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Shen J, Hao Z, Luo Y, Zhen H, Liu Y, Wang J, Hu J, Liu X, Li S, Zhao Z, Liu Y, Yang S, Wang L. Deep Small RNA Sequencing Reveals Important miRNAs Related to Muscle Development and Intramuscular Fat Deposition in Longissimus dorsi Muscle From Different Goat Breeds. Front Vet Sci 2022; 9:911166. [PMID: 35769318 PMCID: PMC9234576 DOI: 10.3389/fvets.2022.911166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/09/2022] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been shown to play important post-transcriptional regulatory roles in the growth and development of skeletal muscle tissues. However, limited research into the effect of miRNAs on muscle development in goats has been reported. In this study, Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotype difference in meat production performance were selected and the difference in Longissimus dorsi muscle tissue expression profile of miRNAs between the two goat breeds was then compared using small RNA sequencing. A total of 1,623 miRNAs were identified in Longissimus dorsi muscle tissues of the two goat breeds, including 410 known caprine miRNAs, 928 known species-conserved miRNAs and 285 novel miRNAs. Of these, 1,142 were co-expressed in both breeds, while 230 and 251 miRNAs were only expressed in LC and ZB goats, respectively. Compared with ZB goats, 24 up-regulated miRNAs and 135 miRNAs down-regulated were screened in LC goats. A miRNA-mRNA interaction network showed that the differentially expressed miRNAs would target important functional genes associated with muscle development and intramuscular fat deposition. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the target genes of differentially expressed miRNAs were significantly enriched in Ras, Rap 1, FoxO, and Hippo signaling pathways. This study suggested that these differentially expressed miRNAs may be responsible for the phenotype differences in meat production performance between the two goat breeds, thereby providing an improved understanding of the roles of miRNAs in muscle tissue of goats.
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Sui M, Zheng Q, Wu H, Zhu L, Ling Y, Wang L, Fang F, Liu Y, Zhang Z, Chu M, Zhang Y. The expression and regulation of miR-1 in goat skeletal muscle and satellite cell during muscle growth and development. Anim Biotechnol 2019; 31:455-462. [PMID: 31179830 DOI: 10.1080/10495398.2019.1622555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNA-1 (miR-1) has been shown to play an important role in muscle growth and development, however, it was mainly discovered in model animals. To explore the function and mechanism of miR-1 in goat, we firstly explored the expression profile of miR-1 in goat tissues and cells. Furthermore, the target gene of miR-1 was predicted, and the relationship between miR-1 and one of its target genes, histone deacetylase 4 (HDAC4), was analyzed through double luciferase reporter assay, real-time PCR, and western blot. It was found that the miR-1 is most abundantly expressed in goat heart and skeletal muscle tissue. Meanwhile, the expression of miR-1 showed an increasing tendency from new-born goats to the 7-month-old goats, and then its expression decreases as the goats mature further. In addition, the expression levels of miR-1 decreased in goat skeletal muscle satellite cells with the algebraic increasing of cells. At last, the results showed that HDAC4 is a target gene of miR-1 in goat, and miR-1 can inhibit the post-transcriptional expression of HDAC4, but had no significant influence on the mRNA level of HDAC4. It was hypothesized that miR-1 promotes muscle development by inhibiting the post-transcriptional expression of HDAC4 in goat.
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Affiliation(s)
- Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Hao Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Lu Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - LiJuan Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Ya Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhai Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, Hefei, Anhui, China
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3
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Capra E, Lazzari B, Frattini S, Chessa S, Coizet B, Talenti A, Castiglioni B, Marsan PA, Crepaldi P, Pagnacco G, Williams JL, Stella A. Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus. BMC Genomics 2018; 19:417. [PMID: 29848285 PMCID: PMC5977473 DOI: 10.1186/s12864-018-4767-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 05/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexual development and mammalian reproduction. In order to identify ncRNAs and to assess their expression patterns, along the HPG axis, we sequenced ncRNA libraries from hypothalamus, pituitary and ovary of three goats. Results Among the medium length noncoding RNAs (mncRNAs) identified, small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs) were found to be more abundant in ovary and hypothalamus, respectively. The observed GC content was representative for different classes of ncRNAs, allowing the identification of a tRNA-derived RNA fragments (tRFs) subclass, which had a peak distribution around 32–38% GC content in the hypothalamus. Differences observed among organs confirmed the specificity of microRNA (miRNA) profiles for each organ system. Conclusions Data on ncRNAs in organs constituting the HPG axis will contribute to understanding their role in the physiological regulation of reproduction in goats. Electronic supplementary material The online version of this article (10.1186/s12864-018-4767-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy
| | - Stefano Frattini
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Stefania Chessa
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Beatrice Coizet
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - Giulio Pagnacco
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.,Parco Tecnologico Padano, Lodi, Italy.,Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milan, Italy
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy. .,Parco Tecnologico Padano, Lodi, Italy.
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Osorio JS, Vailati-Riboni M, Palladino A, Luo J, Loor JJ. Application of nutrigenomics in small ruminants: Lactation, growth, and beyond. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Atambayeva S, Niyazova R, Ivashchenko A, Pyrkova A, Pinsky I, Akimniyazova A, Labeit S. The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes. BMC Genomics 2017; 18:428. [PMID: 28569192 PMCID: PMC5452331 DOI: 10.1186/s12864-017-3811-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/22/2017] [Indexed: 01/13/2023] Open
Abstract
Background Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications. Results The search of 2,750 human microRNAs (miRNAs) binding sites in 12,175 mRNAs of human genes using the MirTarget program has been completed. For the binding sites of the miR-619-5p the hybridization free energy of the bonds was equal to 100% of the maximum potential free energy. The mRNAs of 201 human genes have complete complementary binding sites of miR-619-5p in the 3’UTR (214 sites), CDS (3 sites), and 5’UTR (4 sites). The mRNAs of CATAD1, ICA1L, GK5, POLH, and PRR11 genes have six miR-619-5p binding sites, and the mRNAs of OPA3 and CYP20A1 genes have eight and ten binding sites, respectively. All of these miR-619-5p binding sites are located in the 3’UTRs. The miR-619-5p binding site in the 5’UTR of mRNA of human USP29 gene is found in the mRNAs of orthologous genes of primates. Binding sites of miR-619-5p in the coding regions of mRNAs of C8H8orf44, C8orf44, and ISY1 genes encode the WLMPVIP oligopeptide, which is present in the orthologous proteins. Binding sites of miR-619-5p in the mRNAs of transcription factor genes ZNF429 and ZNF429 encode the AHACNP oligopeptide in another reading frame. Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes. Conclusions The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3811-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shara Atambayeva
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan.
| | - Raigul Niyazova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anatoliy Ivashchenko
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ilya Pinsky
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigul Akimniyazova
- SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Siegfried Labeit
- Institute for Anaesthesiology and Intensive Operative Care Medical Faculty Mannheim, Mannheim, Germany
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6
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Qu B, Qiu Y, Zhen Z, Zhao F, Wang C, Cui Y, Li Q, Zhang L. Computational identification and characterization of novel microRNA in the mammary gland of dairy goat (Capra hircus). J Genet 2016; 95:625-37. [PMID: 27659334 DOI: 10.1007/s12041-016-0674-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many studies have indicated that microRNAs (miRNAs) influence the development of the mammary gland by posttranscriptionally affecting their target genes. The objective of this research was to identify novel miRNAs in the mammary gland of dairy goats with a bioinformatics approach that was based on expressed sequence tag (EST) and genome survey sequence (GSS) analyses. We applied all known major mammals, miRNAs to search against the goat EST and GSS databases for the first time to identify new miRNAs. We, then, validated these newly predicted miRNAs with stem-loop reverse transcription followed by a SYBR Green polymerase chain reaction assay. Finally, 29 mature miRNAs were identified and verified, and of these, 14 were grouped into 13 families based on seed sequence identity and 85 potential target genes of newly verified miRNAs were subsequently predicted, most of which seemed to encode the proteins participating in regulation of metabolism, signal transduction, growth and development. The predicting accuracy of the new miRNAs was 70.37%, which confirmed that the methods used in this study were efficient and reliable. Detailed analyses of the sequence characteristics of the novel miRNAs of the goat mammary gland were performed. In conclusion, these results provide a reference for further identification of miRNAs in animals without a complete genome and thus improve the understanding of miRNAs in the caprine mammary gland.
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Affiliation(s)
- Bo Qu
- Faculty of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of
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7
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Zhu L, Chen T, Sui M, Han C, Fang F, Ma Y, Chu M, Zhang X, Liu C, Ling Y. Comparative profiling of differentially expressed microRNAs between the follicular and luteal phases ovaries of goats. SPRINGERPLUS 2016; 5:1233. [PMID: 27610292 PMCID: PMC4993730 DOI: 10.1186/s40064-016-2902-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022]
Abstract
To explore if the regulation at post-transcriptional level of follicular phase (Fols) to luteal phase (Luts) transition occurs in the ovaries of Anhuai goats, the differentially expressed microRNAs (miRNAs) of ovaries in the Fols and Luts were analyzed using Solexa sequencing in the study. In total, 320 known miRNAs were co-expressed in the two phases, 339 and 353 known miRNAs were expressed in the ovary in the Fols and Luts, respectively. In addition, 45 novel miRNAs were co-expressed in the two phases, 70 and 94 novel miRNAs were expressed in the ovary in the Fols and Luts, respectively. Let-7f was the highest expressed significantly different known miRNA in the two phases, and mir-159 was the highest expressed significantly different novel miRNA in the two phases, which may participate in the follicular-luteal transition of Anhuai goats. GO annotation and KEGG pathway analysis were applied to analyze the target genes of differentially expressed miRNAs detected in the two phases. The results will help to further understand the role of miRNAs in the regulation of follicular to luteal transition in goat ovaries.
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Affiliation(s)
- Long Zhu
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Tao Chen
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Chunyang Han
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Yuehui Ma
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Institute of Animal Science, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Institute of Animal Science, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Cuiyan Liu
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang west road, Hefei, 230036 Anhui China.,Local animal genetic resources conservation and biobreeding laboratory of Anhui province, 130 Changjiang west road, Hefei, 230036 Anhui China
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8
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Characterization and analysis of differentially expressed microRNAs in hircine ovaries during the follicular and luteal phases. Anim Reprod Sci 2016; 166:47-57. [DOI: 10.1016/j.anireprosci.2016.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/15/2015] [Accepted: 01/04/2016] [Indexed: 11/20/2022]
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9
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The properties of binding sites of miR-619-5p, miR-5095, miR-5096, and miR-5585-3p in the mRNAs of human genes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:720715. [PMID: 25162022 PMCID: PMC4137733 DOI: 10.1155/2014/720715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 11/17/2022]
Abstract
The binding of 2,578 human miRNAs with the mRNAs of 12,175 human genes was studied. It was established that miR-619-5p, miR-5095, miR-5096, and miR-5585-3p bind with high affinity to the mRNAs of the 1215, 832, 725, and 655 genes, respectively. These unique miRNAs have binding sites in the coding sequences and untranslated regions of mRNAs. The mRNAs of many genes have multiple miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites. Groups of mRNAs in which the ordering of the miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites differ were established. The possible functional and evolutional properties of unique miRNAs are discussed.
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10
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Wang Y, Zhang C, Fang X, Zhao Y, Chen X, Sun J, Zhou Y, Wang J, Wang Y, Lan X, Chen H. Identification and profiling of microRNAs and their target genes from developing caprine skeletal Muscle. PLoS One 2014; 9:e96857. [PMID: 24818606 PMCID: PMC4018397 DOI: 10.1371/journal.pone.0096857] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
Goat is an important agricultural animal for meat production. Functional studies have demonstrated that microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although studies on miRNAs expression profiles have been performed in various animals, relatively limited information about goat muscle miRNAs has been reported. To investigate the miRNAs involved in regulating different periods of skeletal muscle development, we herein performed a comprehensive research for expression profiles of caprine miRNAs during two developmental stages of skeletal muscles: fetal stage and six month-old stage. As a result, 15,627,457 and 15,593,721 clean reads were obtained from the fetal goat library (FC) and the six month old goat library (SMC), respectively. 464 known miRNAs and 83 novel miRNA candidates were identified. Furthermore, by comparing the miRNA profile, 336 differentially expressed miRNAs were identified and then the potential targets of the differentially expressed miRNAs were predicted. To understand the regulatory network of miRNAs during muscle development, the mRNA expression profiles for the two development stages were characterized and 7322 differentially expressed genes (DEGs) were identified. Then the potential targets of miRNAs were compared to the DEGs, the intersection of the two gene sets were screened out and called differentially expressed targets (DE-targets), which were involved in 231 pathways. Ten of the 231 pathways that have smallest P-value were shown as network figures. Based on the analysis of pathways and networks, we found that miR-424-5p and miR-29a might have important regulatory effect on muscle development, which needed to be further studied. This study provided the first global view of the miRNAs in caprine muscle tissues. Our results help elucidation of complex regulatory networks between miRNAs and mRNAs and for the study of muscle development.
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Affiliation(s)
- Yanhong Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xingtang Fang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Yulong Zhao
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xiaohui Chen
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Jiajie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Yang Zhou
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Jianjin Wang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Yongan Wang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
- * E-mail:
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11
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Ling YH, Ren CH, Guo XF, Xu LN, Huang YF, Luo JC, Zhang YH, Zhang XR, Zhang ZJ. Identification and characterization of microRNAs in the ovaries of multiple and uniparous goats (Capra hircus) during follicular phase. BMC Genomics 2014; 15:339. [PMID: 24886377 PMCID: PMC4035069 DOI: 10.1186/1471-2164-15-339] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 04/30/2014] [Indexed: 12/14/2022] Open
Abstract
Background Superior kidding rate is an important economic trait in production of meat goat, and ovulation rate is the precondition of kidding rate. MicroRNAs (miRNAs) play critical roles in almost all ovarian biological processes, including folliculogenesis, follicle development, follicle atresia, luteal development and regression. To find out the different ovarian activity and follicle recruitment with miRNA-mediated posttranscriptional regulation, the small RNAs expressed pattern in the ovarian tissues of multiple and uniparous Anhui White goats during follicular phase was analyzed using Solexa sequencing data. Results 1008 miRNAs co-expressed, 309 and 433 miRNAs specifically expressed in the ovaries of multiple and uniparous goats during follicular phase were identified. The 10 most highly expressed miRNAs in the multiple library were also the highest expressed in the uniparous library, and there were no significantly different between each other. The highest specific expressed miRNA in the multiple library was miR-29c, and the one in the uniparous library was miR-6406. 35 novel miRNAs were predicted in total. GO annotation and KEGG Pathway analyses were implemented on target genes of all miRNA in two libraries. RT-PCR was applied to detect the expression level of 5 randomly selected miRNAs in multiple and uniparous hircine ovaries, and the results were consistent with the Solexa sequencing data. Conclusions In the present study, the different expression of miRNAs in the ovaries of multiple and uniparous goats during follicular phase were characterized and investigated using deep sequencing technology. The result will help to further understand the role of miRNAs in kidding rate regulation and also may help to identify miRNAs which could be potentially used to increase hircine ovulation rate and kidding rate in the future. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-339) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiao-Rong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, No, 130 Changjiang west road, Hefei 230036, P,R, China.
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