1
|
Xu Z, Liu Q, Ning C, Yang M, Zhu Q, Li D, Wang T, Li F. miRNA profiling of chicken follicles during follicular development. Sci Rep 2024; 14:2212. [PMID: 38278859 PMCID: PMC10817932 DOI: 10.1038/s41598-024-52716-x] [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: 07/30/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024] Open
Abstract
MicroRNAs (miRNAs) play a crucial role as transcription regulators in various aspects of follicular development, including steroidogenesis, ovulation, apoptosis, and gene regulation in poultry. However, there is a paucity of studies examining the specific impact of miRNAs on ovarian granulosa cells (GCs) across multiple grades in laying hens. Consequently, this study aims to investigate the roles of miRNAs in chicken GCs. By constructing miRNA expression profiles of GCs at 10 different time points, encompassing 4 pre-hierarchical, 5 preovulatory, and 1 postovulatory follicles stage, we identified highly expressed miRNAs involved in GC differentiation (miR-148a-3p, miR-143-3p), apoptosis (let7 family, miR-363-3p, miR-30c-5p, etc.), and autophagy (miR-128-3p, miR-21-5p). Furthermore, we discovered 48 developmentally dynamic miRNAs (DDMs) that target 295 dynamic differentially expressed genes (DDGs) associated with follicular development and selection (such as oocyte meiosis, progesterone-mediated oocyte maturation, Wnt signaling pathway, TGF-β signaling pathway) as well as follicular regression (including autophagy and cellular senescence). These findings contribute to a more comprehensive understanding of the intricate mechanisms underlying follicle recruitment, selection, and degeneration, aiming to enhance poultry's reproductive capacity.
Collapse
Affiliation(s)
- Zhongxian Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qian Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Maosen Yang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Tao Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Feng Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, China.
| |
Collapse
|
2
|
Jahantigh D, Mirani Sargazi F, Sargazi S, Saravani R, Ghazaey Zidanloo S, Heidari Nia M, Piri M. Relationship between Functional miR-143/145 Cluster Variants and Susceptibility to Type 2 Diabetes Mellitus: A Preliminary Case-Control Study and Bioinformatics Analyses. Endocr Res 2021; 46:129-139. [PMID: 33870836 DOI: 10.1080/07435800.2021.1914079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Purpose: To investigate the link between two variants (rs4705342 and rs4705343) in the promoter of the miR-143/145 cluster with Type 2 diabetes mellitus (T2DM) risk. Methods:A total of 1200 subjects were genotyped using the ARMS-PCR method. Results: The rs4705342 variant enhanced the risk of T2DM under codominant CC (OR = 3.24; 95% CI: 1.89-5.60), recessive TT+TC (OR = 3.02; 95% CI: 1.77-5.17), and dominant TC+CC (OR = 1.35; 95% CI: 1.08-1.71) genetic models. Individuals carrying the C allele of rs4705342 conferred a 1.43 fold increased risk of T2DM. As regards rs4705343, decreased risk of T2DM was observed under codominant TC (OR = 0.53; 95% CI: 0.42-0.67), over-dominant TT+CC (OR = 0.51; 95% CI: 0.40-0.64), and dominant TC+CC (OR = 0.59; 95% CI: 0.48-0.75) models. Haplotype analysis of the variants showed a 1.941-fold increased risk of T2DM regarding the C T combination. Significant associations were noticed between different haplotypes and lipid indices of T2DM patients. There were no notable changes in p-values after adjustment for BMI. Computational analysis revealed that miR143 and/or miR145 target important genes involved in glucose and lipid metabolism. Conclusions: Functional miR-143/145 variants might influence the risk of T2DM. Hence, clarifying the precise regulatory mechanisms of gene expression in the development of T2DM will significantly guide researchers to find a novel target for therapeutic intervention.
Collapse
Affiliation(s)
- Danial Jahantigh
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Fariba Mirani Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Maryam Piri
- Diabetes Center, Ali Asghar Hospital, Zahedan University of Medical Sciences, Zahedan, IR Iran
| |
Collapse
|
3
|
Sargazi S, Heidari Nia M, Mirani Sargazi F, Sheervalilou R, Saravani R, Bahrami S, Mirinejad S, Alidadi A. Functional miR143/145 Cluster Variants and Haplotypes Are Associated with Chronic Kidney Disease: a Preliminary Case-Control Study and Computational Analyses. Appl Biochem Biotechnol 2021; 193:1532-1544. [PMID: 33484447 DOI: 10.1007/s12010-021-03489-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
MiR-143/145 cluster is a novel transcriptional target of many signaling pathways, with variations within this cluster contributed to the risk of multiple diseases. To date, no data regarding the link between miR143/145 cluster polymorphisms and the risk of developing chronic kidney disease (CKD) has been reported. Hence, we aimed to examine such association in a population of Iranian ancestry. In this preliminary study, 276 CKD patients and 300 unrelated age and sex-matched healthy controls were recruited. Genotyping was performed by PCR-RFLP and allele-specific-PCR methods. Computational analyses were performed to predict the potential effects of the variants. Our findings indicated that rs41291957, rs12659504, and rs353292 polymorphisms were positively associated with CKD, while rs4705342 and rs4705343 polymorphisms demonstrated a significant negative association with the disease. Moreover, a significant association was observed between CC + TC and TT genotypes and CKD stages. We found that AACTT, AATTC, AATTT, GATTC, GATTT, and GGCTT haplotypes significantly enhanced the risk of CKD compared with the Grs41291957AArs12659504Crs353292Trs4705342Trs4705343 haplotype. Computational analysis showed that rs353292, rs4705342, and rs4705343 might alter the binding of the transcription factors in this gene cluster. We found that miR-143/145 cluster polymorphisms were associated with CKD risk in a sample of the Iranian population. Replicated studies on different ethnicities are necessary to investigate the association between these promoter variants and clinical outcomes.
Collapse
Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fariba Mirani Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Roghayeh Sheervalilou
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sara Bahrami
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Alidadi
- Nephrology Department, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| |
Collapse
|
4
|
El-Far YM, Khodir AE, Emarah ZA, Ebrahim MA, Al-Gayyar MMH. Fucoidan Ameliorates Hepatocellular Carcinoma Induced in Rats: Effect on miR143 and Inflammation. Nutr Cancer 2020; 73:1498-1510. [DOI: 10.1080/01635581.2020.1798478] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yousra M. El-Far
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Ahmed E. Khodir
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, Mansoura, Dakhilya, Egypt
| | - Ziad A. Emarah
- Internal Medicine Department, Medical Oncology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mohamed A. Ebrahim
- Medical Oncology Unit, Oncology Center, Mansoura University, Mansoura, Egypt
| | - Mohammed M. H. Al-Gayyar
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
| |
Collapse
|
5
|
Liu L, Wang Q, Qiu Z, Kang Y, Liu J, Ning S, Yin Y, Pang D, Xu S. Noncoding RNAs: the shot callers in tumor immune escape. Signal Transduct Target Ther 2020; 5:102. [PMID: 32561709 PMCID: PMC7305134 DOI: 10.1038/s41392-020-0194-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/17/2023] Open
Abstract
Immunotherapy, designed to exploit the functions of the host immune system against tumors, has shown considerable potential against several malignancies. However, the utility of immunotherapy is heavily limited due to the low response rate and various side effects in the clinical setting. Immune escape of tumor cells may be a critical reason for such low response rates. Noncoding RNAs (ncRNAs) have been identified as key regulatory factors in tumors and the immune system. Consequently, ncRNAs show promise as targets to improve the efficacy of immunotherapy in tumors. However, the relationship between ncRNAs and tumor immune escape (TIE) has not yet been comprehensively summarized. In this review, we provide a detailed account of the current knowledge on ncRNAs associated with TIE and their potential roles in tumor growth and survival mechanisms. This review bridges the gap between ncRNAs and TIE and broadens our understanding of their relationship, providing new insights and strategies to improve immunotherapy response rates by specifically targeting the ncRNAs involved in TIE.
Collapse
Affiliation(s)
- Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Yujuan Kang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Jiena Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China. .,Heilongjiang Academy of Medical Sciences, Harbin, 150086, China.
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
| |
Collapse
|
6
|
Ebrahimi R, Bahiraee A, Niazpour F, Emamgholipour S, Meshkani R. The role of microRNAs in the regulation of insulin signaling pathway with respect to metabolic and mitogenic cascades: A review. J Cell Biochem 2019; 120:19290-19309. [PMID: 31364207 DOI: 10.1002/jcb.29299] [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: 01/18/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022]
Abstract
Insulin resistance (IR) is a shared pathological condition among type 2 diabetes, obesity, cardiovascular disease, and other metabolic disorders. It is growing significantly all over the world and consequently, a substantial effort is needed for developing the potential novel diagnostics and therapeutics. An insulin signaling pathway is tightly modulated by different mechanisms including the epigenetic modifications. Today, a deal of great attention has been shifted towards the regulatory role of noncoding RNAs on target proteins of the insulin signaling pathway. Noncoding RNAs are a major area of the epigenetics which control gene expression at the posttranscriptional levels and include a large class of microRNAs (miRNAs). With this in view, many studies have implicated the mediatory effects of miRNAs on the downstream metabolic and mitogenic proteins of the insulin signaling pathway. Since providing new biomarkers for the early diagnosis of IR and related metabolic traits are very significant, we intended to review the possible role of miRNAs in the regulation of the insulin signaling pathway, with a primary focus on the downstream target proteins of the metabolic and mitogenic cascades.
Collapse
Affiliation(s)
- Reyhane Ebrahimi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahiraee
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farshad Niazpour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Solaleh Emamgholipour
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Meshkani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
Jaeger A, Hadlich F, Kemper N, Lübke-Becker A, Muráni E, Wimmers K, Ponsuksili S. MicroRNA expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli in vitro. BMC Genomics 2017; 18:660. [PMID: 28836962 PMCID: PMC5571640 DOI: 10.1186/s12864-017-4070-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022] Open
Abstract
Background Coliform mastitis is a symptom of postpartum dysgalactia syndrome (PDS), a multifactorial infectious disease of sows. Our previous study showed gene expression profile change after bacterial challenge of porcine mammary epithelial cells (PMECs). These mRNA expression changes may be regulated through microRNAs (miRNAs) which play critical roles in biological processes. Therefore, miRNA expression profile was investigated in PMECs. Results PMECs were isolated from three lactating sows and challenged with heat-inactivated potential mastitis-causing pathogen Escherichia coli (E. coli) for 3 h and 24 h, in vitro. At 3 h post-challenge with E. coli, target gene prediction identified a critical role of miRNAs in regulation of host immune responses and homeostasis of PMECs mediated by affecting pathways including cytokine binding (miR-202, miR-3277, miR-4903); IL-10/PPAR signaling (miR-3277, miR-4317, miR-548); and NF-ĸB/TNFR2 signaling (miR-202, miR-2262, miR-885-3p). Target genes of miRNAs in PMECs at 24 h were significantly enriched in pathways associated with interferon signaling (miR-210, miR-23a, miR-1736) and protein ubiquitination (miR-125, miR-128, miR-1280). Conclusions This study provides first large-scale miRNA expression profiles and their predicted target genes in PMECs after contact with a potential mastitis-causing E. coli strain. Both, highly conserved miRNAs known from other species as well as novel miRNAs were identified in PMECs, representing candidate predictive biomarkers for PDS. Time-dependent pathogen clearance suggests an important role of PMECs in inflammatory response of the first cellular barrier of the porcine mammary gland. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4070-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- A Jaeger
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - F Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - N Kemper
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine Hannover, Foundation, D-30559, Hannover, Germany
| | - A Lübke-Becker
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine at the Freie Universität Berlin, D-14163, Berlin, Germany
| | - E Muráni
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - K Wimmers
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - S Ponsuksili
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany.
| |
Collapse
|
8
|
Luo J, Liu J, Liu H, Zhang T, Wang J, He H, Han C. Enrichment and verification of differentially expressed miRNAs in bursa of Fabricius in two breeds of duck. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:920-929. [PMID: 27660025 PMCID: PMC5495669 DOI: 10.5713/ajas.16.0325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/06/2016] [Accepted: 09/15/2016] [Indexed: 12/03/2022]
Abstract
Objective The bursa of Fabricius (BF) is a central humoral immune organ belonging specifically to avians. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Methods Using Illumina next-generation sequencing, the miRNAs libraries of ducks were established. Results The results showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which are involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability. By gene ontology analysis and enriching KEGG pathway, the targets of differential expressed miRNAs were mainly involved in immunity and disease, supporting that there were differences in the BF immune functions between the two duck breeds. In addition, the metabolic pathway had the maximum enriched target genes and some enriched pathways that were related to cell cycle, protein synthesis, cell proliferation and apoptosis. It indicted that the difference of metabolism may be one of the reasons leading the immune difference between the BF of two duck breeds. Conclusion This data lists the main differences in the BF at miRNAs level between two genetically disparate duck breeds and lays a foundation to carry out molecular assisted breeding of poultry in the future.
Collapse
Affiliation(s)
- Jun Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Junying Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Tao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| |
Collapse
|
9
|
Lv X, Sun W, Yin J, Ni R, Su R, Wang Q, Gao W, Bao J, Yu J, Wang L, Chen L. An Integrated Analysis of MicroRNA and mRNA Expression Profiles to Identify RNA Expression Signatures in Lambskin Hair Follicles in Hu Sheep. PLoS One 2016; 11:e0157463. [PMID: 27404636 PMCID: PMC4942090 DOI: 10.1371/journal.pone.0157463] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/30/2016] [Indexed: 12/27/2022] Open
Abstract
Wave patterns in lambskin hair follicles are an important factor determining the quality of sheep’s wool. Hair follicles in lambskin from Hu sheep, a breed unique to China, have 3 types of waves, designated as large, medium, and small. The quality of wool from small wave follicles is excellent, while the quality of large waves is considered poor. Because no molecular and biological studies on hair follicles of these sheep have been conducted to date, the molecular mechanisms underlying the formation of different wave patterns is currently unknown. The aim of this article was to screen the candidate microRNAs (miRNA) and genes for the development of hair follicles in Hu sheep. Two-day-old Hu lambs were selected from full-sib individuals that showed large, medium, and small waves. Integrated analysis of microRNA and mRNA expression profiles employed high-throughout sequencing technology. Approximately 13, 24, and 18 differentially expressed miRNAs were found between small and large waves, small and medium waves, and medium and large waves, respectively. A total of 54, 190, and 81 differentially expressed genes were found between small and large waves, small and medium waves, and medium and large waves, respectively, by RNA sequencing (RNA-seq) analysis. Differentially expressed genes were classified using gene ontology and pathway analyses. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport, and were associated with MAPK and the Notch signaling pathway. Reverse transcription-polymerase chain reaction (RT-PCR) analyses of differentially-expressed miRNA and genes were consistent with sequencing results. Integrated analysis of miRNA and mRNA expression indicated that, compared to small waves, large waves included 4 downregulated miRNAs that had regulatory effects on 8 upregulated genes and 3 upregulated miRNAs, which in turn influenced 13 downregulated genes. Compared to small waves, medium waves included 13 downregulated miRNAs that had regulatory effects on 64 upregulated genes and 4 upregulated miRNAs, which in turn had regulatory effects on 22 downregulated genes. Compared to medium waves, large waves consisted of 13 upregulated miRNAs that had regulatory effects on 48 downregulated genes. These differentially expressed miRNAs and genes may play a significant role in forming different patterns, and provide evidence for the molecular mechanisms underlying the formation of hair follicles of varying patterns.
Collapse
Affiliation(s)
- Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- * E-mail:
| | - Jinfeng Yin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Rong Ni
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Rui Su
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qingzeng Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wen Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jianjun Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiarui Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lihong Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ling Chen
- Animal Science and Veterinary Medicine Bureau of Suzhou City, Suzhou, China
| |
Collapse
|
10
|
Liu X, Tu J, Yuan J, Liu X, Zhao L, Dawar FU, Khattak MNK, Hegazy AM, Chen N, Vakharia VN, Lin L. Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection. Int J Mol Sci 2016; 17:ijms17020154. [PMID: 26821019 PMCID: PMC4783888 DOI: 10.3390/ijms17020154] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in mediating multiple biological processes in eukaryotes and are being increasingly studied to evaluate their roles associated with cellular changes following viral infection. Snakehead fish Vesiculovirus (SHVV) has caused mass mortality in snakehead fish during the past few years. To identify specific miRNAs involved in SHVV infection, we performed microRNA deep sequencing on a snakehead fish cell line (SSN-1) with or without SHVV infection. A total of 205 known miRNAs were identified when they were aligned with the known zebrafish miRNAs, and nine novel miRNAs were identified using MiRDeep2 software. Eighteen and 143 of the 205 known miRNAs were differentially expressed at three and 24 h post-infection (poi), respectively. From the differentially-expressed miRNAs, five were randomly selected to validate their expression profiles using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and their expression profiles were consistent with the microRNA sequencing results. In addition, the target gene prediction of the SHVV genome was performed for the differentially-expressed host miRNAs, and a total of 10 and 58 differentially-expressed miRNAs were predicted to bind to the SHVV genome at three and 24 h poi, respectively. The effects of three selected miRNAs (miR-130-5p, miR-214 and miR-216b) on SHVV multiplication were evaluated using their mimics and inhibitors via qRT-PCR and Western blotting. The results showed that all three miRNAs were able to inhibit the multiplication of SHVV; whereas the mechanisms underlying the SHVV multiplication inhibited by the specific miRNAs need to be further characterized in the future.
Collapse
Affiliation(s)
- Xiaodan Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Jiagang Tu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Xueqin Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Lijuan Zhao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Farman Ullah Dawar
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Department of Zoology, Hazara University, Mansehra, Khyber Pakhtoonkhwa 21300, Pakistan.
| | | | - Abeer M Hegazy
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Central Laboratory for Environmental Quality Monitoring (CLEQM), National Water Research Center (NWRC), Cairo 13621, Egypt.
| | - Nan Chen
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| | - Vikram N Vakharia
- Institute of Marine and Environmental Technology, University of Maryland, Baltimore, MD 21202, USA.
| | - Li Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.
| |
Collapse
|
11
|
Yuan B, Yu WY, Dai LS, Gao Y, Ding Y, Yu XF, Chen J, Zhang JB. Expression of microRNA‑26b and identification of its target gene EphA2 in pituitary tissues in Yanbian cattle. Mol Med Rep 2015; 12:5753-61. [PMID: 26252447 PMCID: PMC4581756 DOI: 10.3892/mmr.2015.4192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 04/22/2015] [Indexed: 01/11/2023] Open
Abstract
microRNAs (miRNAs/miRs) are a class of single-stranded non-coding RNA molecules of 19–24 nucleotides (nt) in length. They are widely expressed in animals, plants, bacteria and viruses. Via specific mRNA complementary pairing of target genes, miRNAs are able to regulate the expression of mRNA levels or inhibit protein translation following transcription. miRNA expression has a time- and space specificity, and it is involved in cell proliferation and differentiation, apoptosis, development, tumor metastasis occurrence and other biological processes. miR-26b is an miRNA of 22 nt and is important in the regulation of cellular processes. With the advancement of molecular biology techniques in recent years, there have been extensive investigations into miR-26b. Numerous studies have observed that miR-26b is involved in early embryonic development, cell proliferation regulation, pituitary hormone secretion and other physiological activities. miRNAs are associated with the function of propagation. The present study used reverse transcription quantitative polymerase chain reaction to detect the relative expression levels of miR-26b in the pituitary tissue of Yanbian cattle at different developmental stages. The 2−ΔΔCt method was used to calculate the relative gene expression levels. The miRNA target gene database TargetScan and RNA22 were used for prediction of the miR-26b target gene and selective recognition was also performed. The results demonstrated that miR-26b is expressed in the pituitary tissues of Yanbian cattle at 6 and 24 months of age. The relative expression levels of miR-26b in the pituitary tissues of 24-month-old Yanbian cattle were 2.41 times that of those in the six-month-old Yanbian cattle, demonstrating significant differences in the relative expression (P<0.01). The relative expression of the candidate target genes, EphA2 and miR-26b, exhibited the opposite expression pattern. The relative expression levels in the pituitary tissues of six-month-old Yanbian cattle were 3.34 times that of those in 24-month-old Yanbian cattle (P<0.01). There are miR-26b binding sites in the 3′-untranslated region (3′-UTR) of EphA2 in bovine, human, murine and other mammalian mRNAs, suggesting that the EphA2 gene may be a target gene of miR-26b. The results of a Luciferase reporter system assay revealed that miR-26b is able to suppress EphA2 expression at the transcription level. Following the site-directed mutagenesis of plasmid EphA2 3′-UTR pmirGLO-MUT- and miR-26b mimic-transfected HeLa cells, the dual-luciferase reporter gene assay revealed that there were three consecutive nucleotide mutations in the 3′-UTR, binding with the predicted seed region. This may have caused the miR-26b inhibition of luciferase activity to decrease from 60% in the wild-type to 26%, suggesting that miR-26b achieved its function via binding with the TACTTGAA sequence of the 3′-UTR in EphA2. In conclusion, the present study successfully assessed the expression pattern of miR-26b in the pituitary tissue of Yanbian cattle, and also confirmed that EphA2 was a target gene of miR-26b in Yanbian cattle in vitro. The present study provided the theoretical basis to further investigate the role of miR-26b in early embryonic development, pituitary hormone secretion and other reproductive functions.
Collapse
Affiliation(s)
- Bao Yuan
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Wang-Yang Yu
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Li-Sheng Dai
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Yan Gao
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Yu Ding
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Xian-Feng Yu
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Jian Chen
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| | - Jia-Bao Zhang
- Laboratory Animal Center, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, P.R. China
| |
Collapse
|
12
|
Huang Y, Ren HT, Zou Q, Wang YQ, Zhang JL, Yu XL. Computational identification and characterization of miRNAs and their target genes from five cyprinidae fishes. Saudi J Biol Sci 2015; 24:1126-1135. [PMID: 28855803 PMCID: PMC5562384 DOI: 10.1016/j.sjbs.2015.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a kind of small single-strand RNA molecules with lengths of 18–25 nt, which do not encode any proteins. They play an essential role in gene expression regulation by binding to their target genes, leading to translational repression or transcript degradation. In this study, 23 miRNAs were predicted from five cyprinidae fishes by using a bioinformatics-based gene search based on blasting ESTs and GSS in NCBI, of which 21 miRNA genes have not been previously reported. To prove their validity, five of the computationally predicted miRNAs were verified by RTPCR, their transcripts were successfully detected, and, 46 potential target genes for these miRNAs were predicted, most target genes encode transcription factors, they are involved in signal transduction, metabolism and development processes.
Collapse
Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong-Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, China
| | - Yu-Qin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Ji-Liang Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xue-Li Yu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
13
|
Zhu XL, Wen SY, Ai ZH, Wang J, Xu YL, Teng YC. Screening for characteristic microRNAs between pre-invasive and invasive stages of cervical cancer. Mol Med Rep 2015; 12:55-62. [PMID: 25695263 PMCID: PMC4438941 DOI: 10.3892/mmr.2015.3363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 12/12/2014] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to investigate the characteristic microRNAs (miRNAs) expressed during the pre-invasive and invasive stages of cervical cancer. A gene expression profile (GSE7803) containing 21 invasive squamous cell cervical carcinoma samples, 10 normal squamous cervical epithelium samples and seven high-grade squamous intraepithelial cervical lesion samples, was obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified using significance analysis of microarray software, and a Gene Ontology (GO) enrichment analysis was conducted using the Database for Annotation, Visualization and Integrated Discovery. The miRNAs that interacted with the identified DEGs were selected, based on the TarBase v5.0 database. Regulatory networks were constructed from these selected miRNAs along with their corresponding target genes among the DEGs. The regulatory networks were visualized using Cytoscape. A total of 1,160 and 756 DEGs were identified in the pre-invasive and invasive stages of cervical cancer, respectively. The results of the GO enrichment demonstrated that the DEGs were predominantly involved in the immune response and the cell cycle, in the pre-invasive and invasive stages, respectively. Furthermore, a total of 18 and 26 characteristic miRNAs were screened in the pre-invasive and invasive stages, respectively. These miRNAs may be potential biomarkers and targets for the diagnosis and treatment of the different stages of cervical cancer.
Collapse
Affiliation(s)
- Xiao-Lu Zhu
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Shang-Yun Wen
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Zhi-Hong Ai
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Juan Wang
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Yan-Li Xu
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| | - Yin-Cheng Teng
- Department of Obstetrics and Gynecology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, P.R. China
| |
Collapse
|
14
|
Zhong W, Qin S, Zhu B, Pu M, Liu F, Wang L, Ye G, Yi Q, Yan D. Oxysterol-binding protein-related protein 8 (ORP8) increases sensitivity of hepatocellular carcinoma cells to Fas-mediated apoptosis. J Biol Chem 2015; 290:8876-87. [PMID: 25596532 DOI: 10.1074/jbc.m114.610188] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Indexed: 12/16/2022] Open
Abstract
Human hepatoma (HCC) has been reported to be strongly resistant to Fas-mediated apoptosis. However, the underlying mechanisms are poorly understood. In this study the function of oxysterol-binding protein-related protein 8 (ORP8) in human hepatoma cells apoptosis was assessed. We found that ORP8 is down-regulated, whereas miR-143, which controls ORP8 expression, is up-regulated in clinical HCC tissues as compared with liver tissue from healthy subjects. ORP8 overexpression triggered apoptosis in primary HCC cells and cell lines, which coincided with a relocation of cytoplasmic Fas to the cell plasma membrane and FasL up-regulation. Co-culture of HepG2 cells or primary HCC cells with Jurkat T-cells or T-cells, respectively, provided further evidence that ORP8 increases HCC cell sensitivity to Fas-mediated apoptosis. ORP8-induced Fas translocation is p53-dependent, and FasL was induced upon ORP8 overexpression via the endoplasmic reticulum stress response. Moreover, ORP8 overexpression and miR-143 inhibition markedly inhibited tumor growth in a HepG2 cell xenograft model. These results indicate that ORP8 induces HCC cell apoptosis through the Fas/FasL pathway. The role of ORP8 in Fas translocation to the plasma membrane and its down-regulation by miR-143 offer a putative mechanistic explanation for HCC resistance to apoptosis. ORP8 may be a potential target for HCC therapy.
Collapse
Affiliation(s)
- Wenbin Zhong
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Shengying Qin
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Biying Zhu
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Miaoshui Pu
- Department of Hepatobiliary Surgery, Guangzhou General Hospital, Guangzhou 510010, China, and
| | - Fupei Liu
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Lin Wang
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Guilin Ye
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China
| | - Qing Yi
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Daoguang Yan
- From the Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Department of Biotechnology, Jinan University, Guangzhou, 510632, China,
| |
Collapse
|
15
|
Kent OA, McCall MN, Cornish TC, Halushka MK. Lessons from miR-143/145: the importance of cell-type localization of miRNAs. Nucleic Acids Res 2014; 42:7528-38. [PMID: 24875473 PMCID: PMC4081080 DOI: 10.1093/nar/gku461] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
miR-143 and miR-145 are co-expressed microRNAs (miRNAs) that have been extensively studied as potential tumor suppressors. These miRNAs are highly expressed in the colon and are consistently reported as being downregulated in colorectal and other cancers. Through regulation of multiple targets, they elicit potent effects on cancer cell growth and tumorigenesis. Importantly, a recent discovery demonstrates that miR-143 and miR-145 are not expressed in colonic epithelial cells; rather, these two miRNAs are highly expressed in mesenchymal cells such as fibroblasts and smooth muscle cells. The expression patterns of miR-143 and miR-145 and other miRNAs were initially determined from tissue level data without consideration that multiple different cell types, each with their own unique miRNA expression patterns, make up each tissue. Herein, we discuss the early reports on the identification of dysregulated miR-143 and miR-145 expression in colorectal cancer and how lack of consideration of cellular composition of normal tissue led to the misconception that these miRNAs are downregulated in cancer. We evaluate mechanistic data from miR-143/145 studies in context of their cell type-restricted expression pattern and the potential of these miRNAs to be considered tumor suppressors. Further, we examine other examples of miRNAs being investigated in inappropriate cell types modulating pathways in a non-biological fashion. Our review highlights the importance of determining the cellular expression pattern of each miRNA, so that downstream studies are conducted in the appropriate cell type.
Collapse
Affiliation(s)
- Oliver A Kent
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Room 8-703, Toronto Medical Discovery Tower, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Matthew N McCall
- University of Rochester, Department of Biostatistics, Rochester, NY 14642, USA
| | - Toby C Cornish
- Johns Hopkins University, Department of Pathology, Baltimore, MD 21205, USA
| | - Marc K Halushka
- Johns Hopkins University, Department of Pathology, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
The miRNAome of the postpartum dairy cow liver in negative energy balance. BMC Genomics 2014; 15:279. [PMID: 24725334 PMCID: PMC4023597 DOI: 10.1186/1471-2164-15-279] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/08/2014] [Indexed: 01/01/2023] Open
Abstract
Background Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB), short read RNA sequencing was carried out. To identify putative targets of differentially expressed miRNAs among differentially expressed hepatic genes reported previously in dairy cows in SNEB computational target identification was employed. Results Our results indicate that the dairy cow liver expresses 53 miRNAs at a lower threshold of 10 reads per million. Of these, 10 miRNAs accounted for greater than 95% of the miRNAome (miRNA content). Of the highly expressed miRNAs, miR-122 constitutes 75% followed by miR-192 and miR-3596. Five out of thirteen let-7 miRNA family members are also among the highly expressed miRNAs. miR-143, down-regulated in SNEB, was found to have 4 putative up-regulated gene targets associated with SNEB including LRP2 (low density lipoprotein receptor-related protein 2), involved in lipid metabolism and up-regulated in SNEB. Conclusions This is the first liver miRNA-seq profiling study of moderate yielding dairy cows in the early postpartum period. Tissue specific miR-122 and liver enriched miR-192 are two of the most abundant miRNAs in the postpartum dairy cow liver. miR-143 is significantly down-regulated in SNEB and putative targets of miRNA-143 which are up-regulated in SNEB, include a gene involved in lipid metabolism.
Collapse
|
17
|
The Identification of a Novel Transcript Variant of Chicken Lmbr1 and the Sequence Variation Analysis. J Poult Sci 2013. [DOI: 10.2141/jpsa.0120133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
18
|
Polymenidou M, Lagier-Tourenne C, Hutt KR, Bennett CF, Cleveland DW, Yeo GW. Misregulated RNA processing in amyotrophic lateral sclerosis. Brain Res 2012; 1462:3-15. [PMID: 22444279 PMCID: PMC3707312 DOI: 10.1016/j.brainres.2012.02.059] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/24/2012] [Accepted: 02/24/2012] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) research is undergoing an era of unprecedented discoveries with the identification of new genes as major genetic causes of this disease. These discoveries reinforce the genetic, clinical and pathological overlap between ALS and frontotemporal lobar degeneration (FTLD). Common causes of these diseases include mutations in the RNA/DNA-binding proteins, TDP-43 and FUS/TLS and most recently, hexanucleotide expansions in the C9orf72 gene, discoveries that highlight the overlapping pathogenic mechanisms that trigger ALS and FTLD. TDP-43 and FUS/TLS, both of which participate in several steps of RNA processing, are abnormally aggregated and mislocalized in ALS and FTLD, while the expansion in the C9orf72 pre-mRNA strongly suggests sequestration of one or more RNA binding proteins in pathologic RNA foci. Hence, ALS and FTLD converge in pathogenic pathways disrupting the regulation of RNA processing. This article is part of a Special Issue entitled RNA-Binding Proteins.
Collapse
Affiliation(s)
- Magdalini Polymenidou
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093-6070, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
| | - Clotilde Lagier-Tourenne
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093-6070, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
| | - Kasey R. Hutt
- Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
| | - C. Frank Bennett
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093-6070, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
| | - Gene W. Yeo
- Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-6070, USA
| |
Collapse
|
19
|
Zhao S, Zhang J, Hou X, Zan L, Wang N, Tang Z, Li K. OLFML3 expression is decreased during prenatal muscle development and regulated by microRNA-155 in pigs. Int J Biol Sci 2012; 8:459-69. [PMID: 22419891 PMCID: PMC3303172 DOI: 10.7150/ijbs.3821] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/30/2011] [Indexed: 11/25/2022] Open
Abstract
The Olfactomedin-like 3 (OLFML3) gene has matrix-related function involved in embryonic development. MicroRNA-155 (miR-155), 21- to 23-nucleotides (nt) noncoding RNA, regulated myogenesis by target mRNA. Our LongSAGE analysis suggested that OLFML3 gene was differently expressed during muscle development in pig. In this study, we cloned the porcine OLFML3 gene and detected its tissues distribution in adult Tongcheng pigs and dynamical expression in developmental skeletal muscle (12 prenatal and 10 postnatal stages) from Landrace (lean-type) and Tongcheng (obese-type) pigs. Subsequently, we analyzed the interaction between OLFML3 and miR-155. The OLFML3 was abundantly expressed in liver and pancreas, moderately in lung, small intestine and placenta, and weakly in other tissues and postnatal muscle. There were different dynamical expression patterns between Landrace and Tongcheng pigs during prenatal skeletal muscle development. The OLFML3 was down-regulated (33-50 days post coitus, dpc), subsequently up-regulated (50-70 dpc), and then down-regulated (70-100 dpc) in Landrace pigs, while in Tongcheng pigs, it was down-regulated (33-50 dpc), subsequently up-regulated (50-55 dpc) and then down-regulated (55-100 dpc). There was higher expression in Tongcheng than Landrace in prenatal muscle from 33 to 60 dpc, and opposite situation from 65 to 100 dpc. Dual luciferase assay and real time PCR documented that OLFML3 expression was regulated by miR-155 at mRNA level. Our research indicated that OLFML3 gene may affect prenatal skeletal muscle development and was regulated by miR-155. These finding will help understanding biological function and expression regulation of OLFML3 gene in mammal animals.
Collapse
Affiliation(s)
- Shuanping Zhao
- State Key Laboratory for Animal Nutrition, Beijing, P R China
| | | | | | | | | | | | | |
Collapse
|