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Jaglan K, Dhaka SS, Magotra A, Patil CS, Ghanghas A. Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review. Reprod Domest Anim 2024; 59:e14529. [PMID: 38268204 DOI: 10.1111/rda.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAs preservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.
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Affiliation(s)
- Komal Jaglan
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - S S Dhaka
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - C S Patil
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Amandeep Ghanghas
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Hao D, Wang X, Yang Y, Chen H, Thomsen B, Holm LE. MicroRNA sequence variation can impact interactions with target mRNA in cattle. Gene 2023; 868:147373. [PMID: 36934784 DOI: 10.1016/j.gene.2023.147373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Small non-coding microRNAs (miRNAs) are important modulators at post-transcriptional levels. Single-nucleotide polymorphisms (SNPs) located in miRNA genes can alter the secondary structure of pre-miRNA to either impair or promote the miRNA maturation processes. Furthermore, SNPs located in the miRNA seed regions can stabilize or disturb miRNA-target interactions, thereby, quantitatively influence the expression of target genes. Therefore, the main objective of this study was to detect SNPs in bovine miRNAs using the whole-genome re-sequencing datasets of 1632 cattle of five breeds from the 1000 bull genomes project. RESULTS In total, our study identified 1109, 334, and 130 SNPs in the miRNA precursor, mature, and seed regions, respectively. The heterozygosity values were generally less than 0.3, and the minor allele frequencies (MAFs) were mainly less than 0.1. Most SNPs were in Hardy-Weinberg equilibrium (HWE) (HWE-P > 0.05). Furthermore, we found that the majority of SNPs (MAF > 0.1 and HWE-P > 0.05) in the miRNA seed regions altered the repertoire of target genes, which in turn were enriched in different KEGG pathways or GO terms. Thus target prediction for bta-miR-2888 revealed loss of 309 target genes and gain of 691 target genes. The 691 gained target genes were significantly enriched in 60 KEGG pathways and 21 GO terms. CONCLUSION In summary, our study identified candidate SNPs in miRNA precursor, mature, and seed regions that are likely to affect target RNA interactions, thereby potentially influencing cattle phenotypic traits.
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Affiliation(s)
- Dan Hao
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark; College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, 712100, Yangling, Shaanxi, China
| | - Xiao Wang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, 250100, Jinan, China; Konge Larsen ApS, 2800, Kongens Lyngby, Denmark
| | - Yu Yang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, 712100, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, 712100, Yangling, Shaanxi, China.
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.
| | - Lars-Erik Holm
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
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Identification of key adipogenic transcription factors for the pork belly parameters via the association weight matrix. Meat Sci 2023; 195:109015. [DOI: 10.1016/j.meatsci.2022.109015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
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Wang H, Shen Z, Huang R, Zhao A, Jiang J, Li P, Zhou X, Yang S, Hou L. A polymorphism in porcine miR-22 is associated with pork color. Front Vet Sci 2022; 9:939440. [PMID: 35968001 PMCID: PMC9366310 DOI: 10.3389/fvets.2022.939440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs (miRNAs) are posttranscriptional regulators that play key roles in meat color regulation. Changes in miRNA expression affect their target mRNAs, leading to multifunctional effects on biological processes and phenotypes. In this study, a G > A mutation site located upstream of the precursor miR-22 sequence in Suhuai pigs was significantly correlated with the meat color parameter a*(redness) of the porcine longissimus dorsi (LD) muscle. AA genotype individuals had the highest average meat color a* value and the lowest miR-22 level. When G > A mutation was performed in the miR-22 overexpression vector, miR-22 expression significantly decreased. Considering that Ca2+ homeostasis is closely related to pig meat color, our results further demonstrated that ELOVL6 is a direct target of miR-22 in pigs. The effects of miR-22 on skeletal muscle intracellular Ca2+ were partially caused by the suppression of ELOVL6 expression.
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Affiliation(s)
- Han Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Department of Animal Breeding, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Zhonghao Shen
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Department of Animal Breeding, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Ruihua Huang
- Institute of Swine Science, Department of Animal Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ayong Zhao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Department of Animal Breeding, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Jiani Jiang
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | - Pinghua Li
- Institute of Swine Science, Department of Animal Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaolong Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Department of Animal Breeding, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Songbai Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Department of Animal Breeding, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Liming Hou
- Institute of Swine Science, Department of Animal Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Liming Hou
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Yu B, Liu J, Cai Z, Mu T, Gu Y, Xin G, Zhang J. miRNA-mRNA associations with inosine monophosphate specific deposition in the muscle of Jingyuan chicken. Br Poult Sci 2022; 63:821-832. [PMID: 35895079 DOI: 10.1080/00071668.2022.2106777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Inosine monophosphate (IMP), is an essential component for meat flavour and microRNAs (miRNAs) play a vital role in its post-transcriptional regulation. However, the mechanism of how miRNA expression affects muscle-specific IMP deposition is unclear.2. The following study performed transcriptome sequencing and bioinformatics analysis of breast and leg muscle, which have significantly different IMP content in Jingyuan chicken. The differential miRNA-mRNAs were screened out and correlation analysis with IMP content was performed.3. A total of 39 differentially expressed miRNAs (DE miRNAs) and 666 differentially expressed mRNAs (DE mRNAs) were identified between breast muscles and leg muscles. Using miRNA-mRNA integrated analysis, 29 miRNA-target gene pairs were obtained, composed of 13 DE miRNAs and 28 DE mRNAs. Next, purine metabolism, glycolysis/gluconeogenesis, pyruvate metabolism and the biosynthesis of amino acid pathways as necessary for muscle IMP-specific deposition were identified. The differentially expressed gene PKM2, which was significantly enriched in all four pathways, is involved in IMP anabolism in the form of energy metabolism and enzyme activity regulation. The correlation analysis suggested that the gga-miR-107-3p-KLHDC2 negative interaction may be a key regulator in IMP deposition.4. This study explores the functional mechanism of IMP-specific deposition in Jingyuan chicken muscles at the miRNA and mRNA levels and highlights multiple candidate miRNAs and mRNAs for molecular-assisted breeding.
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Affiliation(s)
- Baojun Yu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Jiamin Liu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Zhengyun Cai
- College of Agriculture, Ningxia University, Yinchuan China
| | - Tong Mu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Yaling Gu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Guosheng Xin
- School of Life Sciences, Ningxia University/Ningxia Feed Engineering Technology Research Center, Yinchuan China
| | - Juan Zhang
- College of Agriculture, Ningxia University, Yinchuan China
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6
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Xiao C, Wei T, Liu LX, Liu JQ, Wang CX, Yuan ZY, Ma HH, Jin HG, Zhang LC, Cao Y. Whole-Transcriptome Analysis of Preadipocyte and Adipocyte and Construction of Regulatory Networks to Investigate Lipid Metabolism in Sheep. Front Genet 2021; 12:662143. [PMID: 34394181 PMCID: PMC8358208 DOI: 10.3389/fgene.2021.662143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/09/2021] [Indexed: 01/20/2023] Open
Abstract
Many local sheep breeds in China have poor meat quality. Increasing intramuscular fat (IMF) content can significantly improve the quality of mutton. However, the molecular mechanisms of intramuscular adipocyte formation and differentiation remain unclear. This study compared differences between preadipocytes and mature adipocytes by whole-transcriptome sequencing and constructed systematically regulatory networks according to the relationship predicted among the differentially expressed RNAs (DERs). Sequencing results showed that in this process, there were 1,196, 754, 100, and 17 differentially expressed messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), respectively. Gene Ontology analysis showed that most DERs enriched in Cell Part, Cellular Process, Biological Regulation, and Binding terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the DERs primarily focused on Focal adhesion, phosphoinositide 3-kinase (PI3K)-Akt, mitogen-activated protein kinase (MAPK), peroxisome proliferator-activated receptor (PPAR) signaling pathways. Forty (40) DERs were randomly selected from the core regulatory network to verify the accuracy of the sequence data. The results of qPCR showed that the DER expression trend was consistent with sequence data. Four novel promising candidate miRNAs (miR-336, miR-422, miR-578, and miR-722) played crucial roles in adipocyte differentiation, and they also participated in multiple and important regulatory networks. We verified the expression pattern of the miRNAs and related pathways’ members at five time points in the adipocyte differentiation process (0, 2, 4, 6, 8, 10 days) by qPCR, including miR-336/ACSL4/LncRNA-MSTRG71379/circRNA0002331, miR-422/FOXO4/LncRNA-MSTRG54995/circRNA0000520, miR-578/IGF1/LncRNA-MSTRG102235/circRNA0002971, and miR-722/PDK4/LncRNA-MSTRG107440/circ RNA0002909. In this study, our data provided plenty of valuable candidate DERs and regulatory networks for researching the molecular mechanisms of sheep adipocyte differentiation and will assist studies in improving the IMF.
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Affiliation(s)
- Cheng Xiao
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Tian Wei
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Li Xiang Liu
- Jilin Academy of Agricultural Sciences, Gongzhuling, China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jian Qiang Liu
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Chun Xin Wang
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhi Yu Yuan
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Hui Hai Ma
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Hai Guo Jin
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Li Chun Zhang
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yang Cao
- Jilin Academy of Agricultural Sciences, Gongzhuling, China
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Pawlina-Tyszko K, Semik-Gurgul E, Gurgul A, Oczkowicz M, Szmatoła T, Bugno-Poniewierska M. Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome. Sci Rep 2021; 11:9848. [PMID: 33972633 PMCID: PMC8110958 DOI: 10.1038/s41598-021-89363-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) are recognized as gene expression regulators, indirectly orchestrating a plethora of biological processes. Single nucleotide polymorphism (SNP), one of the most common genetic variations in the genome, is established to affect miRNA functioning and influence complex traits and diseases. SNPs in miRNAs have also been associated with important production traits in livestock. Thus, the aim of our study was to reveal the SNP variability of miRNA genes in the genome of the pig, which is a significant farm animal and large-mammal human model. To this end, we applied the targeted sequencing approach, enabling deep sequencing of specified genomic regions. As a result, 73 SNPs localized in 50 distinct pre-miRNAs were identified. In silico analysis revealed that many of the identified SNPs influenced the structure and energy of the hairpin precursors. Moreover, SNPs localized in the seed regions were shown to alter targeted genes and, as a result, enrich different biological pathways. The obtained results corroborate a significant impact of SNPs on the miRNA processing and broaden the state of knowledge in the field of animal genomics. We also report the targeted sequencing approach to be a promising alternative for the whole genome sequencing in miRNA genes focused studies.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.
| | - Ewelina Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland
| | - Artur Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland
- Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland
| | - Maria Oczkowicz
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland
- Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, The University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059, Kraków, Poland
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Iqbal A, Ping J, Ali S, Zhen G, Juan L, Kang JZ, Ziyi P, Huixian L, Zhihui Z. Role of microRNAs in myogenesis and their effects on meat quality in pig - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1873-1884. [PMID: 32819078 PMCID: PMC7649413 DOI: 10.5713/ajas.20.0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/02/2020] [Accepted: 08/16/2020] [Indexed: 02/02/2023]
Abstract
The demand for food is increasing day by day because of the increasing global population. Therefore, meat, the easiest and largely available source of protein, needs to be produced in large amounts with good quality. The pork industry is a significant shareholder in fulfilling the global meat demands. Notably, myogenesis- development of muscles during embryogenesis- is a complex mechanism which culminates in meat production. But the molecular mechanisms which govern the myogenesis are less known. The involvement of miRNAs in myogenesis and meat quality, which depends on factors such as myofiber composition and intramuscular fat contents which determine the meat color, flavor, juiciness, and water holding capacity, are being extrapolated to increase both the quantity and quality of pork. Various kinds of microRNAs (miRNAs), miR-1, miR-21, miR22, miR-27, miR-34, miR-127, miR-133, miR-143, miR-155, miR-199, miR-206, miR-208, miR-378, and miR-432 play important roles in pig skeletal muscle development. Further, the quality of meat also depends upon myofiber which is developed through the expression of different kinds of miRNAs at different stages. This review will focus on the mechanism of myogenesis, the role of miRNAs in myogenesis, and meat quality with a focus on the pig.
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Affiliation(s)
- Ambreen Iqbal
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jiang Ping
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Shaokat Ali
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Gao Zhen
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Liu Juan
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jin Zi Kang
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Pan Ziyi
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Lu Huixian
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Zhao Zhihui
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
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Gao Z, Sun L, Dai K, Du Y, Wu S, Bao W. Effects of mutations in porcine miRNA-215 precursor sequences on miRNA-215 regulatory function. Gene 2019; 701:131-138. [PMID: 30905811 DOI: 10.1016/j.gene.2019.03.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/12/2019] [Accepted: 03/20/2019] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) play an important role in animal growth and disease development, and sequence variation in microRNAs can alter their functions. Herein, we explored the effects of mutations in the miRNA-215 precursor sequence on the miRNA-215 regulatory network and resistance to Escherichia coli (E. coli). Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) was used to detect sequence variations in Sutai and Meishan pigs. The miR-192 precursor sequence was not mutated, but the miR-215 precursor included an AT insertion mutation at position 6 (start from the first base of the miR-215 precursor) and a C/T mutation at position 43. Wild-type (WT) and mutant miR-215 precursor expression vectors were constructed to investigate the effects of sequence variation on expression of miR-215 and its target genes DLG5 and ALCAM, cytokine levels and E. coli adhesion. Compared with the WT control group, cells harbouring the C/T mutant vector displayed reduced miR-215 expression, increased target gene expression, elevated cytokine levels and rising E. coli adhesion, whereas cells harbouring the AT insertion mutant vector were not significantly changed. The sequence variation in the miRNA-215 precursor may affect the miRNA-215 regulatory network, and alter the stability of intestinal epithelial cells (IPEC-J2 cells) and resistance to E. coli. Our findings provide guidance for future research on the regulatory mechanisms of miR-215 in porcine resistance to E. coli F18, and identifying effective genetic markers against this organism.
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Affiliation(s)
- Zhongcheng Gao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Kaiyu Dai
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulu Du
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China.
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10
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Shi J, Sun G. Effect of pre-miRNA-1658 gene polymorphism on chicken growth and carcass traits. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:455-461. [PMID: 27503275 PMCID: PMC5394830 DOI: 10.5713/ajas.16.0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/30/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022]
Abstract
Objective Polymorphisms occurring in the precursor region of microRNAs (miRNAs) affect the target gene and alter the biogenesis of miRNAs, resulting in phenotypic variation. The purpose of the study was to investigate the genetic effects of rs16681031 (C>G) mutation in the precursor region of gga-miR-1658 on the economic traits of the Gushi-Anka chicken F2 resource population. Methods To explore the effect of miR-1658 polymorphisms on chicken economic traits, the SNP was genotyped by MassArray matrix-assisted laser desorption/ionization-time of flight mass spectrometry. The association between the SNP and chicken body size, growth and carcass traits was determined by linear mixed models. Results The SNP was not only significantly associated with body weight at the age of 6, 8, 10, 12 weeks, respectively, but also with the breadth of the chicken chest, body slanting length and pelvic breadth at 4 weeks, chest depth at 8 weeks of age, and body slanting length at 12 weeks (p<0.05), respectively. Conclusion Our data serve as a useful resource for further analysis of miRNA function, and represent a molecular genetic basis for poultry breeding.
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Affiliation(s)
- Jianzhou Shi
- Institute of Agricultural and Engineering, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Guirong Sun
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou 450002, China
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11
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Liu X, Trakooljul N, Hadlich F, Muráni E, Wimmers K, Ponsuksili S. MicroRNA-mRNA regulatory networking fine-tunes the porcine muscle fiber type, muscular mitochondrial respiratory and metabolic enzyme activities. BMC Genomics 2016; 17:531. [PMID: 27485725 PMCID: PMC4970254 DOI: 10.1186/s12864-016-2850-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/20/2016] [Indexed: 02/02/2023] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in diverse biological processes via regulation of gene expression including in skeletal muscles. In the current study, miRNA expression profile was investigated in longissimus muscle biopsies of malignant hyperthermia syndrome-negative Duroc and Pietrain pigs with distinct muscle metabolic properties in order to explore the regulatory role of miRNAs related to mitochondrial respiratory activity and metabolic enzyme activity in skeletal muscle. Results A comparative analysis of the miRNA expression profile between Duroc and Pietrain pigs was performed, followed by integration with mRNA profiles based on their pairwise correlation and computational target prediction. The identified target genes were enriched in protein ubiquitination pathway, stem cell pluripotency and geranylgeranyl diphosphate biosynthesis, as well as skeletal and muscular system development. Next, we analyzed the correlation between individual miRNAs and phenotypical traits including muscle fiber type, mitochondrial respiratory activity, metabolic enzyme activity and adenosine phosphate concentrations, and constructed the regulatory miRNA-mRNA networks associated with energy metabolism. It is noteworthy that miR-25 targeting BMPR2 and IRS1, miR-363 targeting USP24, miR-28 targeting HECW2 and miR-210 targeting ATP5I, ME3, MTCH1 and CPT2 were highly associated with slow-twitch oxidative fibers, fast-twitch oxidative fibers, ADP and ATP concentration suggesting an essential role of the miRNA-mRNA regulatory networking in modulating the mitochondrial energy expenditure in the porcine muscle. In the identified miRNA-mRNA network, a tight relationship between mitochondrial and ubiquitin proteasome system at the level of gene expression was observed. It revealed a link between these two systems contributing to energy metabolism of skeletal muscle under physiological conditions. Conclusions We assembled miRNA-mRNA regulatory networks based on divergent muscle properties between different pig breeds and further with the correlation analysis of expressed genes and phenotypic measurements. These complex networks relate to muscle fiber type, metabolic enzyme activity and ATP production and may contribute to divergent muscle phenotypes by fine-tuning the expression of genes. Altogether, the results provide an insight into a regulatory role of miRNAs in muscular energy metabolisms and may have an implication on meat quality and production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2850-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuan Liu
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Muráni
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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12
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Shen L, Chen L, Zhang S, Zhang Y, Wang J, Zhu L. MicroRNA-23a reduces slow myosin heavy chain isoforms composition through myocyte enhancer factor 2C (MEF2C) and potentially influences meat quality. Meat Sci 2016; 116:201-6. [DOI: 10.1016/j.meatsci.2016.02.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/09/2015] [Accepted: 02/11/2016] [Indexed: 11/16/2022]
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13
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Effect of polymorphism within miRNA-1606 gene on growth and carcass traits in chicken. Gene 2015; 566:8-12. [DOI: 10.1016/j.gene.2015.03.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/28/2015] [Accepted: 03/16/2015] [Indexed: 11/21/2022]
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14
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Zhang W, Wang L, Zhou P, Song G, Shen M, Gan S, Shi G. Identification and analysis of genetic variations in pri-miRNAs expressed specifically or at a high level in sheep skeletal muscle. PLoS One 2015; 10:e0117327. [PMID: 25699993 PMCID: PMC4336289 DOI: 10.1371/journal.pone.0117327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/23/2014] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators in miRNA-mediated gene regulatory networks and play important roles in many biological processes, such as growth and development of mammals. In this study, we used microarrays to detect 261 miRNAs that are expressed in sheep skeletal muscle. We found 22 miRNAs that showed high levels of expression and equated to 89% of the total miRNA. Genetic variations in these 22 pri-miRNAs were further investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing. A total of 49 genetic variations, which included 41 single nucleotide polymorphisms (SNPs) and 8 deletions/insertions, were identified in four sheep breeds. Three variations were further researched in a larger sample set, including five sheep breeds with different meat production performances. We found that the genotype and allele frequencies of the CCC deletion/insertion in pri-miR-133a were significantly related to the sheep meat production trait. Finally, cell assays and quantitative reverse transcription PCR (qRT-PCR) were employed to investigate the effect of pri-miRNA genetic variation on the miRNA biogenesis process. The results confirmed that genetic variations can influence miRNA biogenesis and increase or decrease the levels of mature miRNAs, in accordance with the energy and stability change of hair-pin secondary structures. Our findings will help to further the understanding of the functions of genetic variations in sheep pri-miRNAs in skeletal muscle growth and development.
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Affiliation(s)
- Wei Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Limin Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Guangchao Song
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Shangquan Gan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- * E-mail: (SG); (GS)
| | - Guoqing Shi
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- * E-mail: (SG); (GS)
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15
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Kim JM, Lim KS, Hong JS, Kang JH, Lee YS, Hong KC. A polymorphism in the porcine miR-208b is associated with microRNA biogenesis and expressions of SOX-6 and MYH7 with effects on muscle fibre characteristics and meat quality. Anim Genet 2014; 46:73-7. [PMID: 25530254 DOI: 10.1111/age.12255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2014] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRNAs) encoded by the myosin heavy chain (MHC) genes are muscle-specific miRNAs (myomiRs) and regulate the expression of MHC isoforms in skeletal muscle. These miRNAs have been implicated in muscle fibre types and their characteristics by affecting the heterogeneity of myosin. In pigs, miR-208b and miR-499 are embedded in introns of MYH7 and MYH7b respectively. Here, we identified a novel single nucleotide polymorphism (SNP) in intron 30 of MYH7 by which porcine miR-208b is encoded. Based on the association study using a total of 487 pigs including Berkshire (n = 164), Landrace (n = 121) and Yorkshire (n = 202), the miR-208b SNP (g.17104G>A) had significant effects on the proportions of types I and IIb fibre numbers (P < 0.010) among muscle fibre characteristics and on drip loss (P = 0.012) in meat quality traits. Moreover, the SNP affected the processing of primary miR-208b into precursor miR-208b with a marginal trend towards significance (P = 0.053), thereby leading to significant changes in the levels of mature miR-208b (P = 0.009). These SNP-dependent changes in mature miR-208b levels were negatively correlated with the expression levels of its target gene, SOX-6 (P = 0.038), and positively associated with the expression levels of its host gene, MYH7 (P = 0.046). Taken together, our data suggest that the porcine miR-208b SNP differentially represses the expression of SOX-6 by regulating miRNA biogenesis, thereby affecting the expression of MYH7 and the traits of muscle fibre characteristics and meat quality.
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Affiliation(s)
- J M Kim
- College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, South Korea; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, 4072, Australia
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16
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Stratz P, Wimmers K, Meuwissen THE, Bennewitz J. Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs. J Anim Breed Genet 2014; 131:473-82. [PMID: 25047461 DOI: 10.1111/jbg.12107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/24/2014] [Indexed: 12/29/2022]
Abstract
The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the PorcineSNP60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome-wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis were matched with the results from the recently conducted genome-wide association study for economical relevant traits to investigate putative overlaps of chromosomal regions. A small subdivision of the population with regard to the geographical origin of the individuals was observed. The extent of LD was determined genome-wide using r(2) values for SNP pairs with a distance ≤5 Mb and was on average 0.34. This comparable low r(2) value indicates a high genetic diversity in the Piétrain population. Six REHH values having a p-value < 0.001 were genome-wide detected. These were located on SSC1, 2, 6 and 17. Three positional candidate genes with potential biological roles were suggested, called LOC100626459, LOC100626014 and MIR1. The results imply that for genome-wide analysis especially in this population, a higher marker density and higher sample sizes are required. For a number of nine SNPs, which were successfully annotated to core regions, the REHH test was applied. However, no selection signatures were found for those regions (p-value < 0.1).
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Affiliation(s)
- P Stratz
- Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany
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17
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Abstract
microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.
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Affiliation(s)
- Attia Fatima
- Department of Bioinformatics, National University of Ireland Galway, Galway, Ireland; and
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Mellows Campus, Athenry, Co. Galway, Ireland
| | - Dermot G. Morris
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Mellows Campus, Athenry, Co. Galway, Ireland
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