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Joshi M, Andrabi SW, Yadav RK, Sankhwar SN, Gupta G, Rajender S. Qualitative and quantitative assessment of sperm miRNAs identifies hsa-miR-9-3p, hsa-miR-30b-5p and hsa-miR-122-5p as potential biomarkers of male infertility and sperm quality. Reprod Biol Endocrinol 2022; 20:122. [PMID: 35971175 PMCID: PMC9377062 DOI: 10.1186/s12958-022-00990-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In contrast with the preceding stages of the germ cells, spermatozoa are unusually rich in small non-coding RNAs in comparison to the coding RNAs. These small RNAs may have had an essential role in the process of spermatogenesis or may have critical roles in the post-fertilization development. Sporadic efforts have identified a few differentially expressed miRNAs in infertile individuals, which do not replicate in other studies. METHODS In order to identify miRNAs signatures of infertility or poor sperm quality, we compared miRNA differential expression data across nine datasets, followed by their analysis by real-time PCR in a case-control study. This was followed by the validation of potential biomarkers in yet another set of cases and controls. For this, total RNA was isolated from 161 sperm samples. miRNA expression levels in infertile cases and fertile controls were measured using TaqMan real-time PCR. Meta-analyses of two miRNAs (hsa-miR-9-3p and hsa-miR-122-5p) were performed using Comprehensive Meta-Analysis Software (version 2). All statistical analyses were performed with the help of GraphPad Prism Software (version 8). RESULTS Literature search identified seven miRNAs (hsa-let-7a-5p, hsa-miR-9-3p, hsa-miR-22-5p, has-miR-30b-5p, hsa-miR-103-3p, hsa-miR-122-5p and hsa-miR-335-5p) showing consistent dysregulation in infertility across a minimum of four studies. In the discovery phase, six miRNAs showed strong association with infertility with four (hsa-miR-9-3p, hsa-miR-30b-5p, hsa-miR-103-3p and hsa-miR-122-5p) showing consistent differential regulation across all sub-groups. Receiver operating characteristic (ROC) curve analysis showed that the area under curve of > 0.75 was achieved by three (hsa-mir-9-3p, hsa-miR-30b-5p and hsa-miR-122-5p) miRNAs. In the validation phase, these three miRNAs showed consistent association with infertility (hsa-mir-9-3p, hsa-miR-30b-5p, and hsa-miR-122-5p). Meta-analysis on hsa-miR-122-5p showed its significant quantitative association with infertility [Hedge's g = -2.428, p = 0.001 (Random effects)]. CONCLUSIONS Three miRNAs (hsa-miR-9-3p, hsa-miR-30b-5p and hsa-miR-122-5p) have strong linkage with infertility and a high potential as sperm quality biomarkers.
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Affiliation(s)
- Meghali Joshi
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | | | | | | | - Gopal Gupta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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MicroRNA-dependent regulation of targeted mRNAs for improved muscle texture in crisp grass carp fed with broad bean. Food Res Int 2022; 155:111071. [DOI: 10.1016/j.foodres.2022.111071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/19/2022]
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miR-128a Acts as a Regulator in Cardiac Development by Modulating Differentiation of Cardiac Progenitor Cell Populations. Int J Mol Sci 2020; 21:ijms21031158. [PMID: 32050579 PMCID: PMC7038042 DOI: 10.3390/ijms21031158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRs) appear to be major, yet poorly understood players in regulatory networks guiding cardiogenesis. We sought to identify miRs with unknown functions during cardiogenesis analyzing the miR-profile of multipotent Nkx2.5 enhancer cardiac progenitor cells (NkxCE-CPCs). Besides well-known candidates such as miR-1, we found about 40 miRs that were highly enriched in NkxCE-CPCs, four of which were chosen for further analysis. Knockdown in zebrafish revealed that only miR-128a affected cardiac development and function robustly. For a detailed analysis, loss-of-function and gain-of-function experiments were performed during in vitro differentiations of transgenic murine pluripotent stem cells. MiR-128a knockdown (1) increased Isl1, Sfrp5, and Hcn4 (cardiac transcription factors) but reduced Irx4 at the onset of cardiogenesis, (2) upregulated Isl1-positive CPCs, whereas NkxCE-positive CPCs were downregulated, and (3) increased the expression of the ventricular cardiomyocyte marker Myl2 accompanied by a reduced beating frequency of early cardiomyocytes. Overexpression of miR-128a (4) diminished the expression of Isl1, Sfrp5, Nkx2.5, and Mef2c, but increased Irx4, (5) enhanced NkxCE-positive CPCs, and (6) favored nodal-like cardiomyocytes (Tnnt2+, Myh6+, Shox2+) accompanied by increased beating frequencies. In summary, we demonstrated that miR-128a plays a so-far unknown role in early heart development by affecting the timing of CPC differentiation into various cardiomyocyte subtypes.
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Salas-Huetos A, James ER, Aston KI, Jenkins TG, Carrell DT, Yeste M. The Expression of miRNAs in Human Ovaries, Oocytes, Extracellular Vesicles, and Early Embryos: A Systematic Review. Cells 2019; 8:cells8121564. [PMID: 31817143 PMCID: PMC6952888 DOI: 10.3390/cells8121564] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 01/10/2023] Open
Abstract
The recent discovery of microRNAs (miRNAs) in human reproductive tissues and cells indicates a possible functional role in reproductive function. However, the studies published to date in female reproductive tissues/cells and embryos are inconclusive and sometimes controversial. In order to update the knowledge of this field, the present study aimed to discuss, through a systematic review, the role of miRNAs in female human reproduction and early embryogenesis. We conducted a systematic review of the published literature in MEDLINE and EMBASE databases through June 2018 (plus a complementary search until July 2019), in accordance with the PRISMA guidelines. We have included descriptive and observational studies, in which fertile/infertile women were well-defined. The primary outcome was the miRNA expression in ovaries, oocytes, extracellular vesicles, and embryos. We identified 25,204 articles, of which 28 were selected for qualitative analysis: 18 in ovaries and extracellular vesicles, three in oocytes, and seven in embryos. The present systematic review of descriptive and observational studies demonstrates that aberrant miRNA expression in female reproductive tissues/cells and embryos is related with infertility and embryogenesis errors. The expression of specific miRNAs, particularly in extracellular vesicles, may be used in the future as biomarkers of infertility and prognostic tools of embryo development.
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Affiliation(s)
- Albert Salas-Huetos
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; (E.R.J.); (K.I.A.); (T.G.J.); (D.T.C.)
- Correspondence: (A.S.-H.); (M.Y.); Tel.: +34-972419514 (M.Y.)
| | - Emma R. James
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; (E.R.J.); (K.I.A.); (T.G.J.); (D.T.C.)
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Kenneth I. Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; (E.R.J.); (K.I.A.); (T.G.J.); (D.T.C.)
| | - Timothy G. Jenkins
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; (E.R.J.); (K.I.A.); (T.G.J.); (D.T.C.)
| | - Douglas T. Carrell
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84108, USA; (E.R.J.); (K.I.A.); (T.G.J.); (D.T.C.)
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Unit of Cell Biology, Department of Biology, Institute of Food and Agricultural Technology, Faculty of Sciences, University of Girona, 17003 Girona, Spain
- Correspondence: (A.S.-H.); (M.Y.); Tel.: +34-972419514 (M.Y.)
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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Salas‐Huetos A, James ER, Aston KI, Carrell DT, Jenkins TG, Yeste M. The role of miRNAs in male human reproduction: a systematic review. Andrology 2019; 8:7-26. [DOI: 10.1111/andr.12714] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022]
Affiliation(s)
- A. Salas‐Huetos
- Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine Salt Lake City UT USA
| | - E. R. James
- Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine Salt Lake City UT USA
- Department of Human Genetics University of Utah School of Medicine Salt Lake City UT USA
| | - K. I. Aston
- Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine Salt Lake City UT USA
| | - D. T. Carrell
- Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine Salt Lake City UT USA
- Department of Human Genetics University of Utah School of Medicine Salt Lake City UT USA
- Department of Obstetrics and Gynecology University of Utah School of Medicine Salt Lake City UT USA
| | - T. G. Jenkins
- Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine Salt Lake City UT USA
| | - M. Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm) Unit of Cell Biology Department of Biology Faculty of Sciences Institute of Food and Agricultural Technology University of Girona Girona Spain
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Tafrihi M, Hasheminasab E. MiRNAs: Biology, Biogenesis, their Web-based Tools, and Databases. Microrna 2019; 8:4-27. [PMID: 30147022 DOI: 10.2174/2211536607666180827111633] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/11/2018] [Accepted: 08/20/2018] [Indexed: 05/25/2023]
Abstract
INTRODUCTION MicroRNAs (miRNAs), which are evolutionarily conserved, and endogenous non-coding RNAs, participate in the post-transcriptional regulation of eukaryotic genes. The biogenesis of miRNAs occurs in the nucleus. Then, in the cytoplasm, they are assembled along with some proteins in a ribonucleoprotein complex called RISC. miRNA component of the RISC complex binds to the complementary sequence of mRNA target depending on the degree of complementarity, and leads to mRNA degradation and/or inhibition of protein synthesis. miRNAs have been found in eukaryotes and some viruses play a role in development, metabolism, cell proliferation, growth, differentiation, and death. OBJECTIVE A large number of miRNAs and their targets were identified by different experimental techniques and computational approaches. The principal aim of this paper is to gather information about some miRNA databases and web-based tools for better and quicker access to relevant data. RESULTS Accordingly, in this paper, we collected and introduced miRNA databases and some webbased tools that have been developed by various research groups. We have categorized them into different classes including databases for viral miRNAs, and plant miRNAs, miRNAs in human beings, mice and other vertebrates, miRNAs related to human diseases, and target prediction, and miRNA expression. Also, we have presented relevant statistical information about these databases.
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Affiliation(s)
- Majid Tafrihi
- Molecular & Cell Biology Research Lab. 2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran
| | - Elham Hasheminasab
- Molecular & Cell Biology Research Lab. 2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran
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Wu S, Guo J, Zhu L, Yang J, Chen S, Yang X. Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels' spermatozoa by Solexa sequencing. Br Poult Sci 2018; 59:371-380. [PMID: 29667432 DOI: 10.1080/00071668.2018.1464123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels' spermatozoa. 2. A small RNA library of cockerels' spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.
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Affiliation(s)
- S Wu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Guo
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - L Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - S Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - X Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
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Mok GF, Lozano-Velasco E, Münsterberg A. microRNAs in skeletal muscle development. Semin Cell Dev Biol 2017; 72:67-76. [PMID: 29102719 DOI: 10.1016/j.semcdb.2017.10.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signaling molecules, transcription factors and more recently non-coding RNAs that contribute to this process have been identified. This has facilitated advances in our understanding of the molecular mechanisms underlying the control of cell fate choice. Here we will review the role of non-coding RNAs, in particular microRNAs (miRNAs), in embryonic muscle development and differentiation, and in satellite cells of adult muscle, which are essential for muscle growth and regeneration. Some of these short post-transcriptional regulators of gene expression are restricted to skeletal muscle, but their expression can also be more widespread. In addition, we discuss a few examples of long non-coding RNAs, which are numerous but much less well understood.
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Affiliation(s)
- Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Estefania Lozano-Velasco
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Jia H, Zhao Y, Li T, Zhang Y, Zhu D. miR-30e is negatively regulated by myostatin in skeletal muscle and is functionally related to fiber-type composition. Acta Biochim Biophys Sin (Shanghai) 2017; 49:392-399. [PMID: 28338991 DOI: 10.1093/abbs/gmx019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Indexed: 01/12/2023] Open
Abstract
Myostatin (MSTN) negatively regulates skeletal myogenesis in which microRNAs (miRNAs) also play critical roles. Using miRNA microarrays of skeletal muscle from MSTN-knockout (MSTN-/-) mice, we recently showed that miR-431 is regulated by MSTN signaling. To identify additional miRNAs regulated by MSTN, we re-analyzed these miRNA arrays and validated their expression by quantitative RT-PCR. Herein, we demonstrated that miR-30e was significantly upregulated in skeletal muscle of MSTN-/- mice compared with that of the wild-type littermates. Importantly, the predicted targets of miR-30e are functionally involved in myocyte differentiation and fiber-type formation. Using luciferase reporter gene assays, we further showed that peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (Pgc1α), is a direct target of miR-30e. Overexpression of miR-30e in C2C12 cells significantly decreased Pgc1α and increased type II form of myosin heavy chain gene expression, suggesting that miR-30e functionally associates with glycolytic myofiber formation. Thus, our data indicate that the altered fiber-type composition in MSTN-/- mice are attributable in part to deregulated expression of miR-30e.
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Affiliation(s)
- Haixue Jia
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Yixia Zhao
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yong Zhang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Dahai Zhu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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Bhattacharya M, Sharma AR, Sharma G, Patra BC, Nam JS, Chakraborty C, Lee SS. The crucial role and regulations of miRNAs in zebrafish development. PROTOPLASMA 2017; 254:17-31. [PMID: 26820151 DOI: 10.1007/s00709-015-0931-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
To comprehend the events during developmental biology, fundamental knowledge about the basic machinery of regulation is a prerequisite. MicroRNA (miRNAs) act as regulators in most of the biological processes and recently, it has been concluded that miRNAs can act as modulatory factors even during developmental process from lower to higher animal. Zebrafish, because of its favorable attributes like tiny size, transparent embryo, and rapid external embryonic development, has gained a preferable status among all other available experimental animal models. Currently, zebrafish is being utilized for experimental studies related to stem cells, regenerative molecular medicine as well drug discovery. Therefore, it is important to understand precisely about the various miRNAs that controls developmental biology of this vertebrate model. In here, we have discussed about the miRNA-controlled zebrafish developmental stages with a special emphasis on different miRNA families such as miR-430, miR-200, and miR-133. Moreover, we have also reviewed the role of various miRNAs during embryonic and vascular development stages of zebrafish. In addition, efforts have been made to summarize the involvement of miRNAs in the development of different body parts such as the brain, eye, heart, muscle, and fin, etc. In each section, we have tried to fulfill the gaps of zebrafish developmental biology with the help of available knowledge of miRNA research. We hope that precise knowledge about the miRNA-regulated developmental stages of zebrafish may further help the researchers to efficiently utilize this vertebrate model for experimental purpose.
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Affiliation(s)
- Manojit Bhattacharya
- Aquaculture Research Unit, Department of Zoology, Vidyasagar University, Midnapore, 721102, West Bengal, India
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Garima Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Bidhan Chandra Patra
- Aquaculture Research Unit, Department of Zoology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Ju-Suk Nam
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea.
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, 201306, India.
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea.
- Department of Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, 200-704, Republic of Korea.
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Hudish LI, Galati DF, Ravanelli AM, Pearson CG, Huang P, Appel B. miR-219 regulates neural progenitors by dampening apical Par protein-dependent Hedgehog signaling. Development 2016; 143:2292-304. [PMID: 27226318 PMCID: PMC4958328 DOI: 10.1242/dev.137844] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/05/2016] [Indexed: 12/25/2022]
Abstract
The transition of dividing neuroepithelial progenitors to differentiated neurons and glia is essential for the formation of a functional nervous system. Sonic hedgehog (Shh) is a mitogen for spinal cord progenitors, but how cells become insensitive to the proliferative effects of Shh is not well understood. Because Shh reception occurs at primary cilia, which are positioned within the apical membrane of neuroepithelial progenitors, we hypothesized that loss of apical characteristics reduces the Shh signaling response, causing cell cycle exit and differentiation. We tested this hypothesis using genetic and pharmacological manipulation, gene expression analysis and time-lapse imaging of zebrafish embryos. Blocking the function of miR-219, a microRNA that downregulates apical Par polarity proteins and promotes progenitor differentiation, elevated Shh signaling. Inhibition of Shh signaling reversed the effects of miR-219 depletion and forced expression of Shh phenocopied miR-219 deficiency. Time-lapse imaging revealed that knockdown of miR-219 function accelerates the growth of primary cilia, revealing a possible mechanistic link between miR-219-mediated regulation of apical Par proteins and Shh signaling. Thus, miR-219 appears to decrease progenitor cell sensitivity to Shh signaling, thereby driving these cells towards differentiation.
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Affiliation(s)
- Laura I. Hudish
- Departments of Pediatrics and Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Domenico F. Galati
- Departments of Pediatrics and Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrew M. Ravanelli
- Departments of Pediatrics and Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chad G. Pearson
- Departments of Pediatrics and Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peng Huang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
| | - Bruce Appel
- Departments of Pediatrics and Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA,Author for correspondence ()
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Franchini P, Xiong P, Fruciano C, Meyer A. The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua. Genome Biol Evol 2016; 8:1543-55. [PMID: 27189980 PMCID: PMC4898811 DOI: 10.1093/gbe/evw097] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany School of Earth Environmental & Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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Wade B, Cummins M, Keyburn A, Crowley TM. Isolation and detection of microRNA from the egg of chickens. BMC Res Notes 2016; 9:283. [PMID: 27215602 PMCID: PMC4877990 DOI: 10.1186/s13104-016-2084-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/11/2016] [Indexed: 11/10/2022] Open
Abstract
Background The egg is a vital part of the chicken developmental process and an important protein source for humans. Despite the chicken egg being a subject of intense research little attention has been given to the role of microRNAs within the egg. Findings We report a method for the reproducible and reliable isolation of miRNA from the albumen and yolk of chicken eggs. We also report the detection via real-time PCR of a number of miRNAs from both of these biological fluids. Conclusions These findings provide an interesting look into the chicken egg and raise questions as to the role that miRNAs maybe playing in the chicken egg. This method of detecting miRNAs in chicken eggs will allow researchers to investigate the presence of an additional level of epigenetic programming in chick development previously unknown and also how this impacts the nutritional value of eggs for human consumption.
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Affiliation(s)
- Ben Wade
- School of Medicine, MMR, Bioinformatics Core Research Facility, Deakin University, Pigdons Road, Waurn Ponds, VIC, 3216, Australia.,CSIRO, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,Poultry Cooperative Research Centre, University of New England, Armidale, NSW, 2351, Australia
| | - Michelle Cummins
- School of Medicine, MMR, Bioinformatics Core Research Facility, Deakin University, Pigdons Road, Waurn Ponds, VIC, 3216, Australia.,CSIRO, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,Poultry Cooperative Research Centre, University of New England, Armidale, NSW, 2351, Australia
| | - Anthony Keyburn
- CSIRO, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,Poultry Cooperative Research Centre, University of New England, Armidale, NSW, 2351, Australia
| | - Tamsyn M Crowley
- School of Medicine, MMR, Bioinformatics Core Research Facility, Deakin University, Pigdons Road, Waurn Ponds, VIC, 3216, Australia. .,CSIRO, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia. .,Poultry Cooperative Research Centre, University of New England, Armidale, NSW, 2351, Australia.
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16
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Pinch M, Güth R, Samanta MP, Chaidez A, Unguez GA. The myogenic electric organ of Sternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome. PeerJ 2016; 4:e1828. [PMID: 27114860 PMCID: PMC4841239 DOI: 10.7717/peerj.1828] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 02/29/2016] [Indexed: 12/13/2022] Open
Abstract
In most electric fish species, the electric organ (EO) derives from striated muscle cells that suppress many muscle properties. In the gymnotiform Sternopygus macrurus, mature electrocytes, the current-producing cells of the EO, do not contain sarcomeres, yet they continue to make some cytoskeletal and sarcomeric proteins and the muscle transcription factors (MTFs) that induce their expression. In order to more comprehensively examine the transcriptional regulation of genes associated with the formation and maintenance of the contractile sarcomere complex, results from expression analysis using qRT-PCR were informed by deep RNA sequencing of transcriptomes and miRNA compositions of muscle and EO tissues from adult S. macrurus. Our data show that: (1) components associated with the homeostasis of the sarcomere and sarcomere-sarcolemma linkage were transcribed in EO at levels similar to those in muscle; (2) MTF families associated with activation of the skeletal muscle program were not differentially expressed between these tissues; and (3) a set of microRNAs that are implicated in regulation of the muscle phenotype are enriched in EO. These data support the development of a unique and highly specialized non-contractile electrogenic cell that emerges from a striated phenotype and further differentiates with little modification in its transcript composition. This comprehensive analysis of parallel mRNA and miRNA profiles is not only a foundation for functional studies aimed at identifying mechanisms underlying the transcription-independent myogenic program in S. macrurus EO, but also has important implications to many vertebrate cell types that independently activate or suppress specific features of the skeletal muscle program.
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Affiliation(s)
- Matthew Pinch
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Robert Güth
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | | | - Alexander Chaidez
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Graciela A. Unguez
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
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17
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Shang FF, Xia QJ, Liu W, Xia L, Qian BJ, You L, He M, Yang JL, Wang TH. miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle. Sci Rep 2016; 6:22884. [PMID: 26964899 PMCID: PMC4786822 DOI: 10.1038/srep22884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/23/2016] [Indexed: 02/06/2023] Open
Abstract
Acetylcholine receptors (AChRs) serve as connections between motor neurons and skeletal muscle and are essential for recovery from spinal cord transection (SCT). Recently, microRNAs have emerged as important potential biotherapeutics for several diseases; however, whether miRNAs operate in the modulation of AChRs remains unknown. We found increased AChRs numbers and function scores in rats with SCT; these increases were reduced following the injection of a eukaryotic translation initiation factor 5A1 (eIF5A1) shRNA lentivirus into the hindlimb muscle. Then, high-throughput screening for microRNAs targeting eIF5A1 was performed, and miR-434-3p was found to be robustly depleted in SCT rat skeletal muscle. Furthermore, a highly conserved miR-434-3p binding site was identified within the mRNA encoding eIF5A1 through bioinformatics analysis and dual-luciferase assay. Overexpression or knockdown of miR-434-3p in vivo demonstrated it was a negative post-transcriptional regulator of eIF5A1 expression and influenced AChRs expression. The microarray-enriched Gene Ontology (GO) terms regulated by miR-434-3p were muscle development terms. Using a lentivirus, one functional gene (map2k6) was confirmed to have a similar function to that of miR-434-3p in GO terms. Finally, HRM and MeDIP-PCR analyses revealed that DNA demethylation also up-regulated eIF5A1 after SCT. Consequently, miR-434-3p/eIF5A1 in muscle is a promising potential biotherapy for SCI repair.
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Affiliation(s)
- Fei-Fei Shang
- Institute of Neurological Disease, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Qing-Jie Xia
- Institute of Neurological Disease, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Wei Liu
- Department of Anesthesiology and Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Lei Xia
- Department of Anesthesiology and Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Bao-Jiang Qian
- Institute of Neuroscience, Kunming medical University, Kunming, 650031, P.R. China
| | - Ling You
- Institute of Neuroscience, Kunming medical University, Kunming, 650031, P.R. China
| | - Mu He
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Jin-Liang Yang
- Institute of Neurological Disease, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Ting-Hua Wang
- Institute of Neurological Disease, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
- Institute of Neuroscience, Kunming medical University, Kunming, 650031, P.R. China
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
- Department of Anesthesiology and Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
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18
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The functional consequences of age-related changes in microRNA expression in skeletal muscle. Biogerontology 2016; 17:641-54. [PMID: 26922183 PMCID: PMC4889642 DOI: 10.1007/s10522-016-9638-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 02/18/2016] [Indexed: 01/07/2023]
Abstract
A common characteristic of ageing is disrupted homeostasis between growth and atrophy of skeletal muscle resulting in loss of muscle mass and function, which is associated with sarcopenia. Sarcopenia is related to impaired balance, increased falls and decline in quality of life of older people. Ageing-related transcriptome and proteome changes in skeletal muscle have been characterised, however the molecular mechanisms underlying sarcopenia are still not fully understood. microRNAs are novel regulators of gene expression known to modulate skeletal muscle development and homeostasis. Expression of numerous microRNAs is disrupted in skeletal muscle with age however, the functional consequences of this are not yet understood. Given that a single microRNA can simultaneously affect multiple signalling pathways, microRNAs are potent modulators of pathophysiological changes occurring during ageing. Here we use microRNA and transcript expression profiling together with microRNA functional assays to show that disrupted microRNA:target interactions play an important role in maintaining muscle homeostasis. We identified miR-181a as a regulator of the sirtuin1 (Sirt1) gene expression in skeletal muscle and show that the expression of miR-181a and its target gene is disrupted in skeletal muscle from old mice. Moreover, we show that miR-181a:Sirt1 interactions regulate myotube size. Our results demonstrate that disrupted microRNA:target interactions are likely related to the pathophysiological changes occurring in skeletal muscle during ageing.
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19
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Jönsson ME, Nelander Wahlestedt J, Åkerblom M, Kirkeby A, Malmevik J, Brattaas PL, Jakobsson J, Parmar M. Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor. Development 2016; 142:3166-77. [PMID: 26395143 PMCID: PMC4582174 DOI: 10.1242/dev.122747] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
MicroRNAs (miRNAs) have been implicated in regulating multiple processes during brain development in various species. However, the function of miRNAs in human brain development remains largely unexplored. Here, we provide a comprehensive analysis of miRNA expression of regionalized neural progenitor cells derived from human embryonic stem cells and human foetal brain. We found miR-92b-3p and miR-130b-5p to be specifically associated with neural progenitors and several miRNAs that display both age-specific and region-specific expression patterns. Among these miRNAs, we identified miR-10 to be specifically expressed in the human hindbrain and spinal cord, while being absent from rostral regions. We found that miR-10 regulates a large number of genes enriched for functions including transcription, actin cytoskeleton and ephrin receptor signalling. When overexpressed, miR-10 influences caudalization of human neural progenitor cells. Together, these data confirm a role for miRNAs in establishing different human neural progenitor populations. This dataset also provides a comprehensive resource for future studies investigating the functional role of different miRNAs in human brain development. Summary: The profiling of neural progenitors derived from human ESCs and foetal brain shows that miRNAs display region-specific expression patterns, suggesting that they contribute to establishing regional identity.
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Affiliation(s)
- Marie E Jönsson
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Jenny Nelander Wahlestedt
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Malin Åkerblom
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Agnete Kirkeby
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Josephine Malmevik
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Per Ludvik Brattaas
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Johan Jakobsson
- Lab of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund 221 84, Sweden
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20
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TGF-β induces miR-30d down-regulation and podocyte injury through Smad2/3 and HDAC3-associated transcriptional repression. J Mol Med (Berl) 2015; 94:291-300. [PMID: 26432290 DOI: 10.1007/s00109-015-1340-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/06/2015] [Accepted: 09/07/2015] [Indexed: 01/23/2023]
Abstract
The microRNA-30 family plays important roles in maintaining kidney homeostasis. Patients with focal segmental glomerulosclerosis (FSGS) have reduced miR-30 levels in glomerulus. TGF-β represses miR-30s in kidney podocytes, which leads to cytoskeleton damage and podocyte apoptosis. In this study, we investigated the mechanism by which TGF-β represses miR-30d in vitro. The human miR-30d promoter contains multiple copies of Smad binding element-like sequences. A fragment of 150 base pairs close to the transcription start site was negatively regulated by TGF-β to a similar extent as the 1.8 kb promoter, which was blocked by histone-deacetylase inhibition. TGF-β specifically enhanced HDAC3 expression. Knockdown of HDAC3 by shRNA or a selective inhibitor RGFP966 significantly relieved the repression of miR-30d mRNA and the promoter transcription. TGF-β promoted HDAC3 association with Smad2/3 and NCoR and caused their accumulation at the putative Smad binding site on the miR-30d promoter, which was prohibited by TSA or RGFP966. Furthermore, TSA or RGFP966 treatment reversed TGF-β-induced up-regulation of miR-30d targets Notch1 and p53 and alleviated the podocyte cytoskeleton damage and apoptosis. Taken together, these findings pinpoint that TGF-β represses miR-30d through a Smad2/3-HDAC3-NCoR repression complex and provide novel insights into a potential target for the treatment of podocyte injury-associated glomerulopathies. Key message: MiR-30d promoter is negatively regulated by TGF-β. TGF-β down-regulates miR-30 through Smad signaling pathway. HDAC3 and NCoR are recruited by Smad2/3 to mediate miR-30d repression by TGF-β. HDAC3 acts as a critical player in TGF-β-induced miR-30d repression and podocyte injuries.
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21
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Calloni R, Bonatto D. Scaffolds for Artificial miRNA Expression in Animal Cells. Hum Gene Ther Methods 2015; 26:162-74. [PMID: 26406928 DOI: 10.1089/hgtb.2015.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Artificial miRNAs (amiRNAs) are molecules that have been developed to promote gene silencing in a similar manner to naturally occurring miRNAs. amiRNAs are generally constructed by replacing the mature miRNA sequence in the pre-miRNA stem-loop with a sequence targeting a gene of interest. These molecules offer an interesting alternative to silencing approaches that are based on shRNAs and siRNAs because they present the same efficiency as these options and are less cytotoxic. amiRNAs have mostly been applied to gene knockdown in plants; they have been examined to a lesser extent in animal cells. Therefore, this article reviews the amiRNAs that have been developed for animal cells and focuses on the miRNA scaffolds that can already be applied to construct the artificial counterparts, as well as on the different approaches that have been described to promote amiRNA expression and silencing efficiency. Furthermore, the availability of amiRNA libraries and other tools that can be used to design and construct these molecules is briefly discussed, along with an overview of the therapeutic applications for which amiRNAs have already been evaluated.
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Affiliation(s)
- Raquel Calloni
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
| | - Diego Bonatto
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
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22
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Zhang YR, Gui LS, Li YK, Jiang BJ, Wang HC, Zhang YY, Zan LS. Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus). Int J Mol Sci 2015. [PMID: 26225956 PMCID: PMC4581179 DOI: 10.3390/ijms160816966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p < 0.05) except SNP1/8 (p > 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p < 0.05) greater body length than those with Hap2/Hap2. Our results indicate that variations in the SMO gene could affect body size traits of Qinchuan cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.
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Affiliation(s)
- Ya-Ran Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lin-Sheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Yao-Kun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Bi-Jie Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Hong-Cheng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ying-Ying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
- National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, Shaanxi, China.
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23
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Kaitetzidou E, Xiang J, Antonopoulou E, Tsigenopoulos CS, Sarropoulou E. Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax). Physiol Genomics 2015; 47:158-69. [DOI: 10.1152/physiolgenomics.00001.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/23/2015] [Indexed: 01/06/2023] Open
Abstract
Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass ( Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA.
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Affiliation(s)
- E. Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - J. Xiang
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, New York
| | - E. Antonopoulou
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - C. S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
| | - E. Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
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24
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Ma J, Wang H, Liu R, Jin L, Tang Q, Wang X, Jiang A, Hu Y, Li Z, Zhu L, Li R, Li M, Li X. The miRNA Transcriptome Directly Reflects the Physiological and Biochemical Differences between Red, White, and Intermediate Muscle Fiber Types. Int J Mol Sci 2015; 16:9635-53. [PMID: 25938964 PMCID: PMC4463610 DOI: 10.3390/ijms16059635] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/24/2015] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that can regulate their target genes at the post-transcriptional level. Skeletal muscle comprises different fiber types that can be broadly classified as red, intermediate, and white. Recently, a set of miRNAs was found expressed in a fiber type-specific manner in red and white fiber types. However, an in-depth analysis of the miRNA transcriptome differences between all three fiber types has not been undertaken. Herein, we collected 15 porcine skeletal muscles from different anatomical locations, which were then clearly divided into red, white, and intermediate fiber type based on the ratios of myosin heavy chain isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e., red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. Furthermore, we constructed small RNA libraries for PL, PMM, and LDM using a deep sequencing approach. Results showed that the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism that achieves the phenotypic diversity of skeletal muscles.
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Affiliation(s)
- Jideng Ma
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Hongmei Wang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Rui Liu
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Long Jin
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Qianzi Tang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Xun Wang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Anan Jiang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Yaodong Hu
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Zongwen Li
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Li Zhu
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Mingzhou Li
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| | - Xuewei Li
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
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25
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Overexpression of NF90-NF45 Represses Myogenic MicroRNA Biogenesis, Resulting in Development of Skeletal Muscle Atrophy and Centronuclear Muscle Fibers. Mol Cell Biol 2015; 35:2295-308. [PMID: 25918244 DOI: 10.1128/mcb.01297-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/18/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in the progression and suppression of various diseases through translational inhibition of target mRNAs. Therefore, the alteration of miRNA biogenesis induces several diseases. The nuclear factor 90 (NF90)-NF45 complex is known as a negative regulator in miRNA biogenesis. Here, we showed that NF90-NF45 double-transgenic (dbTg) mice develop skeletal muscle atrophy and centronuclear muscle fibers in adulthood. Subsequently, we found that the levels of myogenic miRNAs, including miRNA 133a (miR-133a), which promote muscle maturation, were significantly decreased in the skeletal muscle of NF90-NF45 dbTg mice compared with those in wild-type mice. However, levels of primary transcripts of the miRNAs (pri-miRNAs) were clearly elevated in NF90-NF45 dbTg mice. This result indicated that the NF90-NF45 complex suppressed miRNA production through inhibition of pri-miRNA processing. This finding was supported by the fact that processing of pri-miRNA 133a-1 (pri-miR-133a-1) was inhibited via binding of NF90-NF45 to the pri-miRNA. Finally, the level of dynamin 2, a causative gene of centronuclear myopathy and concomitantly a target of miR-133a, was elevated in the skeletal muscle of NF90-NF45 dbTg mice. Taken together, we conclude that the NF90-NF45 complex induces centronuclear myopathy through increased dynamin 2 expression by an NF90-NF45-induced reduction of miR-133a expression in vivo.
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Nachtigall PG, Dias MC, Carvalho RF, Martins C, Pinhal D. MicroRNA-499 expression distinctively correlates to target genes sox6 and rod1 profiles to resolve the skeletal muscle phenotype in Nile tilapia. PLoS One 2015; 10:e0119804. [PMID: 25793727 PMCID: PMC4368118 DOI: 10.1371/journal.pone.0119804] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 02/02/2015] [Indexed: 11/22/2022] Open
Abstract
A class of small non-coding RNAs, the microRNAs (miRNAs), has been shown to be essential for the regulation of specific cell pathways, including skeletal muscle development, maintenance and homeostasis in vertebrates. However, the relative contribution of miRNAs for determining the red and white muscle cell phenotypes is far from being fully comprehended. To better characterize the role of miRNA in skeletal muscle cell biology, we investigated muscle-specific miRNA (myomiR) signatures in Nile tilapia fish. Quantitative (RT-qPCR) and spatial (FISH) expression analyses revealed a highly differential expression (forty-four-fold) of miR-499 in red skeletal muscle compared to white skeletal muscle, whereas the remaining known myomiRs were equally expressed in both muscle cell types. Detailed examination of the miR-499 targets through bioinformatics led us to the sox6 and rod1 genes, which had low expression in red muscle cells according to RT-qPCR, FISH, and protein immunofluorescence profiling experiments. Interestingly, we verified that the high expression of miR-499 perfectly correlates with a low expression of sox6 and rod1 target genes, as verified by a distinctive predominance of mRNA destabilization and protein translational decay to these genes, respectively. Through a genome-wide comparative analysis of SOX6 and ROD1 protein domains and through an in silico gene regulatory network, we also demonstrate that both proteins are essentially similar in vertebrate genomes, suggesting their gene regulatory network may also be widely conserved. Overall, our data shed light on the potential regulation of targets by miR-499 associated with the slow-twitch muscle fiber type phenotype. Additionally the results provide novel insights into the evolutionary dynamics of miRNA and target genes enrolled in a putative constrained molecular pathway in the skeletal muscle cells of vertebrates.
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Affiliation(s)
- Pedro G. Nachtigall
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Marcos C. Dias
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
- Health Sciences Institute, Federal University of Mato Grosso (UFMT), Sinop, Mato Grosso, 78550-000, Brazil
| | - Robson F. Carvalho
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Danillo Pinhal
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
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miR-30 family microRNAs regulate myogenic differentiation and provide negative feedback on the microRNA pathway. PLoS One 2015; 10:e0118229. [PMID: 25689854 PMCID: PMC4331529 DOI: 10.1371/journal.pone.0118229] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022] Open
Abstract
microRNAs (miRNAs) are short non-coding RNAs that can mediate changes in gene expression and are required for the formation of skeletal muscle (myogenesis). With the goal of identifying novel miRNA biomarkers of muscle disease, we profiled miRNA expression using miRNA-seq in the gastrocnemius muscles of dystrophic mdx4cv mice. After identifying a down-regulation of the miR-30 family (miR-30a-5p, -30b, -30c, -30d and -30e) when compared to C57Bl/6 (WT) mice, we found that overexpression of miR-30 family miRNAs promotes differentiation, while inhibition restricts differentiation of myoblasts in vitro. Additionally, miR-30 family miRNAs are coordinately down-regulated during in vivo models of muscle injury (barium chloride injection) and muscle disuse atrophy (hindlimb suspension). Using bioinformatics tools and in vitro studies, we identified and validated Smarcd2, Snai2 and Tnrc6a as miR-30 family targets. Interestingly, we show that by targeting Tnrc6a, miR-30 family miRNAs negatively regulate the miRNA pathway and modulate both the activity of muscle-specific miR-206 and the levels of protein synthesis. These findings indicate that the miR-30 family may be an interesting biomarker of perturbed muscle homeostasis and muscle disease.
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Alli Shaik A, Wee S, Li RHX, Li Z, Carney TJ, Mathavan S, Gunaratne J. Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome. J Proteome Res 2014; 13:5536-50. [DOI: 10.1021/pr5005136] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Asfa Alli Shaik
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Sheena Wee
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Rachel Hai Xia Li
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Zhen Li
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Tom J. Carney
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
| | - Sinnakaruppan Mathavan
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Jayantha Gunaratne
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
- Department
of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
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Salas-Huetos A, Blanco J, Vidal F, Mercader JM, Garrido N, Anton E. New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa. Fertil Steril 2014; 102:213-222.e4. [PMID: 24794309 DOI: 10.1016/j.fertnstert.2014.03.040] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To characterize the microRNA (miRNA) expression profile in spermatozoa from human fertile individuals and their implications in human fertility. DESIGN The expression levels of 736 miRNAs were evaluated using TaqMan arrays. Ontologic analyses were performed to determine the presence of enriched biological processes among their targets. SETTING University research and clinical institutes. PATIENT(S) Ten individuals with normal seminogram, standard karyotype, and proven fertility. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Expression levels of 736 miRNAs, presence of enriched metabolic routes among their targets, homogeneity of the population, influence of demographic features in the results, presence of miRNA stable pairs, and best miRNA normalizing candidates. RESULT(S) A total of 221 miRNAs were consistently present in all individuals, 452 were only detected in some individuals, and 63 did not appear in any sample. The ontologic analysis of the 2,356 potential targets of the ubiquitous miRNAs showed an enrichment of processes related to cell differentiation, development, morphogenesis, and embryogenesis. None of the miRNAs were significantly correlated with age, semen volume, sperm concentration, motility, or morphology. Correlations between samples were statistically significant, indicating a high homogeneity of the population. A set of 48 miRNA pairs displayed a stable expression, a particular behavior that is discussed in relationship to their usefulness as fertility biomarkers. Hsa-miR-532-5p, hsa-miR-374b-5p, and hsa-miR-564 seemed to be the best normalizing miRNA candidates. CONCLUSION(S) Human sperm contain a stable population of miRNAs potentially related to embryogenesis and spermatogenesis.
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Affiliation(s)
- Albert Salas-Huetos
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Joan Blanco
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Francesca Vidal
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - Josep M Mercader
- Joint Institution for Research in Biomedicine-Barcelona Supercomputing Center Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Nicolás Garrido
- Laboratorio de Andrología y Banco de Semen, Instituto Valenciano de Infertilidad Valencia, Valencia, Spain
| | - Ester Anton
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain.
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Zhang Y, Yang WQ, Zhu H, Qian YY, Zhou L, Ren YJ, Ren XC, Zhang L, Liu XP, Liu CG, Ming ZJ, Li B, Chen B, Wang JR, Liu YB, Yang JM. Regulation of autophagy by miR-30d impacts sensitivity of anaplastic thyroid carcinoma to cisplatin. Biochem Pharmacol 2013; 87:562-70. [PMID: 24345332 DOI: 10.1016/j.bcp.2013.12.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 12/11/2022]
Abstract
miR-30d has been observed to be significantly down-regulated in human anaplastic thyroid carcinoma (ATC), and is believed to be an important event in thyroid cell transformation. In this study, we found that miR-30d has a critical role in modulating sensitivity of ATC cells to cisplatin, a commonly used chemotherapeutic drug for treatment of this neoplasm. Using a mimic of miR-30d, we demonstrated that miR-30d could negatively regulate the expression of beclin 1, a key autophagy gene, leading to suppression of the cisplatin-activated autophagic response that protects ATC cells from apoptosis. A reporter gene assay demonstrated that the binding sequences of miR-30d in the beclin 1-3' UTR was the region required for the inhibition of beclin 1 expression by this miRNA. We further showed that inhibition of the beclin 1-mediated autophagy by the miR-30d mimic sensitized ATC cells to cisplatin both in vitro (cell culture) and in vivo (animal xenograft model). These results suggest that dysregulation of miR-30d in ATC cells is responsible for the insensitivity to cisplatin by promoting autophagic survival. Thus, miR-30d may be exploited as a potential target for therapeutic intervention in the treatment of ATC.
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Affiliation(s)
- Y Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China.
| | - W Q Yang
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - H Zhu
- Department of Surgery, School of Medicine, Ohio State University, USA
| | - Y Y Qian
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - L Zhou
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - Y J Ren
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - X C Ren
- Pharmacology and The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - L Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - X P Liu
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX, USA
| | - C G Liu
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX, USA
| | - Z J Ming
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - B Li
- Department of Surgery, School of Medicine, Ohio State University, USA
| | - B Chen
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - J R Wang
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China
| | - Y B Liu
- Department of General Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - J M Yang
- Department of Pharmacology, College of Pharmaceutical Sciences, Hematology Center of Cyrus Tang Medical Institute, Affiliated Changshu Hospital, Soochow University, Suzhou, Jiangsu Province, China; Pharmacology and The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
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