The emerging role of MicroRNAs in the regulation of gene expression by nutrients

Journal of Nutrigenetics and Nutrigenomics

Volumn 6, Issue 1, 2013, Pages 16-31

  García Segura, Laura ^a   Pérez Andrade, Martha ^a   Miranda Ríos, Juan ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Diet; Gene expression; MicroRNAs

Indexed keywords

AMINO ACID; CARBOHYDRATE; FATTY ACID; MICRORNA; MICRORNA 103; MICRORNA 107; MICRORNA 122; MICRORNA 125B; MICRORNA 143; MICRORNA 155; MICRORNA 16; MICRORNA 182; MICRORNA 222; MICRORNA 351; MICRORNA 451; MICRORNA 669C; PLANT MEDICINAL PRODUCT; TRACE ELEMENT; UNCLASSIFIED DRUG; VITAMIN;

ALPHA TOCOPHEROL DEFICIENCY; CARBOHYDRATE INTAKE; DIETARY INTAKE; FAT INTAKE; FOOD INTAKE; GENE EXPRESSION REGULATION; GENE FUNCTION; HUMAN; INTERVENTION STUDY; LIPID DIET; MACRONUTRIENT; NONHUMAN; NUTRITIONAL STATUS; PHARMACOGENETICS; PRIORITY JOURNAL; REVIEW; VITAMIN INTAKE;

ANIMALS; FOOD; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS;

EID: 84874265965     PISSN: 16616499     EISSN: 16616758     Source Type: Journal    
DOI: 10.1159/000345826     Document Type: Review

References (79)

1. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD: Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334:105-108.
2. Fenech M, El-Sohemy A, Cahill L, Ferguson LR, French TA, Tai ES, Milner J, Koh WP, Xie L, Zucker M, Buckley M, Cosgrove L, Lockett T, Fung KY, Head R: Nutrigenetics and nutrigenomics: viewpoints on the current status and applications in nutrition research and practice. J Nutrigenet Nutrigenomics 2011; 4:69-89.
3. Thomason MK, Storz G: Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet 2010; 44: 167-188.
4. Carthew RW, Sontheimer EJ: Origins and mechanisms of miRNAs and siRNAs. Cell 2009; 136: 642-655.
5. Fang Z, Rajewsky N: The impact of miRNA target sites in coding sequences and in 3'UTRs. PLoS One 2011; 6:e18067.
6. Zhang X, Rossi JJ: Phylogenetic comparison of small RNA-triggered transcriptional gene silencing. J Biol Chem 2011; 286:29443-29448.
7. Friedman RC, Farh KK, Burge CB, Bartel DP: Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19: 92-105.
8. Chiou TJ: The role of microRNAs in sensing nutrient stress. Plant Cell Environ 2007; 30:323-332.
9. Holtz J, Pasquinelli AE: Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabdi-tis elegans. RNA 2009; 15:400-405.
10. Leung AK, Sharp PA: MicroRNA functions in stress responses. Mol Cell 2010; 40:205-215.
11. Dolganiuc A, Petrasek J, Kodys K, Catalano D, Mandrekar P, Velayudham A, Szabo G: MicroRNA expression profile in Lieber-DeCarli diet-induced alcoholic and methionine-choline deficient diet-induced nonalcoholic steatohepatitis models in mice. Alcohol Clin Exp Res 2009; 33:1704-1710.
12. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W: Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 2006; 125:1111-1124.
13. Drummond, MJ, Glynn, EL, Fry CS, Dhanani S, Volpi E, Rasmussen BB: Essential amino acids increase micro-RNA-499,-208b, and-23a and downregulate myostatin and myocyte enhancer factor 2C mRNA expression in human skeletal muscle. J Nutr 2009; 139: 2279-2284.
14. Druz A, Betenbaugh M, Shiloach J: Glucose depletion activates mmu-miR-466h-5p expression through oxidative stress and inhibition of histone deacetylation. Nucleic Acids Res 2012; 40:7291-7302.
15. Dey N, Das F, Mariappan MM, Mandal CC, Ghosh-Choudhury N, Kasinath BS, Choudhury GG: MicroRNA-21 orchestrates high glucose-induced signals to TOR complex 1, resulting in renal cell pathology in diabetes. J Biol Chem 2011; 286:25586-25603.
16. Long J, Wang Y, Wang W, Chang BH, Danesh FR: MicroRNA-29c is a signature microRNA under high glucose conditions that targets Sprouty homolog 1, and its in vivo knockdown prevents progression of diabetic nephropathy. J Biol Chem 2011; 286:11837-11848.
17. Tzur G, Levy A, Meiri E, Barad O, Spector Y, Bentwich Z, Mizrahi L, Katzenellenbogen M, Ben-Shushan E, Reubinoff BE, Galun E: MicroRNA expression patterns and function in endodermal differentiation of human embryonic stem cells. PLoS One 2008; 3:e3726.
18. Davidson LA, Wang N, Shah MS, Lupton JR, Ivanov I, Chapkin RS: n-3 polyunsaturated fatty acids modulate carcinogen-directed non-coding microRNA signatures in rat colon. Carcinogenesis 2009; 30:2077-2084.
19. Parra P, Serra F, Palou A: Expression of adipose microRNAs is sensitive to dietary conjugated linoleic acid treatment in mice. PLoS One 2010; 5:e13005.
20. Zhang J, Zhang F, Didelot X, Bruce KD, Cagampang FR, Vatish M, Hanson M, Lehnert H, Ceriello A, Byrne CD: Maternal high fat diet during pregnancy and lactation alters hepatic expression of insulin like growth factor-2 and key microRNAs in the adult offspring. BMC Genomics 2009; 10: 478.
21. Brueckner B, Stresemann C, Kuner R, Mund C, Musch T, Meister M, Sultmann H, Lyko F: The human let-7a-3 locus contains an epigenetically regulated microRNA gene with oncogenic function. Cancer Res 2007; 67:1419-1423.
22. Alisi A, Da Sacco L, Bruscalupi G, Piemonte F, Panera N, De Vito R, Leoni S, Bottazzo GF, Masotti A, Nobili V: Mir-nome analysis reveals novel molecular determinants in the pathogenesis of diet-induced nonalcoholic fatty liver disease. Lab Invest 2011; 91:283-293.
23. Park JH, Ahn J, Kim S, Kwon DY, Ha TY: Murine hepatic miRNAs expression and regulation of gene expression in diet-induced obese mice. Mol Cells 2011; 31:33-38.
24. Trajkovski M, Hausser J, Soutschek J, Bhat B, Akin A, Zavolan M, Heim MH, Stoffel M: MicroRNAs 103 and 107 regulate insulin sensitivity. Nature 2011; 474: 649-653.
25. Jordan SD, Krüger M, Willmes DM, Redemann N, Wunderlich FT, Brönneke HS, Merkwirth C, Kashkar H, Olkkonen VM, Böttger T, Braun T, Seibler J, Brüning JC: Obesity-induced overexpression of miRNA-143 inhibits insulin-stimulated AKT activation and impairs glucose metabolism. Nat Cell Biol 2011; 13: 434-446.
26. Melnick A, Licht JD: Deconstructing a disease: RARalpha, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia. Blood 1999; 93: 3167-3215.
27. Garzon R, Pichiorri F, Palumbo T, Visentini M, Aqeilan R, Cimmino A, Wang H, Sun H, Volinia S, Alder H, Calin GA, Liu CG, Andreeff M, Croce CM: MicroRNA gene expression during retinoic acid-induced differentiation of human acute promyelocytic leukemia. Oncogene 2007; 26: 4148-4157.
28. Kawasaki H, Taira K: Functional analysis of microRNAs during the retinoic acid-induced neuronal differentiation of human NT2 cells. Nucleic Acids Res Suppl 2003; 3: 243-244.
29. Zhao JJ, Sun DG, Wang J, Liu SR, Zhang CY, Zhu MX, Ma X: Retinoic acid downregulates microRNAs to induce abnormal development of spinal cord in spina bifida ratmodel. Childs Nerv Syst 2008; 24:485-492.
30. Meseguer S, Mudduluru G, Escamilla JM, Allgayer H, Barettino D: MicroRNAs-10a and-10b contribute to retinoic acid-induced differentiation of neuroblastoma cells and target the alternative splicing regulatory factor SFRS1 (SF2/ASF). J Biol Chem 2011, 286: 4150-4164.
31. Foley NH, Bray I, Watters KM, Das S, Bryan K, Bernas T, Prehn JH, Stallings RL: MicroRNAs 10a and 10b are potent inducers of neuroblastoma cell differentiation through targeting of nuclear receptor corepressor 2. Cell Death Differ 2011; 18: 1089-1098.
32. Terao M, Fratelli M, Kurosaki M, Zanetti A, Guarnaccia V, Paroni G, Tsykin A, Lupi M, Gianni M, Goodall GJ, Ga-rattini E: Induction of miR-21 by retinoic acid in estrogen receptor-positive breast carcinoma cells: biological correlates and molecular targets. J Biol Chem 2011; 286:4027-4042.
33. Marsit CJ, Eddy K, Kelsey KT: MicroRNA responses to cellular stress. Cancer Res 2006; 66:10843-10848.
34. Kutay H, Bai S, Datta J, Motiwala T, Pogribny I, Frankel W, Jacob ST, Ghoshal K: Downregulation of miR-122 in the rodent and human hepatocellular carcinomas. J Cell Biochem 2006; 99: 671-678.
35. Pogribny IP, Tryndyak VP, Ross SA, Beland FA: Differential expression of microRNAs during hepatocarcinogenesis induced by methyl deficiency in rats. Nutr Rev 2008; 66(suppl 1):S33-S35.
36. Tryndyak VP, Ross SA, Beland FA, Pogribny IP: Down-regulation of the microRNAs miR-34a, miR-127, and miR-200b in rat liver during hepatocarcinogenesis induced by a methyl-deficient diet. Mol Carcinog 2009; 48:479-487.
37. Mohri T, Nakajima M, Takagi S, Komagata S, Yokoi T: MicroRNA regulates human vitamin D receptor. Int J Cancer 2009; 125:1328-1333.
38. Komagata S, Nakajima M, Takagi S, Mohri T, Taniya T, Yokoi T: Human CYP24 catalyzing the inactivation of cal-citriol is post-transcriptionally regulated by miR-125b. Mol Pharmacol 2009; 76:702-709.
39. Wang X, Gocek E, Liu CG, Studzinski GP: MicroRNAs181 regulate the expression of p27Kip1 in human myeloid leukemia cells induced to differentiate by 1, 25-dihydroxyvitamin D3. Cell Cycle 2009; 8:736-741.
40. Gocek E, Wang X, Liu X, Liu CG, Studzinski GP: MicroRNA-32 upregulation by 1, 25-dihydroxyvitamin D3 in human myeloid leukemia cells leads to Bim targeting and inhibition of AraC-induced apoptosis. Cancer Res 2011; 71: 6230-6239.
41. Peng X, Vaishnav A, Murillo G, Alimirah F, Torres KE, Mehta RG: Protection against cellular stress by 25-hydroxyvi-tamin D3 in breast epithelial cells. J Cell Biochem 2010; 110:1324-1333.
42. Wang WL, Chatterjee N, Chittur SV, Welsh J, Tenniswood MP: Effects of 1a, 25 dihydroxyvitamin D3 and testosterone on miRNA and mRNA expression in LNCaP cells. Mol Cancer 2011; 10: 58.
43. Gaedicke S, Zhang X, Schmelzer C, Lou Y, Doering F, Frank J, Rimbach G: Vitamin E dependent microRNA regulation in rat liver. FEBS Lett 2008; 582: 3542-3546.
44. Ortega-Cuellar D, Hernandez-Mendoza A, Moreno-Arriola E, Carvajal-Aguilera K, Perez-Vazquez V, Gonzalez-Alvarez R, Velazquez-Arellano A: Biotin starvation with adequate glucose provision causes paradoxical changes in fuel metabolism gene expression similar in rat (Rattus norvegicus), nematode (Caenorhabditis elegans) and yeast (Saccha-romyces cerevisiae). J Nutrigenet Nutrigenomics 2010; 3: 18-30.
45. Bao B, Rodriguez-Melendez R, Wijeratne SS, Zempleni J: Biotin regulates the expression of holocarboxylase synthetase in the miR-539 pathway in HEK-293 cells. J Nutr 2010; 140:1546-1551.
46. Bao B, Rodriguez-Melendez R, Zempleni J: Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells. J Nutr Biochem 2012; 23: 635-639.
47. Schmelzer C, Kitano M, Rimbach G, Niklowitz P, Menke T, Hosoe K, Frank Döring F: Effects of ubiquinol-10 on microRNA-146a expression in vitro and in vivo. Mediators Inflamm 2009; 2009:415437.
48. Wagner AE, Boesch-Saadatmandi C, Dose J, Schultheiss G, Rimbach G: Anti-inflammatory potential of allyl-isothio-cyanate-role of Nrf2, NFKB and microRNA-155. J Cell Mol Med 2012; 16:836-843.
49. Kusuda R, Cadetti F, Ravanelli MI, Sousa TA, Zanon S, De Lucca FL, Lucas G: Differential expression of microRNAs in mouse pain models. Mol Pain 2011; 7:17.
50. Chintharlapalli S, Papineni S, Abdelrahim M, Abudayyeh A, Jutooru I, Chadalapaka G, Wu F, Mertens-Talcott S, Vanderlaag K, Cho SD, Smith R 3rd, Safe S: Oncogenic microRNA-27a is a target for anticancer agent methyl 2-cyano-3, 11-dioxo-18beta-olean-1, 12-dien-30-oate in colon cancer cells. Int J Cancer 2009; 125: 1965-1974.
51. Jutooru I, Chadalapaka G, Abdelrahim M, Riyaz Basha M, Samudio I, Konopleva M, Andreeff M, Safe S: Methyl 2-cyano-3, 12-dioxooleana-1, 9-dien-28-oate decreases specificity protein transcription factors and inhibits pancreatic tumor growth: role of microRNA 27a. Mol Pharmacol 2010; 78:226-236.
52. Sun M, Estrov Z, Ji Y, Coombes KR, Harris DH, Kurzrock R: Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. Mol Cancer Ther 2008; 7:464-473.
53. Ali S, Ahmad A, Banerjee S, Padhye S, Dominiak K, Schaffert JM, Wang Z, Philip PA, Sarkar FH: Gemcitabine sensitivity can be induced in pancreatic cancer cells through modulation of miR-200 and miR-21 expression by curcumin or its analogue CDF. Cancer Res 2010; 70:3606-3617.
54. Yang J, Cao Y, Sun J, Zhang Y: Curcumin reduces the expression of Bcl-2 by upregulating miR-15a and miR-16 in MCF-7 cells. Med Oncol 2010; 27:1114-1118.
55. Zhang J, Zhang T, Ti X, Shi J, Wu C, Ren X, Yin H: Curcumin promotes apoptosis in A549/DDP multidrug-resistant human lung adenocarcinoma cells through an miRNA signaling pathway. Biochem Biophys Res Commun 2010; 399: 1-6.
56. Mudduluru G, George-William JN, Muppala S, Asangani IA, Regalla K, Nelson LD, Allgayer H: Curcumin regulates miR-21 expression and inhibits invasion and metastasis in colorectal cancer. Biosci Rep 2011; 31: 185-197.
57. Saini S, Arora S, Majid S, Shahryari V, Chen Y, Deng G, Yamamura S, Ueno K, Dahiya R: Curcumin modulates mi-croRNA-203 mediated regulation of the Src-Akt axis in bladder cancer. Cancer Prev Res (Phila) 2011; 4: 1698-1709.
58. Tsang WP, Kwok TT: Epigallocatechin gallate up-regulation of miR-16 and induction of apoptosis in human cancer cells. J Nutr Biochem 2010; 21:140-146.
59. Wen XY, Wu SY, Li ZQ, Liu ZQ, Zhang JJ, Wang GF, Jiang ZH, Wu SG: Ellagitannin (BJA3121), an anti-proliferative natural polyphenol compound, can regulate the expression of miRNAs in HepG2 cancer cells. Phytother Res 2009; 23: 778-784.
60. Li Y, VandenBoom TG II, Kong D, Wang Z, Ali S, Philip PA, Sarkar FH: Up-regulation of miR-200 and let-7 by natural agents leads to the reversal of epithelial-to-mesenchymal transition in gemcitabine resistant pancreatic cancer cells. Cancer Res 2009; 69:6704-6712.
61. Li Y, Vandenboom TG II, Wang Z, Kong D, Ali S, Philip PA, Sarkar FH: miR-146a suppresses invasion of pancreatic cancer cells. Cancer Res 2010; 70:1486-1495.
62. Melkamu T, Zhang X, Tan J, Zeng Y, Kassie F: Alteration of microRNA expression in vinyl-carbamate-induced mouse lung tumors and modulation by the chemopreventive agent indole-3-carbinol. Carcinogenesis 2010; 31:252-258.
63. Iorio MV, Croce CM: MicroRNAs in cancer: small molecules with a huge impact. J Clin Oncol 2009; 27: 5848-5856.
64. Li LN, Zhang HD, Zhi R, Yuan SJ: Down-regulation of some miRNAs by degrading their precursors contributes to anti-cancer effect of mistletoe lectin-I. Br J Pharmacol 2011; 162:349-364.
65. Huang W, Li MD: Nicotine modulates expression of miR-140 ∗, which targets the 3-untranslated region of dynamin 1 gene (Dnm1). Int J Neuropsychopharmacol 2009; 12: 537-546.
66. Noratto GD, Angel-Morales G, Talcott ST, Mertens-Talcott SU: Polyphenolics from açaí (Euterpe oleracea Mart.) and red muscadine grape (Vitis rotundifolia) protect human umbilical vascular endothelial cells (HUVEC) from glucose-and lipopolysaccharide (LPS)-induced inflammation and target microRNA-126. J Agric Food Chem 2011; 59: 7999-8012.
67. Boesch-Saadatmandi C, Loboda A, Wagner AE, Stachurska A, Jozkowicz A, Dulak J, Döring F, Wolffram S, Rimbach G: Effect of quercetin and its metabolites isorhamnetin and quercetin-3-glucuronide on inflammatory gene expression: role of miR-155. J Nutr Biochem 2011; 22:293-299.
68. Noratto GD, Kim Y, Talcott ST, Mertens-Talcott SU: Flavonol-rich fractions of yaupon holly leaves (Ilex vomitoria, Aquifoliaceae) induce microRNA-146a and have anti-inflammatory and chemopreventive effects in intestinal myofibroblast CCD-18Co cells. Fitoterapia 2011; 82: 557-569.
69. Tili E, Michaille JJ, Adair B, Alder H, Limagne E, Taccioli C, Ferracin M, Delmas D, Latruffe N, Croce CM: Resvera-trol decreases the levels of miR-155 by upregulating miR-663, a microRNA targeting JunB and JunD. Carcinogenesis 2010; 31:1561-1566.
70. Tili E, Michaille JJ, Alder H, Volinia S, Delmas D, Latruffe N, Croce CM: Resveratrol modulates the levels of microRNAs targeting genes encoding tumor-suppressors and effectors of TGFbeta signaling pathway in SW480 cells. Biochem Pharmacol 2010; 80:2057-2065.
71. Frost RJ, Olson EN: Control of glucose homeostasis and insulin sensitivity by the Let-7 family of microRNAs. Proc Natl Acad Sci USA 2011; 108:21075-21080.
72. Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG, Urbach A, Thornton JE, Triboulet R, Gregory RI, DIAGRAM Consortium, MAGIC Investigators, Altshuler D, Daley GQ: The Lin28/let-7 axis regulates glucose metabolism. Cell 2011; 147: 81-94.
73. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL, Graham M, McKay R, Subramanian A, Propp S, Lollo BA, Freier S, Bennett CF, Bhanot S, Monia BP: miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 2006; 3:87-98.
74. Elmen J, Lindow M, Schüt z S, Lawrence M, Petri A, Obad S, Lindholm M, Hedtjärn M, Hansen HF, Berger U, Gulla ns S, Kearney P, Sarnow P, Straarup EM, Kauppinen S: LNA-mediated microRNA silencing in non-human primates. Nature 2008; 452:896-899.
75. Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY: Exogenous plant miR-168a specifically targets mammalian LDLRAP1:evidence of cross-kingdom regulation by microRNA. Cell Res 2012; 22:107-126.
76. Liu H, Wang X, Wang H-D, Wu J, Ren J, Meng L, Wu Q, Dong H, Wu J, Kao T-Y, Ge Q, Wu Z, Yuh C-H, Shan G: Esch-erichia colinon coding RNAs canaffect gene expression and physiology of Caenorhabditis elegans. Nat Commun 2012; 3:1073.
77. Skalsky RL, Cullen BR: Viruses, microRNAs, and host interactions. Annu Rev Microbiol 2010; 64:123-141.
78. Kosaka N, Izumi H, Sekine K, Ochiya T: microRNA as a new immune-regulatory agent in breast milk. Silence 2010; 1:7.
79. Stenvang J, Petri A, Lindow M, Obad S, Kauppinen S: Inhibition of microRNA function by antimiR oligonucleotides. Silence 2012; 3: 1.