). For RNA sequencing, samples from skin and head kidney were collected. A total of 5658/4140 and 3678/2123 lncRNAs were identified in uninfected/infected Atlantic and Coho salmon transcriptomes, respectively. Species-specific transcription patterns were observed in exclusive lncRNAs according to the tissue analyzed. Furthermore, neighbor gene GO enrichment analysis of the top 100 highly regulated lncRNAs in Atlantic salmon showed that lncRNAs were localized near genes related to the immune response. On the other hand, in Coho salmon the highly regulated lncRNAs were localized near genes involved in tissue repair processes. This study revealed high regulation of lncRNAs closely localized to immune and tissue repair-related genes in Atlantic and Coho salmon, respectively, suggesting putative roles for lncRNAs in salmon against sea lice infestation.
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Affiliation(s)
- Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile.
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20
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Le Béguec C, Wucher V, Lagoutte L, Cadieu E, Botherel N, Hédan B, De Brito C, Guillory AS, André C, Derrien T, Hitte C. Characterisation and functional predictions of canine long non-coding RNAs. Sci Rep 2018; 8:13444. [PMID: 30194329 PMCID: PMC6128939 DOI: 10.1038/s41598-018-31770-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.
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Affiliation(s)
- Céline Le Béguec
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Valentin Wucher
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lætitia Lagoutte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,UMR PEGASE, Agrocampus Ouest, INRA, 35042, Rennes, France
| | - Edouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Clotilde De Brito
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Anne-Sophie Guillory
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
| | - Christophe Hitte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
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21
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Martin SL, Royston KJ, Tollefsbol TO. The Role of Non-Coding RNAs and Isothiocyanates in Cancer. Mol Nutr Food Res 2018; 62:e1700913. [PMID: 29532604 PMCID: PMC6248329 DOI: 10.1002/mnfr.201700913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/28/2018] [Indexed: 12/12/2022]
Abstract
Cancer is the second leading cause of mortalities in the United States, only exceeded by heart disease. Current cancer treatments include chemotherapy, surgery, and/or radiation. Due to the often harsh effects of current cancer therapies, investigators are focusing their efforts on cancer prevention mediated by dietary phytochemicals. Since the discovery that cancer can be initiated by and progressed through both genetic and epigenetic pathways, there has been a significant surge in studies on epigenetic effects mediated by nutritive compounds. Isothiocyanates, naturally occurring molecules found in cruciferous vegetables, have been documented to exhibit many anticarcinogenic activities. Although isothiocyanates have been extensively documented as key players in epigenetic processes such as DNA methylation and histone modifications, their effects on non-coding RNAs is understudied. Non-coding RNAs are molecules that target mRNA production and repress protein translation and are known to be dysregulated in various human malignancies. Studies have used non-coding RNAs as novel targets for exploration in cancer therapy. This review focuses on the exploration of isothiocyanates and their effect on non-coding RNAs in cancer prevention and therapy.
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Affiliation(s)
- Samantha L. Martin
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
| | - Kendra J. Royston
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA
- Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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22
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Vito D, Smales CM. The Long Non-Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed-Batch Conditions. Biotechnol J 2018; 13:e1800122. [PMID: 29781203 DOI: 10.1002/biot.201800122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The role of non-coding RNAs in determining growth, productivity, and recombinant product quality attributes in Chinese hamster ovary (CHO) cells has received much attention in recent years, exemplified by studies into microRNAs in particular. However, other classes of non-coding RNAs have received less attention. One such class are the non-coding RNAs known collectively as long non-coding RNAs (lncRNAs). The authors have undertaken the first landscape analysis of the lncRNA transcriptome in CHO using a mouse based microarray that also provided for the surveillance of the coding transcriptome. The authors report on those lncRNAs present in a model host CHO cell line under batch and fed-batch conditions on two different days and relate the expression of different lncRNAs to each other. The authors demonstrate that the mouse microarray is suitable for the detection and analysis of thousands of CHO lncRNAs and validated a number of these by qRT-PCR. The authors then further analyzed the data to identify those lncRNAs whose expression changed the most between growth and stationary phases of culture or between batch and fed-batch culture to identify potential lncRNA targets for further functional studies with regard to their role in controlling growth of CHO cells. The authors discuss the implications for the publication of this rich dataset and how this may be used by the community.
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Affiliation(s)
- Davide Vito
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| | - Christopher Mark Smales
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
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23
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Abstract
The majority of our genome is transcribed to produce RNA molecules that are mostly noncoding. Among them, long noncoding RNAs (lncRNAs) are the most numerous and functionally versatile class.LncRNAs have emerged as key regulators of gene expression at multiple levels.This section describes bioinformatics aspects important for lncRNA discovery and molecular approaches to perform structure-function characterization of this exciting class of regulatory molecules.
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24
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Miao X, Luo Q, Zhao H, Qin X. An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity. Front Physiol 2017; 8:1049. [PMID: 29326596 PMCID: PMC5736872 DOI: 10.3389/fphys.2017.01049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023] Open
Abstract
In our previous study, we investigated the regulatory relationship between lncRNAs, miRNA, and mRNAs in an effort to shed light onto the regulatory mechanisms involved in sheep fecundity. As an extension of this study, here, we aimed to identify potential regulators of sheep fecundity using a genome-wide analysis of miRNAs and the methylated genes encoding mRNAs and lncRNAs in the ovaries of Dorset sheep (low fecundity) and Small Tail Han ewes (high fecundity) with the genotype BB (Han BB) and the genotype ++ (Han ++) by performing RNA-Seq and MeDIP-Seq analyses. Methylated coding-non-coding gene co-expression networks for Han and Dorset sheep were constructed using the methylated genes encoding the differentially expressed mRNAs and lncRNAs identified in this study. In the Han BB vs. Dorset comparison, the lncRNAs TTC26 and MYH15 had the largest degree. Similarly, the lncRNA NYAP1 had the largest degree in the Han ++ vs. Dorset comparison. None of the methylated genes encoding lncRNAs were co-expressed with the methylated genes encoding mRNAs in the Han BB vs. Han ++ comparison. The methylated genes encoding lncRNAs identified here may play a vital regulatory role in sheep breeding. Our results suggest that miRNAs might play a key role in sheep prolificacy by regulating target genes related to thyroid hormone synthesis, and methylated genes encoding lncRNAs associated with tight junctions might contribute to the high breeding rate in Han sheep. These findings may contribute to a deeper understanding of sheep prolificacy.
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Affiliation(s)
- Xiangyang Miao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingmiao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijing Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyu Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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25
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Salehi S, Taheri MN, Azarpira N, Zare A, Behzad-Behbahani A. State of the art technologies to explore long non-coding RNAs in cancer. J Cell Mol Med 2017. [PMID: 28631377 PMCID: PMC5706582 DOI: 10.1111/jcmm.13238] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell‐specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single‐molecule RNA in situ hybridization (sm‐RNA FISH), cross‐linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions. Here, we review these and other experimental approaches in common use for identification and characterization of lncRNAs, particularly those involved in different types of cancer, with focus on merits and demerits of each technique.
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Affiliation(s)
- Saeede Salehi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Naser Taheri
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azarpira
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolhossein Zare
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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26
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Beaver LM, Kuintzle R, Buchanan A, Wiley MW, Glasser ST, Wong CP, Johnson GS, Chang JH, Löhr CV, Williams DE, Dashwood RH, Hendrix DA, Ho E. Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer. J Nutr Biochem 2017; 42:72-83. [PMID: 28131897 DOI: 10.1016/j.jnutbio.2017.01.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/30/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important in cancer development and progression. The impact of diet on lncRNA expression is largely unknown. Sulforaphane (SFN), obtained from vegetables like broccoli, can prevent and suppress cancer formation. Here we tested the hypothesis that SFN attenuates the expression of cancer-associated lncRNAs. We analyzed whole-genome RNA-sequencing data of normal human prostate epithelial cells and prostate cancer cells treated with 15 μM SFN or dimethylsulfoxide. SFN significantly altered expression of ~100 lncRNAs in each cell type and normalized the expression of some lncRNAs that were differentially expressed in cancer cells. SFN-mediated alterations in lncRNA expression correlated with genes that regulate cell cycle, signal transduction and metabolism. LINC01116 was functionally investigated because it was overexpressed in several cancers, and was transcriptionally repressed after SFN treatment. Knockdown of LINC01116 with siRNA decreased proliferation of prostate cancer cells and significantly up-regulated several genes including GAPDH (regulates glycolysis), MAP1LC3B2 (autophagy) and H2AFY (chromatin structure). A four-fold decrease in the ability of the cancer cells to form colonies was found when the LINC01116 gene was disrupted through a CRISPR/CAS9 method, further supporting an oncogenic function for LINC01116 in PC-3 cells. We identified a novel isoform of LINC01116 and bioinformatically investigated the possibility that LINC01116 could interact with target genes via ssRNA:dsDNA triplexes. Our data reveal that chemicals from the diet can influence the expression of functionally important lncRNAs, and suggest a novel mechanism by which SFN may prevent and suppress prostate cancer.
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Affiliation(s)
- Laura M Beaver
- Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331; Linus Pauling Institute, Oregon State University, 307 Linus Pauling Science Center, Corvallis, OR 97331.
| | - Rachael Kuintzle
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agriculture and Life Sciences Building, Corvallis, OR 97331.
| | - Alex Buchanan
- Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331; Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331.
| | - Michelle W Wiley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agriculture and Life Sciences Building, Corvallis, OR 97331.
| | - Sarah T Glasser
- Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331.
| | - Carmen P Wong
- Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331; Linus Pauling Institute, Oregon State University, 307 Linus Pauling Science Center, Corvallis, OR 97331.
| | - Gavin S Johnson
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, Texas A&M Health Science Center, 2121 W. Holcombe Blvd., Mail Stop 1201, Houston, TX 77030-3303.
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331; Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331.
| | - Christiane V Löhr
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, 105 Magruder Hall, Corvallis, OR 97331.
| | - David E Williams
- Linus Pauling Institute, Oregon State University, 307 Linus Pauling Science Center, Corvallis, OR 97331; Environmental and Molecular Toxicology, Oregon State University, 1007 Agriculture & Life Sciences Building, Corvallis, OR 97331.
| | - Roderick H Dashwood
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, Texas A&M Health Science Center, 2121 W. Holcombe Blvd., Mail Stop 1201, Houston, TX 77030-3303.
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agriculture and Life Sciences Building, Corvallis, OR 97331; The School of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331.
| | - Emily Ho
- Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331; Linus Pauling Institute, Oregon State University, 307 Linus Pauling Science Center, Corvallis, OR 97331; Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331; Moore Family Center, Oregon State University, 103 Milam Hall, Corvallis, OR 97331.
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27
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Long non-coding RNAs (lncRNAs) in skeletal and cardiac muscle: potential therapeutic and diagnostic targets? Clin Sci (Lond) 2016; 130:2245-2256. [DOI: 10.1042/cs20160244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
Abstract
The recent discovery that thousands of RNAs are transcribed by the cell but are never translated into protein, highlights a significant void in our current understanding of how transcriptional networks regulate cellular function. This is particularly astounding when we consider that over 75% of the human genome is transcribed into RNA, but only approximately 2% of RNA is translated into known proteins. This raises the question as to what function the other so-called ‘non-coding RNAs’ (ncRNAs) are performing in the cell. Over the last decade, an enormous amount of research has identified several classes of ncRNAs, predominantly short ncRNAs (<200 nt) that have been confirmed to have functional significance. Recent advances in sequencing technology and bioinformatics have also allowed for the identification of a novel class of ncRNAs, termed long ncRNA (lncRNA) (>200 nt). Several studies have recently shown that long non-coding RNAs (lncRNAs) are associated with tissue development and disease, particularly in cell types that undergo differentiation such as stem cells, cancer cells and striated muscle (skeletal/cardiac). Therefore, understanding the function of these lncRNAs and designing strategies to detect and manipulate them, may present novel therapeutic and diagnostic opportunities. This review will explore the current literature on lncRNAs in skeletal and cardiac muscle and discuss their recent implication in development and disease. Lastly, we will also explore the possibility of using lncRNAs as therapeutic and diagnostic tools and discuss the opportunities and potential shortcomings to these applications.
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28
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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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29
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Shen Y, Mao H, Huang M, Chen L, Chen J, Cai Z, Wang Y, Xu N. Long Noncoding RNA and mRNA Expression Profiles in the Thyroid Gland of Two Phenotypically Extreme Pig Breeds Using Ribo-Zero RNA Sequencing. Genes (Basel) 2016; 7:genes7070034. [PMID: 27409639 PMCID: PMC4962004 DOI: 10.3390/genes7070034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/24/2016] [Accepted: 07/05/2016] [Indexed: 11/16/2022] Open
Abstract
The thyroid gland is an important endocrine organ modulating development, growth, and metabolism, mainly by controlling the synthesis and secretion of thyroid hormones (THs). However, little is known about the pig thyroid transcriptome. Long non-coding RNAs (lncRNAs) regulate gene expression and play critical roles in many cellular processes. Yorkshire pigs have a higher growth rate but lower fat deposition than that of Jinhua pigs, and thus, these species are ideal models for studying growth and lipid metabolism. This study revealed higher levels of THs in the serum of Yorkshire pigs than in the serum of Jinhua pigs. By using Ribo-zero RNA sequencing—which can capture both polyA and non-polyA transcripts—the thyroid transcriptome of both breeds were analyzed and 22,435 known mRNAs were found to be expressed in the pig thyroid. In addition, 1189 novel mRNAs and 1018 candidate lncRNA transcripts were detected. Multiple TH-synthesis-related genes were identified among the 455 differentially-expressed known mRNAs, 37 novel mRNAs, and 52 lncRNA transcripts. Bioinformatics analysis revealed that differentially-expressed genes were enriched in the microtubule-based process, which contributes to THs secretion. Moreover, integrating analysis predicted 13 potential lncRNA-mRNA gene pairs. These data expanded the repertoire of porcine lncRNAs and mRNAs and contribute to understanding the possible molecular mechanisms involved in animal growth and lipid metabolism.
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Affiliation(s)
- Yifei Shen
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Haiguang Mao
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Minjie Huang
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Lixing Chen
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Jiucheng Chen
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Zhaowei Cai
- Laboratory of Animal Research Center, Zhenjiang Chinese Medical University, Hangzhou 310053, China.
| | - Ying Wang
- College of Mechanics, Taiyuan University of Technology, Taiyuan 030024, China.
| | - Ningying Xu
- College of Animal Science, Zhejiang University, Hangzhou 310058, China.
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30
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Jiang X, Lei R, Ning Q. Circulating long noncoding RNAs as novel biomarkers of human diseases. Biomark Med 2016; 10:757-69. [PMID: 27347748 DOI: 10.2217/bmm-2016-0039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs which are longer than ˜200 nucleotides, lacking of protein-encoding capacity and are implicated in the pathogenesis of various diseases. Recently, it was demonstrated that lncRNAs could be released into the circulation and be stable in blood. Circulating lncRNAs have been reported to have potential in distinguishing patients from healthy individuals. Therefore, the detection of circulating lncRNAs may be valuable for improving the diagnosis and prognosis of various diseases. This review summarized the current understanding of circulating lncRNAs as novel biomarkers of various human diseases, such as cancer, cardiovascular diseases, nervous system diseases and other diseases, which highlighted the significance of circulating lncRNAs as novel diagnostic and prognostic biomarkers of human diseases.
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Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Ronghui Lei
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Qilan Ning
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
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