鱼类miRNAs研究新进展
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摘要
<正>MicroRNAs(miRNAs)是一类内生性的、进化上高度保守的单链成熟非编码RNA,长度约21~25个核苷酸,广泛存在植物、动物及微生物中~[1-2],参与生物体的胚胎形成、个体生长发育、机体免疫、疾病防御以及繁殖和糖脂类代谢等生命过程~[3-8]。目前,基于生物信息学预测,miRNAs约占整个基因组的2%~3%~[9]。自Lee等~[10]利用定位克隆法从秀丽隐杆线虫(Caenorhabditis elegans)中克隆到
引文
[1]Bartel D P,Chen C Z.Micromanagers of gene expression:the potentially widespread influence of metazoan microRNAs[J].Nature Reviews Genetics,2004,5(5):396-400.
[2]Carrington J C,Ambros V.Role of microRNAs in plant and animal development[J].Science,2003,301(5631):336-338.
[3]Fu Y,Shi Z,Wu M,et al.Identification and differentia1expression of microRNAs during metamorphosis of the Japanese flounder(Paralichthys olivaceus)[J].PLos One,2011,6(7):e22957.
[4]Bizuayehu T T,Babiak I.MicroRNA in teleost fish[J].Genome Biology and Evolution,2014,6(8):1911-1937.
[5]Tang X L,Xu M J,Li Z H,et al.Effects of vitamin E on expressions of eight microRNAs in the liver of Nile tilapia(Oreochromis niloticus)[J].Fish&Shellfish Immunology,2013,34(6):1470-1475.
[6]唐雪莲,李洪,付京花.鱼类microRNAs研究进展[J].水产科学,2013,32(1):55-58.
[7]Bizuayehu T T,Babiak J,Norberg B,et al.Sex-biased miRNA expression in Atlantic halibut(Hippoglossus hippoglossus)brain and gonads[J].Sexual Development,2012,6(5):257-266.
[8]Zhang Q H,Xie D Z,Wang S Q,et al.miR-17is involved in the regulation of LC-PUFA biosynthesis in vertebrates:effects on liver expression of a fatty acyl desaturase in the marine teleost Siganus canaliculatus[J].Biochimica et Biophysica Acta,2014,1841(7):934-943.
[9]Berezikov E,Guryev V,van de Belt J,et al.Phylogenetic shadowing and computational identification of human microRNA genes[J].Cell,2005,120(1):21-24.
[10]Lee R C,Feinbaum R L,Ambros V.The C.elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity to lin-14[J].Cell,1993,75(5):843-854.
[11]Chen P Y,Manninga H,Slanchev K,et al.The developmental miRNA profiles of zebrafish as determined by small RNA cloning[J].Genes Development,2005,19(11):1288-1293.
[12]Salem M,Xiao C,Womack J,et al.A microRNA repertoire for functional genome research in rainbow trout(Oncorhynchus mykiss)[J].Mar Biotechnol(NY),2010,12(4):410-429.
[13]Chi W,Tong C,Gan X,et al.Characterization and comparative profiling of MiRNA transcriptomes in bighead carp and silver carp[J].PLoS One,2011,6(8):e23549.
[14]Yang L D,He S P.A bioinformatics-based update on microRNAs and their targets in rainbow trout(Oncorhynchus mykiss)[J].Gene,2014,533(1):261-269.
[15]孙君君,卢荣华,杨峰,等.草鱼SREBP-1基因的克隆及糖对其在肝脏中表达的影响[J].水产学报,2014,38(8):1057-1067.
[16]Her G M,Hsu C C,Hong J R,et al.Overexpression of gankyrin induces liver steatosis in zebrafish(Danio rerio)[J].Biochimica et Biophysica Acta,2011,1811(9):536-548.
[17]Horton J D,Goldstein J L,Brown M S.SREBPs:Activators of the complete program cholesterol and fatty acid synthesis in the liver[J].Journal of Clinical Investigation,2002,109(9):1125-1131.
[18]Shao W,Espenshade P J.Expanding roles for SREBP in metabolism[J].Cell Metab,2012,16(4):414-419.
[19]Linhart H G,Ishimura-Oka K,Demayo F,et al.C/EBPαis required for differentiation of white,but not brown,adipose tissue[J].Proc Natl Acad Sci U S A,2001,98(22):12532-12537.
[20]Tanaka T,Yoshida N,Kishimoto T,et al.Defective adipocyte differentiation in mice lacking the C/EBPbeta and/or C/EBPdelta gene[J].EMBO J,1997,16(24):7432-7443.
[21]Wang T,Li M,Guan J,et al.MicroRNAs miR-27a and miR-143regulate porcine adipocyte lipid metabolism[J].International Journal of Molecular Sciences,2011,12(11):7950-7959.
[22]Kida K,Nakajima M,Mohri T,et al.PPARalpha is regulated by miR-21and miR-27bin human liver[J].Pharmaceutical Research,2011,28(10):2467-2476.
[23]Zisoulis D G,Kai Z S,Chang K R,et al.Autoregulation of microRNA biogenesis by let-7and Argonaute[J].Nature,2012,486(7404):541-544.
[24]Hansen T B,Wiklund E B,Bramsen J B,et al.miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA[J].EMBO Journal,2011,30(2):4414-4422.
[25]Iliopoulos D,Drosatos K,Hiyama Y,et al.MicroRNA-370controls the expression of microRNA-122and Cpt1alpha and affects lipid metabolism[J].Journal of Lipid Research,2010,51(6):1513-1523.
[26]Mennigen J A,Panserat S,Larquier M,et al.Postprandial regulation of hepatic MicroRNAs predicted to target the insulin pathway in rainbow trout[J].PLoS One,2012,7(6):e38604.
[27]Davalos A,Goedeke L,Smibert P,et al.miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling[J].Proc Natl Acad Sci U S A,2011,108(22):9232-9237.
[28]Esau C,Davis S,Murray S F,et al.miR-122regulation of lipid metabolism revealed by in vivo antisense targeting[J].Cell Metabolism,2006,3(2):87-98.
[29]Rayner K J,Suarez Y,Davalos A,et al.MiR-33contributes to the regulation of cholesterol homeostasis[J].Science,2011,328(5985):1570-1573.
[30]Mennigen J A,Plagnes-juan E,Figueredo-silva C A,et al.Acute endocrine and nutritional co-regulation of the hepatic omy-miRNA-122band the lipogenic gene fas in rainbow trout,Oncorhynchus mykiss[J].Comp Biochem Physiol B Biochem Mol Biol,2014,169(3):16-24.
[31]Mennigen J A,Martyniuk C J,Seiliez I,et al.Metabolic consequences of microRNA-122 inhibition in rainbow trout,Oncorhynchus mykiss[J].BMC Genomics,2014,15(1):70.
[32]Huang C W,Li Y H,Hu S Y,et al.Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia(Oreochromis niloticus)[J].Journal of Animal Science,2012,90(12):4266-4279.
[33]Yan B,Guo J T,Zhao L H,et al.microRNA expression signature in skeletal muscle of Nile tilapia[J].Aquaculture,2012(364/365):240-246.
[34]Yan X C,Ding L,Li Y C,et al.Identification and profiling of microRNAs from skeletal muscle of the common carp[J].PLoS One,2012,7(1):e30925.
[35]Yi S,Gao Z X,Zhao H,et al.Identification and characterization of microRNAs involved in growth of blunt snout bream(Megalobrama amblycephala)by Solexa sequencing[J].BMC Genomics,2013,14(1):754.
[36]江守文.日本文昌鱼性别差异miRNA的筛选与功能鉴定[D].上海:上海海洋大学,2012.
[37]Memczak S,Jens M,Elefsinioti A,et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature,2013,495(7441):333-338.
[38]Yan B,Guo J T,Zhu C D,et al.miR-203b:a novel regulator of MyoD expression in tilapia skeletal muscle[J].Journal of Experimental Biology,2013,216(3):447-451.
[39]Chiavacci E,Dolfi L,Verduci L,et al.MicroRNA-218mediates the effects of Tbx5aover-expression on zebrafish heart development[J].PLoS One,2012,7(11):e50536.
[40]Lalwani M K,Sharma M,Singh A R,et al.Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity[J].PLoS One,2012,7(12):e52588.
[41]Nakamura Y,He X,Kato H,et al.Sox9is upstream of microRNA-140in cartilage[J].Applied Biochemistry and Biotechnology,2012,166(1):64-71.
[42]Huang J,Zhao L,Xing L,et al.MicroRNA-204regulates Runx2protein expression and mesenchymal progenitor cell differentiation[J].Stem Cells,2010,28(2):357-364.
[43]Li G X,Zhao Y L,Wen L,et al.Identification and characterization of MicroRNAs in the spleen of common carp immune organ[J].Journal of Cellular Biochemistry,2014,115(10):1768-1778.
[44]Li X Y,Ma J G,Fang Q,et al.Transcription alterations of microRNAs,cytochrome P4501A1and 3A65,and AhR and PXR in the liver of zebrafish exposed to crude microcystins[J].Toxicon,2013(73):17-22.
[45]Xu X Y,Shen Y B,Fu J J,et al.MicroRNA-induced negative regulation of TLR-5in grass carp,Ctenopharyngodon idella[J].Sci Rep,2016(6):18595.
[46]Xiao J,Zhong H,Zhou Y,et al.Identification and characterization of microRNAs in ovary and testis of Nile tilapia(Oreochromis niloticus)by using solexa sequencing technology[J].PLoS One,2014,9(1):e86821.
[47]Juanchich A,Le C A,Montfort J,et al.Identification of differentially expressed miRNAs and their potential targets during fish ovarian development[J].Biology of Reproduction,2013,88(5):1-11.
[48]Wang W,Liu W,Liu Q,et al.Coordinated microRNA and messenger RNA expression profiles for understanding sexual dimorphism of gonads and the potential roles of microRNA in the steroidogenesis pathway in Nile tilapia(Oreochromis niloticus)[J].Theriogenology,2016,85(5):970-978.
[49]Eshel O,Shirak A,Dor L,et al.Identification of male-specific amh duplication,sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia(Oreochromis niloticus)[J].BMC Genomics,2014,15(1):774.
[50]Yin V P,Lepilina A,Smith A,et al.Regulation of zebrafish heart regeneration by miR-133[J].Developmental Biology,2012,365(2):319-327.
[51]Chen J F,Mandel E M,Thomson J M,et al.The role of microRNA-1and microRNA-133in skeletal muscle proliferation and differentiation[J].Nature Genetics,2006,38(2):228-233.
[52]Hoppe B,Pietsch S,Franke M,et al.MiR-21is required for efficient kidney regeneration in fish[J].BMC Dev Biol,2015,15(1):1-10.
[53]Plaisance V,Abderrahmani A,Perret-Menoud V J,et al.MicroRNA-9controls the expression of granuphilin/Slp4and the secretory response of insulin-producing cells[J].Journal of Biological Chemistry,2006,281(37):26932-26942.
[54]Yu D,Dos Santos C O,Zhao G,et al.miR-451protects against erythroid oxidant stress by repressing 14-3-3zeta[J].Genes&Development,2010,24(15):1620-1633.
[55]Brzuzan P,Wony M,Wolińska L,et al.Expression profiling in vivo demonstrates rapid changes in liver microRNA levels of whitefish(Coregonus lavaretus)following microcystin-LR exposure[J].Aquatic Toxicology,2012(122/123):188-196.
[56]Jenny M J,Aluru N,Hahn M E.Effects of shortterm exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos[J].Toxicology and Applied Pharmacology,2012,264(2):262-273.
[57]Zhang L,Li Y Y,Zeng H C,et al.MicroRNA expression changes during zebrafish development induced by perfluorooctane sulfonate[J].Journal of Applied Toxicology,2011,31(3):210-222.
[2]Carrington J C,Ambros V.Role of microRNAs in plant and animal development[J].Science,2003,301(5631):336-338.
[3]Fu Y,Shi Z,Wu M,et al.Identification and differentia1expression of microRNAs during metamorphosis of the Japanese flounder(Paralichthys olivaceus)[J].PLos One,2011,6(7):e22957.
[4]Bizuayehu T T,Babiak I.MicroRNA in teleost fish[J].Genome Biology and Evolution,2014,6(8):1911-1937.
[5]Tang X L,Xu M J,Li Z H,et al.Effects of vitamin E on expressions of eight microRNAs in the liver of Nile tilapia(Oreochromis niloticus)[J].Fish&Shellfish Immunology,2013,34(6):1470-1475.
[6]唐雪莲,李洪,付京花.鱼类microRNAs研究进展[J].水产科学,2013,32(1):55-58.
[7]Bizuayehu T T,Babiak J,Norberg B,et al.Sex-biased miRNA expression in Atlantic halibut(Hippoglossus hippoglossus)brain and gonads[J].Sexual Development,2012,6(5):257-266.
[8]Zhang Q H,Xie D Z,Wang S Q,et al.miR-17is involved in the regulation of LC-PUFA biosynthesis in vertebrates:effects on liver expression of a fatty acyl desaturase in the marine teleost Siganus canaliculatus[J].Biochimica et Biophysica Acta,2014,1841(7):934-943.
[9]Berezikov E,Guryev V,van de Belt J,et al.Phylogenetic shadowing and computational identification of human microRNA genes[J].Cell,2005,120(1):21-24.
[10]Lee R C,Feinbaum R L,Ambros V.The C.elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity to lin-14[J].Cell,1993,75(5):843-854.
[11]Chen P Y,Manninga H,Slanchev K,et al.The developmental miRNA profiles of zebrafish as determined by small RNA cloning[J].Genes Development,2005,19(11):1288-1293.
[12]Salem M,Xiao C,Womack J,et al.A microRNA repertoire for functional genome research in rainbow trout(Oncorhynchus mykiss)[J].Mar Biotechnol(NY),2010,12(4):410-429.
[13]Chi W,Tong C,Gan X,et al.Characterization and comparative profiling of MiRNA transcriptomes in bighead carp and silver carp[J].PLoS One,2011,6(8):e23549.
[14]Yang L D,He S P.A bioinformatics-based update on microRNAs and their targets in rainbow trout(Oncorhynchus mykiss)[J].Gene,2014,533(1):261-269.
[15]孙君君,卢荣华,杨峰,等.草鱼SREBP-1基因的克隆及糖对其在肝脏中表达的影响[J].水产学报,2014,38(8):1057-1067.
[16]Her G M,Hsu C C,Hong J R,et al.Overexpression of gankyrin induces liver steatosis in zebrafish(Danio rerio)[J].Biochimica et Biophysica Acta,2011,1811(9):536-548.
[17]Horton J D,Goldstein J L,Brown M S.SREBPs:Activators of the complete program cholesterol and fatty acid synthesis in the liver[J].Journal of Clinical Investigation,2002,109(9):1125-1131.
[18]Shao W,Espenshade P J.Expanding roles for SREBP in metabolism[J].Cell Metab,2012,16(4):414-419.
[19]Linhart H G,Ishimura-Oka K,Demayo F,et al.C/EBPαis required for differentiation of white,but not brown,adipose tissue[J].Proc Natl Acad Sci U S A,2001,98(22):12532-12537.
[20]Tanaka T,Yoshida N,Kishimoto T,et al.Defective adipocyte differentiation in mice lacking the C/EBPbeta and/or C/EBPdelta gene[J].EMBO J,1997,16(24):7432-7443.
[21]Wang T,Li M,Guan J,et al.MicroRNAs miR-27a and miR-143regulate porcine adipocyte lipid metabolism[J].International Journal of Molecular Sciences,2011,12(11):7950-7959.
[22]Kida K,Nakajima M,Mohri T,et al.PPARalpha is regulated by miR-21and miR-27bin human liver[J].Pharmaceutical Research,2011,28(10):2467-2476.
[23]Zisoulis D G,Kai Z S,Chang K R,et al.Autoregulation of microRNA biogenesis by let-7and Argonaute[J].Nature,2012,486(7404):541-544.
[24]Hansen T B,Wiklund E B,Bramsen J B,et al.miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA[J].EMBO Journal,2011,30(2):4414-4422.
[25]Iliopoulos D,Drosatos K,Hiyama Y,et al.MicroRNA-370controls the expression of microRNA-122and Cpt1alpha and affects lipid metabolism[J].Journal of Lipid Research,2010,51(6):1513-1523.
[26]Mennigen J A,Panserat S,Larquier M,et al.Postprandial regulation of hepatic MicroRNAs predicted to target the insulin pathway in rainbow trout[J].PLoS One,2012,7(6):e38604.
[27]Davalos A,Goedeke L,Smibert P,et al.miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling[J].Proc Natl Acad Sci U S A,2011,108(22):9232-9237.
[28]Esau C,Davis S,Murray S F,et al.miR-122regulation of lipid metabolism revealed by in vivo antisense targeting[J].Cell Metabolism,2006,3(2):87-98.
[29]Rayner K J,Suarez Y,Davalos A,et al.MiR-33contributes to the regulation of cholesterol homeostasis[J].Science,2011,328(5985):1570-1573.
[30]Mennigen J A,Plagnes-juan E,Figueredo-silva C A,et al.Acute endocrine and nutritional co-regulation of the hepatic omy-miRNA-122band the lipogenic gene fas in rainbow trout,Oncorhynchus mykiss[J].Comp Biochem Physiol B Biochem Mol Biol,2014,169(3):16-24.
[31]Mennigen J A,Martyniuk C J,Seiliez I,et al.Metabolic consequences of microRNA-122 inhibition in rainbow trout,Oncorhynchus mykiss[J].BMC Genomics,2014,15(1):70.
[32]Huang C W,Li Y H,Hu S Y,et al.Differential expression patterns of growth-related microRNAs in the skeletal muscle of Nile tilapia(Oreochromis niloticus)[J].Journal of Animal Science,2012,90(12):4266-4279.
[33]Yan B,Guo J T,Zhao L H,et al.microRNA expression signature in skeletal muscle of Nile tilapia[J].Aquaculture,2012(364/365):240-246.
[34]Yan X C,Ding L,Li Y C,et al.Identification and profiling of microRNAs from skeletal muscle of the common carp[J].PLoS One,2012,7(1):e30925.
[35]Yi S,Gao Z X,Zhao H,et al.Identification and characterization of microRNAs involved in growth of blunt snout bream(Megalobrama amblycephala)by Solexa sequencing[J].BMC Genomics,2013,14(1):754.
[36]江守文.日本文昌鱼性别差异miRNA的筛选与功能鉴定[D].上海:上海海洋大学,2012.
[37]Memczak S,Jens M,Elefsinioti A,et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature,2013,495(7441):333-338.
[38]Yan B,Guo J T,Zhu C D,et al.miR-203b:a novel regulator of MyoD expression in tilapia skeletal muscle[J].Journal of Experimental Biology,2013,216(3):447-451.
[39]Chiavacci E,Dolfi L,Verduci L,et al.MicroRNA-218mediates the effects of Tbx5aover-expression on zebrafish heart development[J].PLoS One,2012,7(11):e50536.
[40]Lalwani M K,Sharma M,Singh A R,et al.Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity[J].PLoS One,2012,7(12):e52588.
[41]Nakamura Y,He X,Kato H,et al.Sox9is upstream of microRNA-140in cartilage[J].Applied Biochemistry and Biotechnology,2012,166(1):64-71.
[42]Huang J,Zhao L,Xing L,et al.MicroRNA-204regulates Runx2protein expression and mesenchymal progenitor cell differentiation[J].Stem Cells,2010,28(2):357-364.
[43]Li G X,Zhao Y L,Wen L,et al.Identification and characterization of MicroRNAs in the spleen of common carp immune organ[J].Journal of Cellular Biochemistry,2014,115(10):1768-1778.
[44]Li X Y,Ma J G,Fang Q,et al.Transcription alterations of microRNAs,cytochrome P4501A1and 3A65,and AhR and PXR in the liver of zebrafish exposed to crude microcystins[J].Toxicon,2013(73):17-22.
[45]Xu X Y,Shen Y B,Fu J J,et al.MicroRNA-induced negative regulation of TLR-5in grass carp,Ctenopharyngodon idella[J].Sci Rep,2016(6):18595.
[46]Xiao J,Zhong H,Zhou Y,et al.Identification and characterization of microRNAs in ovary and testis of Nile tilapia(Oreochromis niloticus)by using solexa sequencing technology[J].PLoS One,2014,9(1):e86821.
[47]Juanchich A,Le C A,Montfort J,et al.Identification of differentially expressed miRNAs and their potential targets during fish ovarian development[J].Biology of Reproduction,2013,88(5):1-11.
[48]Wang W,Liu W,Liu Q,et al.Coordinated microRNA and messenger RNA expression profiles for understanding sexual dimorphism of gonads and the potential roles of microRNA in the steroidogenesis pathway in Nile tilapia(Oreochromis niloticus)[J].Theriogenology,2016,85(5):970-978.
[49]Eshel O,Shirak A,Dor L,et al.Identification of male-specific amh duplication,sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia(Oreochromis niloticus)[J].BMC Genomics,2014,15(1):774.
[50]Yin V P,Lepilina A,Smith A,et al.Regulation of zebrafish heart regeneration by miR-133[J].Developmental Biology,2012,365(2):319-327.
[51]Chen J F,Mandel E M,Thomson J M,et al.The role of microRNA-1and microRNA-133in skeletal muscle proliferation and differentiation[J].Nature Genetics,2006,38(2):228-233.
[52]Hoppe B,Pietsch S,Franke M,et al.MiR-21is required for efficient kidney regeneration in fish[J].BMC Dev Biol,2015,15(1):1-10.
[53]Plaisance V,Abderrahmani A,Perret-Menoud V J,et al.MicroRNA-9controls the expression of granuphilin/Slp4and the secretory response of insulin-producing cells[J].Journal of Biological Chemistry,2006,281(37):26932-26942.
[54]Yu D,Dos Santos C O,Zhao G,et al.miR-451protects against erythroid oxidant stress by repressing 14-3-3zeta[J].Genes&Development,2010,24(15):1620-1633.
[55]Brzuzan P,Wony M,Wolińska L,et al.Expression profiling in vivo demonstrates rapid changes in liver microRNA levels of whitefish(Coregonus lavaretus)following microcystin-LR exposure[J].Aquatic Toxicology,2012(122/123):188-196.
[56]Jenny M J,Aluru N,Hahn M E.Effects of shortterm exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos[J].Toxicology and Applied Pharmacology,2012,264(2):262-273.
[57]Zhang L,Li Y Y,Zeng H C,et al.MicroRNA expression changes during zebrafish development induced by perfluorooctane sulfonate[J].Journal of Applied Toxicology,2011,31(3):210-222.