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Farrell CE, Liu X, Yagan NO, Suda AC, Cerqueira DM, Bodnar AJ, Kashlan OB, Subramanya AR, Ho J, Butterworth MB. MicroRNA-19 is regulated by aldosterone in a sex-specific manner to alter kidney sodium transport. Am J Physiol Cell Physiol 2024; 326:C282-C293. [PMID: 38047299 PMCID: PMC11192485 DOI: 10.1152/ajpcell.00385.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
A key regulator of blood pressure homeostasis is the steroid hormone aldosterone, which is released as the final signaling hormone of the renin-angiotensin-aldosterone-signaling (RAAS) system. Aldosterone increases sodium (Na+) reabsorption in the kidney distal nephron to regulate blood volume. Unregulated RAAS signaling can lead to hypertension and cardiovascular disease. The serum and glucocorticoid kinase (SGK1) coordinates much of the Na+ reabsorption in the cortical collecting duct (CCD) tubular epithelial cells. We previously demonstrated that aldosterone alters the expression of microRNAs (miRs) in CCD principal cells. The aldosterone-regulated miRs can modulate Na+ transport and the cellular response to aldosterone signaling. However, the sex-specific regulation of miRs by aldosterone in the kidney distal nephron has not been explored. In this study, we report that miR-19, part of the miR-17-92 cluster, is upregulated in female mouse CCD cells in response to aldosterone activation. Mir-19 binding to the 3'-untranslated region of SGK1 was confirmed using a dual-luciferase reporter assay. Increasing miR-19 expression in CCD cells decreased SGK1 message and protein expression. Removal of this cluster using a nephron-specific, inducible knockout mouse model increased SGK1 expression in female mouse CCD cells. The miR-19-induced decrease in SGK1 protein expression reduced the response to aldosterone stimulation and may account for sex-specific differences in aldosterone signaling. By examining evolution of the miR-17-92 cluster, phylogenetic sequence analysis indicated that this cluster arose at the same time that other Na+-sparing and salt regulatory proteins, specifically SGK1, first emerged, indicating a conserved role for these miRs in kidney function of salt and water homeostasis.NEW & NOTEWORTHY Expression of the microRNA-17-92 cluster is upregulated by aldosterone in mouse cortical collecting duct principal cells, exclusively in female mice. MiR-19 in this cluster targets the serum and glucocorticoid kinase (SGK1) to downregulate both mRNA and protein expression, resulting in a decrease in sodium transport across epithelial cells of the collecting duct. The miR-17-92 cluster is evolutionarily conserved and may act as a novel feedback regulator for aldosterone signaling in females.
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Affiliation(s)
- Corinne E Farrell
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Xiaoning Liu
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Nejla Ozbaki Yagan
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Amanda C Suda
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Debora M Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Andrew J Bodnar
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ossama B Kashlan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Michael B Butterworth
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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2
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Tan X, Zhu T, Zhang L, Fu L, Hu Y, Li H, Li C, Zhang J, Liang B, Liu J. miR-669a-5p promotes adipogenic differentiation and induces browning in preadipocytes. Adipocyte 2022; 11:120-132. [PMID: 35094659 PMCID: PMC8803067 DOI: 10.1080/21623945.2022.2030570] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Obesity is a major global health issue that contributes to the occurrence of metabolic disorders. Based on this fact, understanding the underlying mechanisms and to uncover promising therapeutic approaches for obesity have attracted intense investigation. Brown adipose tissue (BAT) can help burns excess calories. Therefore, promoting White adipose tissue (WAT) browning and BAT activation is an attractive strategy for obesity treatment. MicroRNAs (miRNAs) are small, non-coding RNAs, which are involved in regulation of adipogenic processes and metabolic functions. Evidence is accumulating that miRNAs are important regulators for both brown adipocyte differentiation and white adipocyte browning. Here we report that the expression of miR-669a-5p increases during the adipogenic differentiation of 3T3-L1 and C3H10T1/2 adipocytes. miR-669a-5p supplementation promotes adipogenic differentiation and causes browning of 3T3-L1 and C3H10T1/2 cells. Moreover, the expression of miR-669a-5p is upregulated in iWAT of mice exposed to cold. These data demonstrate that miR-669a-5p plays a role in regulating adipocyte differentiation and fat browning.Abbreviations: Acadl: long-chain acyl-Coenzyme A dehydrogenase; Acadm: medium-chain acyl-Coenzyme A dehydrogenase; Acadvl: very long-chain acyl-Coenzyme A dehydrogenase, very long chain; Aco2: mitochondrial aconitase 2; BAT: brown adipose tissue; Bmper: BMP-binding endothelial regulator; Cpt1-b:carnitine palmitoyltransferase 1b; Cpt2: carnitine palmitoyltransferase 2; Crat: carnitine acetyltransferase; Cs: citrate synthase; C2MC: Chromosome 2 miRNA cluster; DMEM: Dulbecco's modified Eagle medium; eWAT: epididymal white adipose tissue; ETC: electron transport chain; FAO: fatty acid oxidation; Fabp4:fatty acid binding protein 4; FBS: fetal bovine serum; Hadha: hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha; Hadhb: hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit beta; HFD: high fat diet; Idh3a: isocitrate dehydrogenase 3 alpha; iWAT: inguinal subcutaneous white adipose tissue; Lpl: lipoprotein lipase; Mdh2: malate dehydrogenase 2; NBCS: NewBorn Calf Serum; mt-Nd1: mitochondrial NADH dehydrogenase 1; Ndufb8:ubiquinone oxidoreductase subunit B8; Nrf1: nuclear respiratory factor 1; Pgc1α: peroxisome proliferative activated receptor gamma coactivator 1 alpha; Pgc1b: peroxisome proliferative activated receptor, gamma, coactivator 1 beta; Pparγ: peroxisome proliferator activated receptor gamma; Prdm16: PR domain containing 16; Rgs4: regulator of G-protein signaling 4; Sdhb: succinate dehydrogenase complex, subunit B; Sdhc: succinate dehydrogenase complex, subunit C; Sdhd: succinate dehydrogenase complex, subunit D; Sh3d21: SH3 domain containing 21; Sfmbt2: Scm-like with four mbt domains 2; TG: triglyceride; TCA: tricarboxylic acid cycle; Tfam: transcription factor A, mitochondrial; TMRE: tetramethylrhodamine, methyl ester; Ucp1: uncoupling protein 1; Uqcrc2: ubiquinol cytochrome c reductase core protein 2; WAT: White adipose tissue.
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Affiliation(s)
- Xiaoqiong Tan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Tingting Zhu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Linqiang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Lin Fu
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Ying Hu
- School of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Huiqin Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Chengbin Li
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingjing Zhang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Bin Liang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Jing Liu
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
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3
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MicroRNA Signature and Cellular Characterization of Undifferentiated and Differentiated House Ear Institute-Organ of Corti 1 (HEI-OC1) Cells. J Assoc Res Otolaryngol 2022; 23:467-489. [PMID: 35546217 PMCID: PMC9094604 DOI: 10.1007/s10162-022-00850-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/20/2022] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expressions and control a wide variety of cellular functions. House Ear Institute-Organ of Corti 1 (HEI-OC1) cells are widely used to screen ototoxic drugs and to investigate cellular and genetic alterations in response to various conditions. HEI-OC1 cells are almost exclusively studied under permissive conditions that promote cell replication at the expense of differentiation. Many researchers suggest that permissive culture condition findings are relevant to understanding human hearing disorders. The mature human cochlea however consists of differentiated cells and lacks proliferative capacity. This study therefore aimed to compare the miRNA profiles and cellular characteristics of HEI-OC1 cells cultured under permissive (P-HEI-OC1) and non-permissive (NP-HEI-OC1) conditions. A significant increase in the level of expression of tubulin β1 class VI (Tubb1), e-cadherin (Cdh1), espin (Espn), and SRY (sex determining region Y)-box2 (Sox2) mRNAs was identified in non-permissive cells compared with permissive cells (P < 0.05, Kruskal–Wallis H test, 2-sided). miR-200 family, miR-34b/c, and miR-449a/b functionally related cluster miRNAs, rodent-specific maternally imprinted gene Sfmbt2 intron 10th cluster miRNAs (-466a/ -467a), and miR-17 family were significantly (P < 0.05, Welch’s t-test, 2-tailed) differentially expressed in non-permissive cells when compared with permissive cells. Putative target genes were significantly predominantly enriched in mitogen-activated protein kinase (MAPK), epidermal growth factor family of receptor tyrosine kinases (ErbB), and Ras signaling pathways in non-permissive cells compared with permissive cells. This distinct miRNA signature of differentiated HEI-OC1 cells could help in understanding miRNA-mediated cellular responses in the adult cochlea.
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Matoba S, Kozuka C, Miura K, Inoue K, Kumon M, Hayashi R, Ohhata T, Ogura A, Inoue A. Noncanonical imprinting sustains embryonic development and restrains placental overgrowth. Genes Dev 2022; 36:483-494. [PMID: 35483741 PMCID: PMC9067403 DOI: 10.1101/gad.349390.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/08/2022] [Indexed: 01/23/2023]
Abstract
In this study, Matoba et al. use a combinatorial maternal KO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, and show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Their findings provide evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth. Genomic imprinting regulates parental origin-dependent monoallelic gene expression. It is mediated by either germline differential methylation of DNA (canonical imprinting) or oocyte-derived H3K27me3 (noncanonical imprinting) in mice. Depletion of Eed, an essential component of Polycomb repressive complex 2, results in genome-wide loss of H3K27me3 in oocytes, which causes loss of noncanonical imprinting (LOI) in embryos. Although Eed maternal KO (matKO) embryos show partial lethality after implantation, it is unknown whether LOI itself contributes to the developmental phenotypes of these embryos, which makes it unclear whether noncanonical imprinting is developmentally relevant. Here, by combinatorial matKO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, we show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Moreover, we found that the placentae of Eed matKO embryos are remarkably enlarged in a manner independent of Xist LOI. Heterozygous deletion screening of individual autosomal noncanonical imprinted genes suggests that LOI of the Sfmbt2 miRNA cluster chromosome 2 miRNA cluster (C2MC), solute carrier family 38 member 4 (Slc38a4), and Gm32885 contributes to the placental enlargement. Taken together, our study provides evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth.
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Affiliation(s)
- Shogo Matoba
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Japan
| | - Chisayo Kozuka
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kento Miura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mami Kumon
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ryoya Hayashi
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.,The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Azusa Inoue
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
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5
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MiR-466b-3p/HDAC7 meditates transgenerational inheritance of testicular testosterone synthesis inhibition induced by prenatal dexamethasone exposure. Biochem Pharmacol 2022; 199:115018. [DOI: 10.1016/j.bcp.2022.115018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 11/23/2022]
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6
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Wu C, Wang C, Zhai B, Zhao Y, Zhao Z, Yuan Z, Zhang M, Tian K, Fu X. Study of microRNA Expression Profile in Different Regions of Ram Epididymis. Reprod Domest Anim 2021; 56:1209-1219. [PMID: 34169586 DOI: 10.1111/rda.13978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
The regional expression of epididymal genes provides a guarantee for sperm maturation. As a class of endogenous non-coding small RNAs, microRNAs (miRNAs) play an important role in spermatogenesis, maturation and fertilization. Currently, the regulatory role of miRNA in the epididymis is poorly understood. Here, transcriptome sequencing was used to analyse miRNA expression profiles in three regions of the epididymis of rams, including caput, corpus and cauda. The results showed that there were 13 known miRNAs between the caput and corpus controls, 29 between the caput and cauda and 22 differences between the corpus and cauda. Based on the analysis of miRNA target genes by GO and KEGG, a negative regulation network of miRNA-mRNA was constructed in which let-7, miR-541-5p, miR-133b and miR-150 may play an important regulatory role in the maturation regulation of ram epididymal sperm. This research provides a reference for studying the regulation mechanism of sperm maturation in male epididymis and improving semen quality and male reproductive performance.
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Affiliation(s)
- Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.,Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China.,Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chunxin Wang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Bo Zhai
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yunhui Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhuo Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhiyu Yuan
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Mingxin Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
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7
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Haig D, Mainieri A. The Evolution of Imprinted microRNAs and Their RNA Targets. Genes (Basel) 2020; 11:genes11091038. [PMID: 32899179 PMCID: PMC7564603 DOI: 10.3390/genes11091038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/19/2022] Open
Abstract
Mammalian genomes contain many imprinted microRNAs. When an imprinted miRNA targets an unimprinted mRNA their interaction may have different fitness consequences for the loci encoding the miRNA and mRNA. In one possible outcome, the mRNA sequence evolves to evade regulation by the miRNA by a simple change of target sequence. Such a response is unavailable if the targeted sequence is strongly constrained by other functions. In these cases, the mRNA evolves to accommodate regulation by the imprinted miRNA. These evolutionary dynamics are illustrated using the examples of the imprinted C19MC cluster of miRNAs in primates and C2MC cluster in mice that are paternally expressed in placentas. The 3′ UTR of PTEN, a gene with growth-related and metabolic functions, appears to be an important target of miRNAs from both clusters.
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Zhang F, Zhang Y, Lv X, Xu B, Zhang H, Yan J, Li H, Wu L. Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells. Mol Biol Evol 2019; 36:663-678. [PMID: 30649414 PMCID: PMC6445303 DOI: 10.1093/molbev/msz001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are important posttranscriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during mammalian spermatogenesis are lacking. Herein, we sequenced small RNAs in highly purified mouse spermatogenic cells at different stages. We found that a family of X-linked miRNAs named spermatogenesis-related miRNAs (spermiRs) is predominantly expressed in the early meiotic phases and has a conserved testis-specific high expression pattern in different mammals. We identified one spermiR homolog in opossum; this homolog might originate from THER1, a retrotransposon that is active in marsupials but extinct in current placental mammals. SpermiRs have expanded rapidly with mammalian evolution and are diverged into two clades, spermiR-L and spermiR-R, which are likely to have been generated at least in part by tandem duplication mediated by flanking retrotransposable elements. Notably, despite having undergone highly frequent lineage-specific duplication events, the sequences encoding all spermiR family members are strictly located between two protein-coding genes, Slitrk2 and Fmr1. Moreover, spermiR-Ls and spermiR-Rs have evolved different expression patterns during spermatogenesis in different mammals. Intriguingly, the seed sequences of spermiRs, which are critical for the recognition of target genes, are highly divergent within and among mammals, whereas spermiR target genes largely overlap. When miR-741, the most highly expressed spermiR, is knocked out in cultured mouse spermatogonial stem cells (SSCs), another spermiR, miR-465a-5p, is dramatically upregulated and becomes the most abundant miRNA. Notably, miR-741−/− SSCs grow normally, and the genome-wide expression levels of mRNAs remain unchanged. All these observations indicate functional compensation between spermiR family members and strong coevolution between spermiRs and their targets.
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Affiliation(s)
- Fengjuan Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaolong Lv
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Hongdao Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haipeng Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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9
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Identification of novel mouse and rat CB1R isoforms and in silico modeling of human CB1R for peripheral cannabinoid therapeutics. Acta Pharmacol Sin 2019; 40:387-397. [PMID: 30202012 DOI: 10.1038/s41401-018-0152-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/18/2018] [Indexed: 01/28/2023] Open
Abstract
Targeting peripheral CB1R is desirable for the treatment of metabolic syndromes without adverse neuropsychiatric effects. We previously reported a human hCB1b isoform that is selectively enriched in pancreatic beta-cells and hepatocytes, providing a potential peripheral therapeutic hCB1R target. It is unknown whether there are peripherally enriched mouse and rat CB1R (mCB1 and rCB1, respectively) isoforms. In this study, we found no evidence of peripherally enriched rodent CB1 isoforms; however, some mCB1R isoforms are absent in peripheral tissues. We show that the mouse Cnr1 gene contains six exons that are transcribed from a single promoter. We found that mCB1A is a spliced variant of extended exon 1 and protein-coding exon 6; mCB1B is a novel spliced variant containing unspliced exon 1, intron 1, and exon 2, which is then spliced to exon 6; and mCB1C is a spliced variant including all 6 exons. Using RNAscope in situ hybridization, we show that the isoforms mCB1A and mCB1B are expressed at a cellular level and colocalized in GABAergic neurons in the hippocampus and cortex. RT-qPCR reveals that mCB1A and mCB1B are enriched in the brain, while mCB1B is not expressed in the pancreas or the liver. Rat rCB1R isoforms are differentially expressed in primary cultured neurons, astrocytes, and microglia. We also investigated modulation of Cnr1 expression by insulin in vivo and carried out in silico modeling of CB1R with JD5037, a peripherally restricted CB1R inverse agonist, using the published crystal structure of hCB1R. The results provide models for future CB1R peripheral targeting.
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Zhang S, An Q, Hu P, Wu X, Pan X, Peng W, Wang R, Gan J, Chen D, Li Z, Wang T, Zhou G. Core regulatory RNA molecules identified in articular cartilage stem/progenitor cells during osteoarthritis progression. Epigenomics 2019; 11:669-684. [PMID: 30775942 DOI: 10.2217/epi-2018-0212] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aim: To assess cartilage-derived stem/progenitor cells (CSPCs) in osteoarthritis (OA) by employing mRNA-miRNA-circRNA-lncRNA network biology approach. Methods: Differentially expressed (DE) RNAs in CSPCs from 2-/4-/8-month-old STR/Ort and CBA mice were identified to construct networks via RNA sequencing. Results: Compared with age-matched CBA mice, 4-/8-month-old STR/Ort mice had cartilage lesions and their CSPCs exhibited lower proliferative and differentiation capacity (decreased CD44 and CD90), and identified 7082 DE RNAs in STR/Ort mice were associated with strain differences or OA progression. OA-related core RNAs were identified via the networks constructed with the predominant DE RNAs, which were involved in the signaling pathways (NF-κB/MAPK/Hippo/Wnt/TGF-β/cytoskeleton organization). The core RNAs (miR-322-5p/miR-493-5p/miR-378c/CPNE1/Cdh2/PRDM16/CTGF/NCAM1) were validated in CSPCs from OA patients. Conclusion: RNA-based networks identifying core RNAs and signaling pathways contribute to CSPC-dependent OA mechanisms.
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Affiliation(s)
- Shuai Zhang
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Qier An
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Peilin Hu
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Xiaomin Wu
- Department of Orthopedic & Traumatology, Shenzhen BaoAn People Hospital Affiliated Southern Medical University, Shenzhen, Guangdong 518101, PR China
| | - Xiaohua Pan
- Department of Orthopedic & Traumatology, Shenzhen BaoAn People Hospital Affiliated Southern Medical University, Shenzhen, Guangdong 518101, PR China
| | - Wenjin Peng
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Rikang Wang
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Jingyi Gan
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Di Chen
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - Zhen Li
- Shenzhen Alps Cell Sci-Tech Co. Ltd, Longhua District, Shenzhen, PR China
| | - Tianfu Wang
- Guangdong Key Laboratory for Biomedical Measurements & Ultrasound Imaging, School of Biomedical Engineering, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Guangqian Zhou
- Department of Medical Cell Biology & Genetics, Guangdong Key Laboratory of Genomic Stability & Disease Prevention, Shenzhen Key Laboratory of Anti-aging & Regenerative Medicine, & Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
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11
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Malnou EC, Umlauf D, Mouysset M, Cavaillé J. Imprinted MicroRNA Gene Clusters in the Evolution, Development, and Functions of Mammalian Placenta. Front Genet 2019; 9:706. [PMID: 30713549 PMCID: PMC6346411 DOI: 10.3389/fgene.2018.00706] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
In mammals, the expression of a subset of microRNA (miRNA) genes is governed by genomic imprinting, an epigenetic mechanism that confers monoallelic expression in a parent-of-origin manner. Three evolutionarily distinct genomic intervals contain the vast majority of imprinted miRNA genes: the rodent-specific, paternally expressed C2MC located in intron 10 of the Sfmbt2 gene, the primate-specific, paternally expressed C19MC positioned at human Chr.19q13.4 and the eutherian-specific, maternally expressed miRNAs embedded within the imprinted Dlk1-Dio3 domains at human 14q32 (also named C14MC in humans). Interestingly, these imprinted miRNA genes form large clusters composed of many related gene copies that are co-expressed with a marked, or even exclusive, localization in the placenta. Here, we summarize our knowledge on the evolutionary, molecular, and physiological relevance of these epigenetically-regulated, recently-evolved miRNAs, by focusing on their roles in placentation and possibly also in pregnancy diseases (e.g., preeclampsia, intrauterine growth restriction, preterm birth).
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Affiliation(s)
- E Cécile Malnou
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - David Umlauf
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Maïlys Mouysset
- Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
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12
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Besharat ZM, Sabato C, Po A, Gianno F, Abballe L, Napolitano M, Miele E, Giangaspero F, Vacca A, Catanzaro G, Ferretti E. Low Expression of miR-466f-3p Sustains Epithelial to Mesenchymal Transition in Sonic Hedgehog Medulloblastoma Stem Cells Through Vegfa-Nrp2 Signaling Pathway. Front Pharmacol 2018; 9:1281. [PMID: 30483126 PMCID: PMC6240675 DOI: 10.3389/fphar.2018.01281] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
High-throughput analysis has improved the knowledge of medulloblastoma (MB), the leading cause of cancer related death in children, allowing a better comprehension of the key molecular pathways in MB pathogenesis. However, despite these advances, 30% of patients still die from the disease and survivors face severe long-term side effects. Cancer stem cells (CSCs) represent a subset of cells that not only drive tumorigenesis, but are also one of the main determinants of chemoresistance. Epithelial mesenchymal transition (EMT) is a hallmark of cancer and up to now few data is available in MB. To give insight into the role of the EMT process in maintaining the mesenchymal phenotype of CSCs, we analyzed the expression of EMT related transcripts and microRNAs in these cells. We firstly isolated CSCs from Sonic Hedgehog (SHH) MB derived from Ptch1 heterozygous mice and compared their expression level of EMT-related transcripts and microRNAs with cerebellar NSCs. We identified two molecules linked to SHH and EMT, Vegfa and its receptor Nrp2, over-expressed in SHH MB CSCs. Inhibition of Vegfa showed impairment of cell proliferation and self-renewal ability of CSCs concurrent with an increase of the expression of the EMT gene, E-cadherin, and a decrease of the EMT marker, Vimentin. Moreover, among deregulated microRNAs, we identified miR-466f-3p, a validated inhibitor of both Vegfa and Nrp2. These results allowed us to describe a new EMT molecular network, involving the down-regulation of miR-466f-3p together with the concordant up-regulation of Vegfa and Nrp2, that sustains the mesenchymal phenotype of SHH MB CSCs.
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Affiliation(s)
| | - Claudia Sabato
- Department of Molecular Medicine, Sapienza University, Rome, Italy.,Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Pathological Science, Sapienza University, Rome, Italy
| | - Luana Abballe
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Evelina Miele
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Pathological Science, Sapienza University, Rome, Italy.,IRCCS Neuromed, Isernia, Italy
| | - Alessandra Vacca
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Rome, Italy.,IRCCS Neuromed, Isernia, Italy
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13
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Trontti K, Väänänen J, Sipilä T, Greco D, Hovatta I. Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression. RNA (NEW YORK, N.Y.) 2018; 24:643-655. [PMID: 29445025 PMCID: PMC5900563 DOI: 10.1261/rna.064881.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism.
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Affiliation(s)
- Kalevi Trontti
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Juho Väänänen
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Tessa Sipilä
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
| | - Dario Greco
- Insitute of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki FI-00790, Finland
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14
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Becker W, Nagarkatti M, Nagarkatti PS. miR-466a Targeting of TGF-β2 Contributes to FoxP3 + Regulatory T Cell Differentiation in a Murine Model of Allogeneic Transplantation. Front Immunol 2018; 9:688. [PMID: 29686677 PMCID: PMC5900016 DOI: 10.3389/fimmu.2018.00688] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/20/2018] [Indexed: 12/25/2022] Open
Abstract
The promise of inducing immunological tolerance through regulatory T cell (Treg) control of effector T cell function is crucial for developing future therapeutic strategies to treat allograft rejection as well as inflammatory autoimmune diseases. In the current study, we used murine allograft rejection as a model to identify microRNA (miRNA) regulation of Treg differentiation from naïve CD4 cells. We performed miRNA expression array in CD4+ T cells in the draining lymph node (dLN) of mice which received syngeneic or allogeneic grafts to determine the molecular mechanisms that hinder the expansion of Tregs. We identified an increase in miRNA cluster 297-669 (C2MC) after allogeneic transplantation, in CD4+ T cells, such that 10 of the 27 upregulated miRNAs were all from this cluster, with one of its members, mmu-miR-466a-3p (miR-466a-3p), targeting transforming growth factor beta 2 (TGF-β2), as identified through reporter luciferase assay. Transfection of miR-466a-3p in CD4+ T cells led to a decreased inducible FoxP3+ Treg generation while inhibiting miR-466a-3p expression through locked nucleic acid resulting in increased Tregs and a reduction in effector T cells. Furthermore, in vivo inhibition of miR-466a-3p in an allogeneic skin-graft model attenuated T cell response against the graft through an increase in TGF-β2. TGF-β2 was as effective as TGF-β1 at both inducing Tregs and through adoptive transfer, mitigating host effector T cell response against the allograft. Together, the current study demonstrates for the first time a new role for miRNA-466a-3p and TGF-β2 in the regulation of Treg differentiation and thus offers novel avenues to control inflammatory disorders.
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Affiliation(s)
| | | | - Prakash S. Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
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15
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Hayder H, O'Brien J, Nadeem U, Peng C. MicroRNAs: crucial regulators of placental development. Reproduction 2018; 155:R259-R271. [PMID: 29615475 DOI: 10.1530/rep-17-0603] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/03/2018] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding single-stranded RNAs that are integral to a wide range of cellular processes mainly through the regulation of translation and mRNA stability of their target genes. The placenta is a transient organ that exists throughout gestation in mammals, facilitating nutrient and gas exchange and waste removal between the mother and the fetus. miRNAs are expressed in the placenta, and many studies have shown that miRNAs play an important role in regulating trophoblast differentiation, migration, invasion, proliferation, apoptosis, vasculogenesis/angiogenesis and cellular metabolism. In this review, we provide a brief overview of canonical and non-canonical pathways of miRNA biogenesis and mechanisms of miRNA actions. We highlight the current knowledge of the role of miRNAs in placental development. Finally, we point out several limitations of the current research and suggest future directions.
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Affiliation(s)
- Heyam Hayder
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Jacob O'Brien
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Uzma Nadeem
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Chun Peng
- Department of BiologyYork University, Toronto, Ontario, Canada
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16
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Liu JT, Bain LJ. Arsenic Induces Members of the mmu-miR-466-669 Cluster Which Reduces NeuroD1 Expression. Toxicol Sci 2018; 162:64-78. [PMID: 29121352 PMCID: PMC6693399 DOI: 10.1093/toxsci/kfx241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Chronic arsenic exposure can result in adverse development effects including decreased intellectual function, reduced birth weight, and altered locomotor activity. Previous in vitro studies have shown that arsenic inhibits stem cell differentiation. MicroRNAs (miRNAs) are small noncoding RNAs that regulate multiple cellular processes including embryonic development and cell differentiation. The purpose of this study was to examine whether altered miRNA expression was a mechanism by which arsenic inhibited cellular differentiation. The pluripotent P19 mouse embryonal carcinoma cells were exposed to 0 or 0.5 μM sodium arsenite for 9 days during cell differentiation, and changes in miRNA expression was analyzed using microarrays. We found that the expression of several miRNAs important in cellular differentiation, such as miR-9 and miR-199 were decreased by 1.9- and 1.6-fold, respectively, following arsenic exposure, while miR-92a, miR-291a, and miR-709 were increased by 3-, 3.7-, and 1.6-fold, respectively. The members of the miR-466-669 cluster and its host gene, Scm-like with 4 Mbt domains 2 (Sfmbt2), were significantly induced by arsenic from 1.5- to 4-fold in a time-dependent manner. Multiple miRNA target prediction programs revealed that several neurogenic transcription factors appear to be targets of the cluster. When consensus anti-miRNAs targeting the miR-466-669 cluster were transfected into P19 cells, arsenic-exposed cells were able to more effectively differentiate. The consensus anti-miRNAs appeared to rescue the inhibitory effects of arsenic on cell differentiation due to an increased expression of NeuroD1. Taken together, we conclude that arsenic induces the miR-466-669 cluster, and that this induction acts to inhibit cellular differentiation in part due to a repression of NeuroD1.
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Affiliation(s)
| | - Lisa J Bain
- Environmental Toxicology Graduate Program
- Department of Biological Sciences, Clemson University, Clemson, South Carolina 29634
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17
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Xiao D, Qu Y, Pan L, Li X, Mu D. MicroRNAs participate in the regulation of oligodendrocytes development in white matter injury. Rev Neurosci 2018; 29:151-160. [DOI: 10.1515/revneuro-2017-0019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/21/2017] [Indexed: 12/21/2022]
Abstract
AbstractWhite matter injury (WMI) often results in cognitive impairment, behavioral disorders, and cerebral palsy and thus imposes a tremendous burden on society. The cells in brain white matter mainly comprise oligodendrocytes (OLs), astrocytes, and microglia. The dysregulation of OLs development is the pathological hallmark of WMI. Recent studies have demonstrated that microRNAs (miRNAs or miRs) participate in the regulation of OLs development, and the dysregulation of this process represents the pathogenesis of WMI. This review summarizes the progress made in this field that will help clinicians and researchers understand the molecular etiology of WMI and develop miRNAs as new agents for the prevention and treatment of WMI.
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18
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Inoue K, Hirose M, Inoue H, Hatanaka Y, Honda A, Hasegawa A, Mochida K, Ogura A. The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene Is Imprinted and Essential for Placental Development. Cell Rep 2018; 19:949-956. [PMID: 28467908 DOI: 10.1016/j.celrep.2017.04.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/16/2017] [Accepted: 04/05/2017] [Indexed: 10/19/2022] Open
Abstract
MicroRNAs (miRNAs) represent small noncoding RNAs that are involved in physiological and developmental processes by posttranscriptionally inhibiting gene expression. One of the largest miRNA clusters in mice is located in intron 10 of the Sfmbt2 gene, containing 72 miRNA precursor sequences. In this study, we generated mice lacking the entire Sfmbt2 miRNA cluster to elucidate its functions during development. The Sfmbt2 miRNAs were expressed predominantly from the paternal allele in the placenta, as is the host Sfmbt2 gene. Loss of the paternal allele resulted in severely impaired development of the placenta, especially the spongiotrophoblast layer, and frequent lethality or defects of fetuses. The predicted target sequences of the miRNAs and gene expression analysis defined at least nine putative target genes, which function as tumor suppressors or apoptosis inducers. Our study has provided experimental evidence for the indispensable roles of placental miRNAs in trophoblast proliferation and thus fetal development.
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Affiliation(s)
- Kimiko Inoue
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Michiko Hirose
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroki Inoue
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Agricultural Science, Faculty of Agriculture, Tohoku University, Sendai, Miyagi 981-8555, Japan
| | - Yuki Hatanaka
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Arata Honda
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Keiji Mochida
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, BioResource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
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19
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Cai M, Kolluru GK, Ahmed A. Small Molecule, Big Prospects: MicroRNA in Pregnancy and Its Complications. J Pregnancy 2017; 2017:6972732. [PMID: 28713594 PMCID: PMC5496128 DOI: 10.1155/2017/6972732] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/18/2017] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs are small, noncoding RNA molecules that regulate target gene expression in the posttranscriptional level. Unlike siRNA, microRNAs are "fine-tuners" rather than "switches" in the regulation of gene expression; thus they play key roles in maintaining tissue homeostasis. The aberrant microRNA expression is implicated in the disease process. To date, numerous studies have demonstrated the regulatory roles of microRNAs in various pathophysiological conditions. In contrast, the study of microRNA in pregnancy and its associated complications, such as preeclampsia (PE), fetal growth restriction (FGR), and preterm labor, is a young field. Over the last decade, the knowledge of pregnancy-related microRNAs has increased and the molecular mechanisms by which microRNAs regulate pregnancy or its associated complications are emerging. In this review, we focus on the recent advances in the research of pregnancy-related microRNAs, especially their function in pregnancy-associated complications and the potential clinical applications. Here microRNAs that associate with pregnancy are classified as placenta-specific, placenta-associated, placenta-derived circulating, and uterine microRNA according to their localization and origin. MicroRNAs offer a great potential for developing diagnostic and therapeutic targets in pregnancy-related disorders.
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Affiliation(s)
- Meng Cai
- Aston Medical Research Institute, Aston Medical School, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Gopi K. Kolluru
- Aston Medical Research Institute, Aston Medical School, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Asif Ahmed
- Aston Medical Research Institute, Aston Medical School, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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20
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Preusse M, Schughart K, Pessler F. Host Genetic Background Strongly Affects Pulmonary microRNA Expression before and during Influenza A Virus Infection. Front Immunol 2017; 8:246. [PMID: 28377766 PMCID: PMC5359533 DOI: 10.3389/fimmu.2017.00246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/20/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Expression of host microRNAs (miRNAs) changes markedly during influenza A virus (IAV) infection of natural and adaptive hosts, but their role in genetically determined host susceptibility to IAV infection has not been explored. We, therefore, compared pulmonary miRNA expression during IAV infection in two inbred mouse strains with differential susceptibility to IAV infection. RESULTS miRNA expression profiles were determined in lungs of the more susceptible strain DBA/2J and the less susceptible strain C57BL/6J within 120 h post infection (hpi) with IAV (H1N1) PR8. Even the miRNomes of uninfected lungs differed substantially between the two strains. After a period of relative quiescence, major miRNome reprogramming was detected in both strains by 48 hpi and increased through 120 hpi. Distinct groups of miRNAs regulated by IAV infection could be defined: (1) miRNAs (n = 39) whose expression correlated with hemagglutinin (HA) mRNA expression and represented the general response to IAV infection independent of host genetic background; (2) miRNAs (n = 20) whose expression correlated with HA mRNA expression but differed between the two strains; and (3) remarkably, miR-147-3p, miR-208b-3p, miR-3096a-5p, miR-3069b-3p, and the miR-467 family, whose abundance even in uninfected lungs differentiated nearly perfectly (area under the ROC curve > 0.99) between the two strains throughout the time course, suggesting a particularly strong association with the differential susceptibility of the two mouse strains. Expression of subsets of miRNAs correlated significantly with peripheral blood granulocyte and monocyte numbers, particularly in DBA/2J mice; miR-223-3p, miR-142-3p, and miR-20b-5p correlated most positively with these cell types in both mouse strains. Higher abundance of antiapoptotic (e.g., miR-467 family) and lower abundance of proapoptotic miRNAs (e.g., miR-34 family) and those regulating the PI3K-Akt pathway (e.g., miR-31-5p) were associated with the more susceptible DBA/2J strain. CONCLUSION Substantial differences in pulmonary miRNA expression between the two differentially susceptible mouse strains were evident even before infection, but evolved further throughout infection and could in part be attributed to differences in peripheral blood leukocyte populations. Thus, pulmonary miRNA expression both before and during IAV infection is in part determined genetically and contributes to susceptibility to IAV infection in this murine host, and likely in humans.
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Affiliation(s)
- Matthias Preusse
- Institute for Experimental Infection Research, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany; University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Centre, Memphis, TN, USA
| | - Frank Pessler
- Institute for Experimental Infection Research, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine, Hannover, Germany
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21
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Yan Y, Yang X, Li TT, Gu KL, Hao J, Zhang Q, Wang Y. Significant differences of function and expression of microRNAs between ground state and serum-cultured pluripotent stem cells. J Genet Genomics 2017; 44:179-189. [PMID: 28411033 DOI: 10.1016/j.jgg.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 01/08/2023]
Abstract
Serum- and 2i-cultured embryonic stem cells (ESCs) show different epigenetic landscapes and transcriptomic profiles. The difference in the function and expression of microRNAs (miRNAs) between these two states remains unclear. Here, we showed that 2i- and serum-cultured ESCs exhibited distinctive miRNA expression profiles with >100 miRNAs differentially expressed, and the expression changes were largely due to transcriptional regulation. We further characterized the function of miRNAs differentially expressed under two conditions and found that ESCs exhibited higher degree of dependency on miRNAs for rapid proliferation; since Dgcr8-/- or Dicer1-/- but not wild-type ESCs showed slower growth rate and more accumulation in the G1 phase under 2i than serum condition. More interestingly, introduction of various self-renewal-silencing miRNAs in wild-type or Dgcr8-/- ESCs failed to silence the self-renewal in 2i medium, but regained the ability to silence the self-renewal upon the addition of serum. Our findings reveal significant differences in the expression and function of miRNAs between serum- and 2i-cultured ESCs.
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Affiliation(s)
- Ying Yan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xi Yang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Ting-Ting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100871, China
| | - Kai-Li Gu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Qiang Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
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22
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Stankevicius V, Vasauskas G, Bulotiene D, Butkyte S, Jarmalaite S, Rotomskis R, Suziedelis K. Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment. BMC Cancer 2016; 16:789. [PMID: 27729023 PMCID: PMC5057255 DOI: 10.1186/s12885-016-2825-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022] Open
Abstract
Background The extracellular matrix (ECM), one of the key components of tumor microenvironment, has a tremendous impact on cancer development and highly influences tumor cell features. ECM affects vital cellular functions such as cell differentiation, migration, survival and proliferation. Gene and protein expression levels are regulated in cell-ECM interaction dependent manner as well. The rate of unsuccessful clinical trials, based on cell culture research models lacking the ECM microenvironment, indicates the need for alternative models and determines the shift to three-dimensional (3D) laminin rich ECM models, better simulating tissue organization. Recognized advantages of 3D models suggest the development of new anticancer treatment strategies. This is among the most promising directions of 3D cell cultures application. However, detailed analysis at the molecular level of 2D/3D cell cultures and tumors in vivo is still needed to elucidate cellular pathways most promising for the development of targeted therapies. In order to elucidate which biological pathways are altered during microenvironmental shift we have analyzed whole genome mRNA and miRNA expression differences in LLC1 cells cultured in 2D or 3D culture conditions. Methods In our study we used DNA microarrays for whole genome analysis of mRNA and miRNA expression differences in LLC1 cells cultivated in 2D or 3D culture conditions. Next, we indicated the most common enriched functional categories using KEGG pathway enrichment analysis. Finally, we validated the microarray data by quantitative PCR in LLC1 cells cultured under 2D or 3D conditions or LLC1 tumors implanted in experimental animals. Results Microarray gene expression analysis revealed that 1884 genes and 77 miRNAs were significantly altered in LLC1 cells after 48 h cell growth under 2D and ECM based 3D cell growth conditions. Pathway enrichment results indicated metabolic pathway, MAP kinase, cell adhesion and immune response as the most significantly altered functional categories in LLC1 cells due to the microenvironmental shift from 2D to 3D. Comparison of the expression levels of selected genes and miRNA between LLC1 cells grown in 3D cell culture and LLC1 tumors implanted in the mouse model indicated correspondence between both model systems. Conclusions Global gene and miRNA expression analysis in LLC1 cells under ECM microenvironment indicated altered immune response, adhesion and MAP kinase pathways. All these processes are related to tumor development, progression and treatment response, suggesting the most promising directions for the development of targeted therapies using the 3D cell culture models. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2825-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vaidotas Stankevicius
- National Cancer Institute, Vilnius, Lithuania.,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gintautas Vasauskas
- National Cancer Institute, Vilnius, Lithuania.,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Stase Butkyte
- Vilnius University Institute of Biotechnology, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sonata Jarmalaite
- National Cancer Institute, Vilnius, Lithuania.,Human Genome Research Centre, Department Botany & Genetics, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ricardas Rotomskis
- National Cancer Institute, Vilnius, Lithuania.,Biophotonics Group of Laser Research Centre, Vilnius University, Vilnius, Lithuania
| | - Kestutis Suziedelis
- National Cancer Institute, Vilnius, Lithuania. .,Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, Vilnius University, Vilnius, Lithuania. .,Laboratory of Molecular Oncology, National Cancer Institute, Santariskiu 1, Vilnius, LT-08660, Lithuania.
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23
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Galloway DA, Moore CS. miRNAs As Emerging Regulators of Oligodendrocyte Development and Differentiation. Front Cell Dev Biol 2016; 4:59. [PMID: 27379236 PMCID: PMC4911355 DOI: 10.3389/fcell.2016.00059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Chronic demyelination is a hallmark of neurological disorders such as multiple sclerosis (MS) and several leukodystrophies. In the central nervous system (CNS), remyelination is a regenerative process that is often inadequate during these pathological states. In the MS context, in situ evidence suggests that remyelination is mediated by populations of oligodendrocyte progenitor cells (OPCs) that proliferate, migrate, and differentiate into mature, myelin-producing oligodendrocytes at sites of demyelinated lesions. The molecular programming of OPCs into mature oligodendrocytes is governed by a myriad of complex intracellular signaling pathways that modulate this process. Recent research has demonstrated the importance of specific and short non-coding RNAs, known as microRNAs (miRNAs), in regulating OPC differentiation and remyelination. Fortunately, it may be possible to take advantage of numerous developmental studies (both human and rodent) that have previously characterized miRNA expression profiles from the early neural progenitor cell to the late myelin-producing oligodendrocyte. Here we review much of the work to date and discuss the impact of miRNAs on OPC and oligodendrocyte biology. Additionally, we consider the potential for miRNA-mediated therapy in the context of remyelination and brain repair.
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Affiliation(s)
- Dylan A Galloway
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland St. John's, NL, Canada
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland St. John's, NL, Canada
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24
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Jacobs ME, Kathpalia PP, Chen Y, Thomas SV, Noonan EJ, Pao AC. SGK1 regulation by miR-466g in cortical collecting duct cells. Am J Physiol Renal Physiol 2016; 310:F1251-7. [PMID: 26911843 PMCID: PMC4935769 DOI: 10.1152/ajprenal.00024.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/22/2016] [Indexed: 11/22/2022] Open
Abstract
Micro-RNAs (miRNAs) are noncoding RNAs that bind target mRNA transcripts and modulate gene expression. In the cortical collecting duct (CCD), aldosterone stimulates the expression of genes that increase activity of the epithelial sodium channel (ENaC); in the early phase of aldosterone induction, one such gene is serum and glucocorticoid regulated kinase 1 (SGK1). We hypothesized that aldosterone regulates the expression of miRNAs in the early phase of induction to control the expression of target genes that stimulate ENaC activity. We treated mpkCCDc14 cells with aldosterone or vehicle for 1 h and used a miRNA microarray to analyze differential miRNA expression. We identified miR-466g as a miRNA that decreased by 57% after 1 h of aldosterone treatment. Moreover, we identified a putative miR-466g binding site in the 3'-untranslated region of SGK1. We constructed an SGK1 3'-untranslated region luciferase reporter and found that cotransfection of miR-466g suppressed luciferase activity in human embryonic kidney-293 cells in a dose-dependent manner. Deletion or introduction of point mutations that disrupt the miR-466g target site attenuated miR-466g-directed suppression of luciferase activity. Finally, we generated stably transduced mpkCCDc14 cell lines overexpressing miR-466g. Cells overexpressing miR-466g demonstrated 12.9-fold lower level of SGK1 mRNA compared with control cells after 6 h of aldosterone induction; moreover, cells overexpressing miR-466g exhibited 25% decrease in amiloride-sensitive current after 6 h of aldosterone induction and complete loss of amiloride-sensitive current after 24 h of aldosterone induction. Our findings implicate miR-466g as a novel early-phase aldosterone responsive miRNA that regulates SGK1 and ENaC in CCD cells.
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Affiliation(s)
- Mollie E Jacobs
- Department of Medicine, Stanford University School of Medicine, Stanford, California; and
| | - Paru P Kathpalia
- Department of Medicine, Stanford University School of Medicine, Stanford, California; and
| | - Yu Chen
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Sheela V Thomas
- Department of Medicine, Stanford University School of Medicine, Stanford, California; and
| | - Emily J Noonan
- Department of Medicine, Stanford University School of Medicine, Stanford, California; and Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Alan C Pao
- Department of Medicine, Stanford University School of Medicine, Stanford, California; and Veterans Affairs Palo Alto Health Care System, Palo Alto, California
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25
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Wu L, Lu Y, Jiao Y, Liu B, Li S, Li Y, Xing F, Chen D, Liu X, Zhao J, Xiong X, Gu Y, Lu J, Chen X, Li X. Paternal Psychological Stress Reprograms Hepatic Gluconeogenesis in Offspring. Cell Metab 2016; 23:735-43. [PMID: 26908462 DOI: 10.1016/j.cmet.2016.01.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 10/09/2015] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
Both epidemiologic and experimental animal studies demonstrate that chronic psychological stress exerts adverse effects on the initiation and/or progression of many diseases. However, intergenerational effects of this environmental information remains poorly understood. Here, using a C57BL/6 mouse model of restraint stress, we show that offspring of stressed fathers exhibit hyperglycemia due to enhanced hepatic gluconeogenesis and elevated expression of PEPCK. Mechanistically, we identify an epigenetic alteration at the promoter region of the Sfmbt2 gene, a maternally imprinted polycomb gene, leading to a downregulation of intronic microRNA-466b-3p, which post-transcriptionally inhibits PEPCK expression. Importantly, hyperglycemia in F1 mice is reversed by RU486 treatment in fathers, and dexamethasone administration in F0 mice phenocopies the roles of restraint stress. Thus, we provide evidence showing the effects of paternal psychological stress on the regulation of glucose metabolism in offspring, which may have profound implications for our understanding of health and disease risk inherited from fathers.
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Affiliation(s)
- Ling Wu
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yan Lu
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Yang Jiao
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Bin Liu
- Hubei Key Laboratory for Kidney Disease Pathogenesis and Intervention, Hubei Polytechnic University School of Medicine, 16 North Guilin Road, Huangshi, Hubei 435003, China
| | - Shangang Li
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Yao Li
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Fengying Xing
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Dongbao Chen
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Xing Liu
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Jiejie Zhao
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Xuelian Xiong
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Yanyun Gu
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Jieli Lu
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China
| | - Xuejin Chen
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China.
| | - Xiaoying Li
- Shanghai Institute of Endocrinology and Metabolism, Shanghai Key Laboratory for Endocrine Tumors, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-Jin 2nd Road, Shanghai 200025, China.
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26
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In silico prediction of microRNAs on fluoride induced sperm toxicity in mice. Food Chem Toxicol 2016; 98:34-49. [PMID: 27012587 DOI: 10.1016/j.fct.2016.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/07/2016] [Accepted: 03/10/2016] [Indexed: 01/06/2023]
Abstract
Fluorosis is an endemic global problem causing male reproductive impairment. F mediates male reproductive toxicity in mice down-regulating 63 genes involved in diverse biological processes - apoptosis, cell cycle, cell signaling, chemotaxis, electron transport, glycolysis, oxidative stress, sperm capacitation and spermatogenesis. We predicted the miRNAs down-regulating these 63 genes using TargetScan, DIANA and MicroCosm. The prediction tools identified 3059 miRNAs targeting 63 genes. Of the predicted interactions, 11 miRNAs (mmu-miR-103, -107, -122, -188a, -199a-5p, -205, -340-5p, -345-3p, -452-5p, -499, -878-3p) were commonly found in the three tools utilized and seven miRNAs (miR-9-5p, miR-511-3p, miR-7b-5p, miR-30e-5p, miR-17-5p, miR-122-5p and miR-541-5p) targeting six genes (Traf3, Rock2, Rgs8, Atp1b2, Cacna2d1 and Aldoa) were already validated experimentally in mice. The miRNA-mRNA network of the predicted miRNAs with its respective targets revealed the complex interaction within a biological process leading to sperm dysfunction on exposure to F. Our findings not only suggest that the predicted miRs furnish evidence, but also have the potential to serve as non-invasive biomarkers on F-induced sperm dysfunction. Our data contribute towards elucidating the function of miRNAs in the fluoride induced infertility. miRNA molecular pathways in F intoxication will open new avenues on the use of antagomirs in recovering fertility.
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27
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Cox B, Leavey K, Nosi U, Wong F, Kingdom J. Placental transcriptome in development and pathology: expression, function, and methods of analysis. Am J Obstet Gynecol 2015; 213:S138-51. [PMID: 26428493 DOI: 10.1016/j.ajog.2015.07.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/18/2022]
Abstract
The placenta is the essential organ of mammalian pregnancy and errors in its development and function are associated with a wide range of human pathologies of pregnancy. Genome sequencing has led to methods for investigation of the transcriptome (all expressed RNA species) using microarrays and next-generation sequencing, and implementation of these techniques has identified many novel species of RNA including: micro-RNA, long noncoding RNA, and circular RNA. These species can physically interact with both each other and regulatory proteins to modify gene expression and messenger RNA to protein translation. Transcriptome analysis is actively used to investigate placental development and dysfunction in pathologies ranging from preeclampsia and fetal growth restriction to preterm labor. Genome-wide gene expression analysis is also being applied to identify prognostic and diagnostic biomarkers of these disorders. In this comprehensive review we summarize transcriptome biology, methods of isolation and analysis, application to placental development and pathology, and use in diagnostic analysis in maternal blood. Key information for analysis methods is organized into quick reference tables where current analysis techniques and tools are cited and compared. We have created this review as a practical guide and starting reference for those interested in beginning an investigation into the transcriptome of the placenta.
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28
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Schmidt A, Morales-Prieto DM, Pastuschek J, Fröhlich K, Markert UR. Only humans have human placentas: molecular differences between mice and humans. J Reprod Immunol 2015; 108:65-71. [DOI: 10.1016/j.jri.2015.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 01/23/2023]
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29
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Li Z, Zhang J, Su J, Liu Y, Guo J, Zhang Y, Lu C, Xing S, Guan Y, Li Y, Sun B, Zhao Z. MicroRNAs in the immune organs of chickens and ducks indicate divergence of immunity against H5N1 avian influenza. FEBS Lett 2014; 589:419-25. [PMID: 25541489 DOI: 10.1016/j.febslet.2014.12.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/10/2014] [Accepted: 12/10/2014] [Indexed: 12/20/2022]
Abstract
Chickens are susceptible to the highly pathogenic H5N1 strain of avian influenza virus (HPAIV), whereas ducks are not. Here, we used high-throughput sequencing to analyse the microRNA expression in the spleen, thymus and bursa of Fabricius of H5N1-HPAIV-infected and non-infected chickens and ducks. We annotated the genomic positions of duck microRNAs and we compared the microRNA repertoires of chickens and ducks. Our results showed that the microRNA expression patterns in the homologous immune organs of specific-pathogen-free (SPF) chickens and ducks diverge substantially. Moreover, there was larger divergence between the microRNA expression patterns in immune organs of HPAIV-infected chickens than HPAIV-infected ducks. Together, our results might help to elucidate the roles of microRNAs in the divergent immunity of chickens and ducks against H5N1 HPAIV.
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Affiliation(s)
- Zezhong Li
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Jinyu Zhang
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Jiazi Su
- Jilin Business and Technology College, Changchun 130507, China
| | - Yinuo Liu
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Jiang Guo
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Yonghong Zhang
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Chunyan Lu
- Experimental Base of Agriculture, Jilin University, Changchun 130062, China
| | - Shenyang Xing
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China
| | - Yuntao Guan
- Harbin Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Harbin 150001, China
| | - Yanbing Li
- Harbin Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Harbin 150001, China
| | - Boxing Sun
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China.
| | - Zhihui Zhao
- College of Animal Science, Jilin University, Changchun 130062, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, Center for Animal Embryo Engineering of Jilin Province, Jilin University, Changchun 130062, China.
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Clancy JL, Patel HR, Hussein SMI, Tonge PD, Cloonan N, Corso AJ, Li M, Lee DS, Shin JY, Wong JJL, Bailey CG, Benevento M, Munoz J, Chuah A, Wood D, Rasko JEJ, Heck AJR, Grimmond SM, Rogers IM, Seo JS, Wells CA, Puri MC, Nagy A, Preiss T. Small RNA changes en route to distinct cellular states of induced pluripotency. Nat Commun 2014; 5:5522. [DOI: 10.1038/ncomms6522] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/08/2014] [Indexed: 12/16/2022] Open
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Abstract
Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei to understand the microevolution of this important class of regulatory genes. Our analysis of three population samples and C. remanei's sister species revealed ongoing natural selection that constrains evolution of all sequence domains within miRNA hairpins. We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence. Despite the ongoing importance of purging of new mutations, we discover a trove of >400 natural miRNA sequence variants that include single nucleotide polymorphisms in seed motifs, indels that ablate miRNA functional domains, and origination of new miRNAs by duplication. Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species. These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past.
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Affiliation(s)
- Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
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32
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Pernaute B, Spruce T, Smith KM, Sánchez-Nieto JM, Manzanares M, Cobb B, Rodríguez TA. MicroRNAs control the apoptotic threshold in primed pluripotent stem cells through regulation of BIM. Genes Dev 2014; 28:1873-8. [PMID: 25184675 PMCID: PMC4197944 DOI: 10.1101/gad.245621.114] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pernaute et al. identify miRNA-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Three miRNA families, miR-20, miR-92, and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the proapoptotic protein BIM. These miRNA families are needed to maintain cell survival in stem cells that are primed for not only differentiation but also cell death. Mammalian primed pluripotent stem cells have been shown to be highly susceptible to cell death stimuli due to their low apoptotic threshold, but how this threshold is regulated remains largely unknown. Here we identify microRNA (miRNA)-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Moreover, we found that three miRNA families, miR-20, miR-92, and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the proapoptotic protein BIM. These families therefore represent an essential buffer needed to maintain cell survival in stem cells that are primed for not only differentiation but also cell death.
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Affiliation(s)
- Barbara Pernaute
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Thomas Spruce
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London W12 0NN, United Kingdom
| | | | - Juan Miguel Sánchez-Nieto
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Miguel Manzanares
- Department of Cardiovascular Developmental and Repair, Centro Nacional de Investigaciones Cardiovasculares-CNIC, 28029 Madrid, Spain
| | - Bradley Cobb
- Royal Veterinary College, London NW1 0TU, United Kingdom
| | - Tristan A Rodríguez
- British Heart Foundation Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London W12 0NN, United Kingdom;
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Diet-induced obesity modulates epigenetic responses to ionizing radiation in mice. PLoS One 2014; 9:e106277. [PMID: 25171162 PMCID: PMC4149562 DOI: 10.1371/journal.pone.0106277] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
Both exposure to ionizing radiation and obesity have been associated with various pathologies including cancer. There is a crucial need in better understanding the interactions between ionizing radiation effects (especially at low doses) and other risk factors, such as obesity. In order to evaluate radiation responses in obese animals, C3H and C57BL/6J mice fed a control normal fat or a high fat (HF) diet were exposed to fractionated doses of X-rays (0.75 Gy ×4). Bone marrow micronucleus assays did not suggest a modulation of radiation-induced genotoxicity by HF diet. Using MSP, we observed that the promoters of p16 and Dapk genes were methylated in the livers of C57BL/6J mice fed a HF diet (irradiated and non-irradiated); Mgmt promoter was methylated in irradiated and/or HF diet-fed mice. In addition, methylation PCR arrays identified Ep300 and Socs1 (whose promoters exhibited higher methylation levels in non-irradiated HF diet-fed mice) as potential targets for further studies. We then compared microRNA regulations after radiation exposure in the livers of C57BL/6J mice fed a normal or an HF diet, using microRNA arrays. Interestingly, radiation-triggered microRNA regulations observed in normal mice were not observed in obese mice. miR-466e was upregulated in non-irradiated obese mice. In vitro free fatty acid (palmitic acid, oleic acid) administration sensitized AML12 mouse liver cells to ionizing radiation, but the inhibition of miR-466e counteracted this radio-sensitization, suggesting that the modulation of radiation responses by diet-induced obesity might involve miR-466e expression. All together, our results suggested the existence of dietary effects on radiation responses (especially epigenetic regulations) in mice, possibly in relationship with obesity-induced chronic oxidative stress.
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Martín-Gómez L, Villalba A, Kerkhoven RH, Abollo E. Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis. INFECTION GENETICS AND EVOLUTION 2014; 27:40-50. [PMID: 25008434 DOI: 10.1016/j.meegid.2014.06.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small (∼22nt) non-coding regulatory single strand RNA molecules that reduce stability and/or translation of sequence-complementary target. miRNAs are a key component of gene regulatory networks and have been involved in a wide variety of biological processes, such as signal transduction, cell proliferation and apoptosis. Many miRNAs are broadly conserved among the animal lineages and even between invertebrates and vertebrates. The European flat oyster Ostrea edulis is highly susceptible to infection with Bonamia ostreae, an intracellular parasite able to survive and proliferate within oyster haemocytes. Mollusc haemocytes play a key role in the immune response of molluscs as main cellular effectors. The roles of miRNAs in the immune response of O. edulis to bonamiosis were analysed using a commercial microarray platform (miRCURY LNA™ v2, Exiqon) for miRNAs. Expression of miRNAs in haemocytes from oysters with different bonamiosis intensity was compared. Differential expression was detected in 63 and 76 miRNAs when comparing heavily-affected with non-affected oysters and with lightly-affected ones, respectively. Among them, 19 miRNAs are known to be linked to immune response, being responsible of proliferation and activation of macrophages, inflammation, apoptosis and/or oxidative damage, which is consistent with the modulation of their expression in oyster haemocytes due to bonamiosis.
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Affiliation(s)
- Laura Martín-Gómez
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, Aptdo 13, 36620 Vilanova de Arousa, Spain.
| | - Antonio Villalba
- Centro de Investigacións Mariñas, Consellería do Mar, Xunta de Galicia, Aptdo 13, 36620 Vilanova de Arousa, Spain
| | - Ron H Kerkhoven
- Central Microarray Facility, NKI (The Netherlands Cancer Institute), Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Elvira Abollo
- Fundación CETMAR - Centro Tecnológico del Mar, Eduardo Cabello s/n., 36208 Vigo, Spain
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Angiotensin II-regulated microRNA 483-3p directly targets multiple components of the renin-angiotensin system. J Mol Cell Cardiol 2014; 75:25-39. [PMID: 24976017 DOI: 10.1016/j.yjmcc.2014.06.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 11/21/2022]
Abstract
Improper regulation of signaling in vascular smooth muscle cells (VSMCs) by angiotensin II (AngII) can lead to hypertension, vascular hypertrophy and atherosclerosis. The extent to which the homeostatic levels of the components of signaling networks are regulated through microRNAs (miRNA) modulated by AngII type 1 receptor (AT1R) in VSMCs is not fully understood. Whether AT1R blockers used to treat vascular disorders modulate expression of miRNAs is also not known. To report differential miRNA expression following AT1R activation by AngII, we performed microarray analysis in 23 biological and technical replicates derived from humans, rats and mice. Profiling data revealed a robust regulation of miRNA expression by AngII through AT1R, but not the AngII type 2 receptor (AT2R). The AT1R-specific blockers, losartan and candesartan antagonized >90% of AT1R-regulated miRNAs and AngII-activated AT2R did not modulate their expression. We discovered VSMC-specific modulation of 22 miRNAs by AngII, and validated AT1R-mediated regulation of 17 of those miRNAs by real-time polymerase chain reaction analysis. We selected miR-483-3p as a novel representative candidate for further study because mRNAs of multiple components of the renin-angiotensin system (RAS) were predicted to contain the target sequence for this miRNA. MiR-483-3p inhibited the expression of luciferase reporters bearing 3'-UTRs of four different RAS genes and the inhibition was reversed by antagomir-483-3p. The AT1R-regulated expression levels of angiotensinogen and angiotensin converting enzyme 1 (ACE-1) proteins in VSMCs are modulated specifically by miR-483-3p. Our study demonstrates that the AT1R-regulated miRNA expression fingerprint is conserved in VSMCs of humans and rodents. Furthermore, we identify the AT1R-regulated miR-483-3p as a potential negative regulator of steady-state levels of RAS components in VSMCs. Thus, miRNA-regulation by AngII to affect cellular signaling is a novel aspect of RAS biology, which may lead to discovery of potential candidate prognostic markers and therapeutic targets.
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Zhang YJ, Yang JH, Shi QS, Zheng LL, Liu J, Zhou H, Zhang H, Qu LH. Rapid birth-and-death evolution of imprinted snoRNAs in the Prader-Willi syndrome locus: implications for neural development in Euarchontoglires. PLoS One 2014; 9:e100329. [PMID: 24945811 PMCID: PMC4063771 DOI: 10.1371/journal.pone.0100329] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/23/2014] [Indexed: 11/24/2022] Open
Abstract
Imprinted small nucleolar RNAs (snoRNAs) are only found in eutherian genomes and closely related to brain functions. A complex human neurological disease, Prader-Willi syndrome (PWS), is primarily attributed to the deletion of imprinted snoRNAs in chromosome 15q11-q13. Here we investigated the snoRNA repertoires in the PWS locus of 12 mammalian genomes and their evolution processes. A total of 613 imprinted snoRNAs were identified in the PWS homologous loci and the gene number was highly variable across lineages, with a peak in Euarchontoglires. Lineage-specific gene gain and loss events account for most extant genes of the HBII-52 (SNORD115) and the HBII-85 (SNORD116) gene family, and remarkable high gene-birth rates were observed in the primates and the rodents. Meanwhile, rapid sequence substitution occurred only in imprinted snoRNA genes, rather than their flanking sequences or the protein-coding genes located in the same imprinted locus. Strong selective constraints on the functional elements of these imprinted snoRNAs further suggest that they are subjected to birth-and-death evolution. Our data suggest that the regulatory role of HBII-52 on 5-HT2CR pre-mRNA might originate in the Euarchontoglires through adaptive process. We propose that the rapid evolution of PWS-related imprinted snoRNAs has contributed to the neural development of Euarchontoglires.
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Affiliation(s)
- Yi-Jun Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Qiao-Su Shi
- Laboratory of Liver Disease Hospital, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Ling-Ling Zheng
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hui Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail:
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Yelamanchili SV, Morsey B, Harrison EB, Rennard DA, Emanuel K, Thapa I, Bastola DR, Fox HS. The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins. Cell Death Dis 2014; 5:e982. [PMID: 24407235 PMCID: PMC4040694 DOI: 10.1038/cddis.2013.498] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 10/18/2013] [Accepted: 11/05/2013] [Indexed: 12/26/2022]
Abstract
Regulation of cellular proliferation and differentiation during brain development results from processes requiring several regulatory networks to function in synchrony. MicroRNAs are part of this regulatory system. Although many microRNAs are evolutionarily conserved, recent evolution of such regulatory molecules can enable the acquisition of new means of attaining specialized functions. Here we identify and report the novel expression and functions of a human and higher primate-specific microRNA, miR-1290, in neurons. Using human fetal-derived neural progenitors, SH-SY5Y neuroblastoma cell line and H9-ESC-derived neural progenitors (H9-NPC), we found miR-1290 to be upregulated during neuronal differentiation, using microarray, northern blotting and qRT-PCR. We then conducted knockdown and overexpression experiments to look at the functional consequences of perturbed miR-1290 levels. Knockdown of miR-1290 inhibited differentiation and induced proliferation in differentiated neurons; correspondingly, miR-1290 overexpression in progenitors led to a slowing down of the cell cycle and differentiation to neuronal phenotypes. Consequently, we identified that crucial cell cycle proteins were aberrantly changed in expression level. Therefore, we conclude that miR-1290 is required for maintaining neurons in a differentiated state.
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Affiliation(s)
- S V Yelamanchili
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - B Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - E B Harrison
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - D A Rennard
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - K Emanuel
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - I Thapa
- School of Interdisciplinary Informatics, University of Nebraska-Omaha, Omaha, NE, USA
| | - D R Bastola
- School of Interdisciplinary Informatics, University of Nebraska-Omaha, Omaha, NE, USA
| | - H S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
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Luo Y, Liu Y, Liu M, Wei J, Zhang Y, Hou J, Huang W, Wang T, Li X, He Y, Ding F, Yuan L, Cai J, Zheng F, Yang JY. Sfmbt2 10th intron-hosted miR-466(a/e)-3p are important epigenetic regulators of Nfat5 signaling, osmoregulation and urine concentration in mice. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:97-106. [PMID: 24389345 DOI: 10.1016/j.bbagrm.2013.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
Sfmbt2-hosted miR-466a-3p and its close relatives are often among the most significantly up-regulated or down-regulated miRNAs in responses to numerous deleterious environmental stimuli. The exact roles of these miRNAs in cellular stress responses, however, are not clear. Here we showed that many Sfmbt2-hosted miRNAs were highly hypertonic stress responsive in vitro and in vivo. In renal medulla, water deprivation induced alterations in the expression of miR-466(a/b/c/e/p)-3p in a pattern similar to that of miR-200b-3p, a known regulator of osmoresponsive transcription factor Nfat5. Remarkably, exposure of mIMCD3 cells to an arginine vasopressin analog time-dependently down-regulated the expression of miR-466(a/b/c/e/p)-3p and miR-200b-3p, which provides a novel regulatory mechanism for these osmoresponsive miRNAs. In cultured mIMCD3 cells we further demonstrated that miR-466a-3p and miR-466g were capable of targeting Nfat5 by interacting with its 3'UTR. In transgenic mice overexpressing miR-466a-3p, significant down-regulation of Nfat5 and many other osmoregulation-related genes was observed in both the renal cortex and medulla. Moreover, sustained transgenic over-expression of miR-466a-3p was found to be associated with polydipsia, polyuria and disturbed ion homeostasis and kidney morphology. Since the mature sequence of miR-466a-3p is completely equivalent to that of miR-466e-3p and that the seed sequence of miR-466a-3p is completely equivalent to that of miR-297(a/b/c)-3p, miR-466d-3p, miR-467g and miR-669d-3p, and that miR-466a-3p differs from miR-466(b/c/p)-3p only in a 5' nucleotide, we propose that miR-466a-3p and many of its close relatives are important epigenetic regulators of renal Nfat5 signaling, osmoregulation and urine concentration in mice.
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Affiliation(s)
- Yu Luo
- School of Nursing, The Third Military Medical University, Chongqing 400038, China; State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Ying Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Meng Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Jie Wei
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Yunyun Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Jinpao Hou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Weifeng Huang
- The First Affiliated Hospital of Xiamen University, Xiamen 361005, China
| | - Tao Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Xun Li
- The First Affiliated Hospital of Xiamen University, Xiamen 361005, China
| | - Ying He
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China; Fujian Provincial Transgenic Core, Xiamen University Laboratory Animal Center, Xiang'an, Xiamen 361102, China
| | - Feng Ding
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China; Fujian Provincial Transgenic Core, Xiamen University Laboratory Animal Center, Xiang'an, Xiamen 361102, China
| | - Li Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Biology, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Jianchun Cai
- Zhongshan Hospital, Xiamen University, Xiamen 361005, China
| | - Feng Zheng
- Department of Nephrology and Basic Science Laboratory, Union Hospital, Fujian Medical University, Fuzhou 350001, China
| | - James Y Yang
- School of Nursing, The Third Military Medical University, Chongqing 400038, China; Fujian Provincial Transgenic Core, Xiamen University Laboratory Animal Center, Xiang'an, Xiamen 361102, China.
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Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, Plastow GS, Guan LL, Stothard P. Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics 2013; 14:609. [PMID: 24020371 PMCID: PMC3847189 DOI: 10.1186/1471-2164-14-609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022] Open
Abstract
Background Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species. Results We analyzed miRNA and mRNA transcriptomes generated by Illumina sequencing from whole blood samples of cattle and a closely related non-ruminant species, pig. We found evidence of expansion of cattle-specific miRNAs by analyzing miRNA conservation among 57 vertebrate species. The emergence of cattle-specific miRNAs was accompanied by accelerated sequence evolution at their target sites. Further, the target genes of cattle-specific miRNAs show markedly reduced expression compared to their pig and human orthologues. We found that target genes with conserved or non-conserved target sites of cattle-specific miRNAs exhibit reduced expression. One of the significantly enriched KEGG pathway terms for the target genes of the cattle-specific miRNAs is the insulin signalling pathway, raising the possibility that some of these miRNAs may modulate insulin resistance in ruminants. Conclusions We provide evidence of rapid miRNA-mediated regulatory evolution in the ruminant lineage. Cattle-specific miRNAs play an important role in shaping gene expression divergence between ruminant and non-ruminant species, by influencing the expression of targets genes through both conserved and cattle-specific target sites.
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Affiliation(s)
- Hua Bao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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40
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Mor E, Shomron N. Species-specific microRNA regulation influences phenotypic variability: perspectives on species-specific microRNA regulation. Bioessays 2013; 35:881-8. [PMID: 23864354 DOI: 10.1002/bies.201200157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phenotypic divergence among animal species may be due in part to species-specific (SS) regulation of gene expression by small, non-coding regulatory RNAs termed "microRNAs". This phenomenon can be modulated by several variables. First, microRNA genes vary by their level of conservation, many of them being SS, or unique to a particular evolutionary lineage. Second, microRNA expression levels vary spatially and temporally in different species. Lastly, while microRNAs bind the 3'UTR of target genes in order to silence their expression, the binding sites themselves are often non-conserved. The variability of the miRNA-target paradigm between different species is thus multifactorial, and this paradigm has only just started to gain attention from researchers in various fields. Here we present and discuss recent findings regarding the characteristics and implications of SS microRNA regulation.
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Affiliation(s)
- Eyal Mor
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Gurtan AM, Sharp PA. The role of miRNAs in regulating gene expression networks. J Mol Biol 2013; 425:3582-600. [PMID: 23500488 DOI: 10.1016/j.jmb.2013.03.007] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression. They are conserved across species, expressed across cell types, and active against a large proportion of the transcriptome. The sequence-complementary mechanism of miRNA activity exploits combinatorial diversity, a property conducive to network-wide regulation of gene expression, and functional evidence supporting this hypothesized systems-level role has steadily begun to accumulate. The emerging models are exciting and will yield deep insight into the regulatory architecture of biology. However, because of the technical challenges facing the network-based study of miRNAs, many gaps remain. Here, we review mammalian miRNAs by describing recent advances in understanding their molecular activity and network-wide function.
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Affiliation(s)
- Allan M Gurtan
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA.
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Du ZQ, Yang CX, Rothschild MF, Ross JW. Novel microRNA families expanded in the human genome. BMC Genomics 2013; 14:98. [PMID: 23402294 PMCID: PMC3602292 DOI: 10.1186/1471-2164-14-98] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 01/31/2013] [Indexed: 12/28/2022] Open
Abstract
Background Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scale (<1 kb) could also contribute to microRNA expansion, as demonstrated in this study. Results Using comparative genome analysis and bioinformatics methods, we found nine novel expanded microRNA families enriched in short duplicated sequences in the human genome. Furthermore, novel genomic regions were found to contain microRNA paralogs for microRNA families previously analyzed to be related to segmental duplications. We found that for microRNA families expanded in the human genome, 14 families are specific to the primate lineage, and nine are non-specific, respectively. Two microRNA families (hsa-mir-1233 and hsa-mir-622) appear to be further expanded in the human genome, and were confirmed by fluorescence in situ hybridization. These novel microRNA families expanded in the human genome were mostly embedded in or close to proteins with conserved functions. Furthermore, besides the Alu element, L1 elements could also contribute to the origination of microRNA paralog families. Conclusions Together, we found that small duplication events could also contribute to microRNA expansion, which could provide us novel insights on the evolution of human genome structure and function.
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Affiliation(s)
- Zhi-Qiang Du
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA.
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Iwama H, Kato K, Imachi H, Murao K, Masaki T. Human microRNAs originated from two periods at accelerated rates in mammalian evolution. Mol Biol Evol 2012; 30:613-26. [PMID: 23171859 PMCID: PMC3563971 DOI: 10.1093/molbev/mss262] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that modulate genes posttranscriptionally. Frequent gains and losses of miRNA genes have been reported to occur during evolution. However, little is known systematically about the periods of evolutionary origin of the present miRNA gene repertoire of an extant mammalian species. Thus, in this study, we estimated the evolutionary periods during which each of 1,433 present human miRNA genes originated within 15 periods, from human to platypus-human common ancestral branch and a class "conserved beyond theria," primarily using multiple genome alignments of 38 species, plus the pairwise genome alignments of five species. The results showed two peak periods in which the human miRNA genes originated at significantly accelerated rates. The most accelerated rate appeared in the period of the initial phase of hominoid lineage, and the second appeared shortly before Laurasiatherian divergence. Approximately 53% of the present human miRNA genes have originated within the simian lineage to human. In particular, approximately 28% originated within the hominoid lineage. The early phase of placental mammal radiation comprises approximately 28%, while no more than 15% of human miRNAs have been conserved beyond placental mammals. We also clearly showed a general trend, in which the miRNA expression level decreases as the miRNA becomes younger. Intriguingly, amid this decreasing trend of expression, we found one significant rise in the expression level that corresponded to the initial phase of the hominoid lineage, suggesting that increased functional acquisitions of miRNAs originated at this particular period.
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Affiliation(s)
- Hisakazu Iwama
- Life Science Research Center, Kagawa University, Kita-gun, Kagawa, Japan.
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Zhang T, Luo Y, Wang T, Yang JY. MicroRNA-297b-5p/3p target Mllt3/Af9 to suppress lymphoma cell proliferation, migration and invasion in vitro and tumor growth in nude mice. Leuk Lymphoma 2012; 53:2033-40. [PMID: 22448917 DOI: 10.3109/10428194.2012.678005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mllt3/Af9 is a proto-oncogene capable of deregulating the expression of genes critical for leukemia. However, the regulation of its expression remains incompletely elucidated. Herein, we show that the microRNAs miR-297b-5p/3p are capable of regulating Mllt3/Af9 expression negatively by binding to its 3'-untranslated region. Overexpression of miR-297b-5p/3p also led to altered expression of p27(Kip1) and proliferating cell nuclear antigen, abnormal cell cycle arrest, decreased cell proliferation, migration and invasion in vitro in cell cultures, and suppressed xenograft tumor growth in vivo in the nude mouse. These data demonstrate that miR-297b-5p/3p and Mllt3/Af9 might be critical regulators of lymphoma cell proliferation or carcinogenesis. Together our findings suggest that miR-297b-5p/3p might be useful molecular targets for diagnosis or treatment of cancers associated with abnormal expression of Mllt3/Af9.
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Affiliation(s)
- Tiantian Zhang
- State Key Laboratory of Cellular Stress Biology and Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen, China
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