An NTD-Associated Polymorphism in the 3' UTR of MTHFD1L can Affect Disease Risk by Altering miRNA Binding

Human Mutation

Volumn 35, Issue 1, 2014, Pages 96-104

  Minguzzi, Stefano ^a   Selcuklu, S Duygu ^b   Spillane, Charles ^b   Parle Mcdermott, Anne ^a  

^a DUBLIN CITY UNIVERSITY   (Ireland)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Folate; MicroRNA 197; MicroRNA 9; MTHFD1L; NTDs; Rs7646; SNP

Indexed keywords

MICRORNA; MICRORNA 197; MICRORNA 9; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; BINDING AFFINITY; BINDING SITE; CELL STRAIN HEK293; CELL STRAIN MCF 7; CONTROLLED STUDY; DOWN REGULATION; GENE; GENE EXPRESSION; GENE REPRESSION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; MTHFD1L GENE; NEURAL TUBE DEFECT; NONHUMAN; PRIORITY JOURNAL; RNA BINDING; SINGLE NUCLEOTIDE POLYMORPHISM; THERMODYNAMICS;

FOLATE; MICRORNA-197; MICRORNA-9; MTHFD1L; NTDS; RS7646; SNP;

3' UNTRANSLATED REGIONS; ALLELES; AMINOHYDROLASES; BINDING SITES; FORMATE-TETRAHYDROFOLATE LIGASE; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOTYPE; HEK293 CELLS; HUMANS; MCF-7 CELLS; METHYLENETETRAHYDROFOLATE DEHYDROGENASE (NADP); MICRORNAS; MODELS, MOLECULAR; MULTIENZYME COMPLEXES; NEURAL TUBE DEFECTS; POLYMORPHISM, SINGLE NUCLEOTIDE; THERMODYNAMICS;

EID: 84890695946     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22459     Document Type: Article

References (40)

1. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281-297.
2. Bressler J, Folsom AR, Couper DJ, Volcik KA, Boerwinkle E. 2010. Genetic variants identified in a European genome-wide association study that were found to predict incident coronary heart disease in the atherosclerosis risk in communities study. Am J Epidemiol 171(1):14-23.
3. Chen K, Rajewsky N. 2006. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38(12):1452-1456.
4. Czeizel AE, Dudas I. 1992. Prevention of the first occurrence of neural-tube defects by periconceptional vitamin supplementation. N Engl J Med 327(26):1832-1835.
5. Du L, Schageman JJ, Subauste MC, Saber B, Hammond SM, Prudkin L, Wistuba II, Ji L, Roth JA, Minna JD, Pertsemlidis A. 2009. miR-93, miR-98, and miR-197 regulate expression of tumor suppressor gene FUS1. Mol Cancer Res 7(8):1234-1243.
6. Haas U, Sczakiel G, Laufer SD. 2012. MicroRNA-mediated regulation of gene expression is affected by disease-associated SNPs within the 3'-UTR via altered RNA structure. RNA Biol 9(6).
7. Jain M, Nilsson R, Sharma S, Madhusudhan N, Kitami T, Souza AL, Kafri R, Kirschner MW, Clish CB, Mootha VK. 2012. Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science 336(6084):1040-1044.
8. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. 2007. The role of site accessibility in microRNA target recognition. Nat Genet 39(10):1278-1284.
9. Khew-Goodall Y, Goodall GJ. 2010. Myc-modulated miR-9 makes more metastases. Nat Cell Biol 12(3):209-211.
10. Kirke PN, Scott JM. 2005. Pre-conception nutrition and prevention of neural tube defects. In: Sadler MJ, Strain JJ, Caballero B, editors. Encyclopaedia of human nutrition. New York: Oxford Academic Press. p 15-27.
11. Laios A, O'Toole S, Flavin R, Martin C, Kelly L, Ring M, Finn SP, Barrett C, Loda M, Gleeson N, D'Arcy T, McGuinness E, et al. 2008. Potential role of miR-9 and miR-223 in recurrent ovarian cancer. Mol Cancer 7:35.
12. Lehmann U, Streichert T, Otto B, Albat C, Hasemeier B, Christgen H, Schipper E, Hille U, Kreipe HH, Langer F. 2010. Identification of differentially expressed microRNAs in human male breast cancer. BMC Cancer 10:109.
13. Lujambio A, Calin GA, Villanueva A, Ropero S, Sanchez-Cespedes M, Blanco D, Montuenga LM, Rossi S, Nicoloso MS, Faller WJ, Gallagher WM, Eccles SA, et al. 2008. A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA 105(36):13556-13561.
14. Lukiw WJ. 2007. Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. Neuroreport 18(3):297-300.
15. Maes OC, Chertkow HM, Wang E, Schipper HM. 2009. MicroRNA: implications for Alzheimer Disease and other Human CNS Disorders. Curr Genomics 10(3):154-168.
16. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288(5):911-940.
17. McEntee G, Minguzzi S, O'Brien K, Ben Larbi N, Loscher C, O'Fagain C, Parle-McDermott A. 2011. The former annotated human pseudogene dihydrofolate reductase-like 1 (DHFRL1) is expressed and functional. Proc Natl Acad Sci USA 108(37):15157-15162.
18. Mishra PJ, Humeniuk R, Mishra PJ, Longo-Sorbello GS, Banerjee D, Bertino JR. 2007. A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA 104(33):13513-13518.
19. Momb J, Lewandowski JP, Bryant JD, Fitch R, Surman DR, Vokes SA, Appling DR. 2013. Deletion of Mthfd1l causes embryonic lethality and neural tube and craniofacial defects in mice. Proc Natl Acad Sci USA 110(2):549-554.
20. MRC Vitamin Study Research Group. 1991. Prevention of neural tube defects: results of the Medical Research Council Vitamin Study. MRC Vitamin Study Research Group. Lancet 338(8760):131-137.
21. Naj AC, Beecham GW, Martin ER, Gallins PJ, Powell EH, Konidari I, Whitehead PL, Cai G, Haroutunian V, Scott WK, Vance JM, Slifer MA, et al. 2010. Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities. PLoS Genet 6(9).
22. Parle-McDermott A, Pangilinan F, O'Brien KK, Mills JL, Magee AM, Troendle J, Sutton M, Scott JM, Kirke PN, Molloy AM, Brody LC. 2009. A common variant in MTHFD1L is associated with neural tube defects and mRNA splicing efficiency. Hum Mutat 30(12):1650-1656.
23. Pereira PM, Marques JP, Soares AR, Carreto L, Santos MA. 2010. MicroRNA expression variability in human cervical tissues. PLoS One 5(7):e11780.
24. Pike ST, Rajendra R, Artzt K, Appling DR. 2010. Mitochondrial C1-tetrahydrofolate synthase (MTHFD1L) supports the flow of mitochondrial one-carbon units into the methyl cycle in embryos. J Biol Chem 285(7):4612-4620.
25. Prasannan P, Appling DR. 2009. Human mitochondrial C1-tetrahydrofolate synthase: submitochondrial localization of the full-length enzyme and characterization of a short isoform. Arch Biochem Biophys 481(1):86-93.
26. Prasannan P, Pike S, Peng K, Shane B, Appling DR. 2003. Human mitochondrial C1-tetrahydrofolate synthase: gene structure, tissue distribution of the mRNA, and immunolocalization in Chinese hamster ovary calls. J Biol Chem 278(44):43178-43187.
27. Rampersaud E ME, Speer MC. 2006. Nonsyndromic neural tube defects: Genetic basis and genetic investigations. New York: Oxford Univ Press.
28. Samani NJ, Erdmann J, Hall AS, Hengstenberg C, Mangino M, Mayer B, Dixon RJ, Meitinger T, Braund P, Wichmann HE, Barrett JH, Konig IR, et al. 2007. Genomewide association analysis of coronary artery disease. N Engl J Med 357(5):443-453.
29. Saunders MA, Liang H, Li WH. 2007. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA 104(9):3300-3305.
30. Schonrock N, Humphreys DT, Preiss T, Gotz J. 2012. Target gene repression mediated by miRNAs miR-181c and miR-9 both of which are down-regulated by amyloid-beta. J Mol Neurosci 46(2):324-335.
31. Selcuklu SD, Donoghue MT, Rehmet K, de Souza Gomes M, Fort A, Kovvuru P, Muniyappa MK, Kerin MJ, Enright AJ, Spillane C. 2012. MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells. J Biol Chem 287(35):29516-29528.
32. Song F, Zheng H, Liu B, Wei S, Dai H, Zhang L, Calin GA, Hao X, Wei Q, Zhang W, Chen K. 2009. An miR-502-binding site single-nucleotide polymorphism in the 3'-untranslated region of the SET8 gene is associated with early age of breast cancer onset. Clin Cancer Res 15(19):6292-6300.
33. Sugiura T, Nagano Y, Inoue T, Hirotani K. 2004. A novel mitochondrial C1-tetrahydrofolate synthetase is upregulated in human colon adenocarcinoma. Biochem Biophys Res Commun 315(1):204-211.
34. Wuchty S, Fontana W, Hofacker IL, Schuster P. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49(2):145-165.
35. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, Calin GA, Liu CG, et al. 2006. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9(3):189-198.
36. Yu Z, Li Z, Jolicoeur N, Zhang L, Fortin Y, Wang E, Wu M, Shen SH. 2007. Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers. Nucleic Acids Res 35(13):4535-4541.
37. Yuva-Aydemir Y, Simkin A, Gascon E, Gao FB. 2011. MicroRNA-9: functional evolution of a conserved small regulatory RNA. RNA Biol 8(4):557-564.
38. Zhang L, Liu Y, Song F, Zheng H, Hu L, Lu H, Liu P, Hao X, Zhang W, Chen K. 2011. Functional SNP in the microRNA-367 binding site in the 3' UTR of the calcium channel ryanodine receptor gene 3 (RYR3) affects breast cancer risk and calcification. Proc Natl Acad Sci USA 108(33):13653-13658.
39. Zhang L, Ren A, Li Z, Hao L, Tian Y, Li Z. 2006. Folate concentrations and folic acid supplementation among women in their first trimester of pregnancy in a rural area with a high prevalence of neural tube defects in Shanxi, China. Birth Defects Res A Clin Mol Teratol 76(6):461-466.
40. Zheng D, Haddadin S, Wang Y, Gu LQ, Perry MC, Freter CE, Wang MX. 2011. Plasma microRNAs as novel biomarkers for early detection of lung cancer. Int J Clin Exp Pathol 4(6):575-586.