The importance of nutrition in gene expression, replication, repair and prevention of DNA damage

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, College of Agriculture, Shahid Bahonar University of Kerman

2 Assistant Professor, Department of Plant Pathology, Rafsanjan Branch, Islamic Azad University, Rafsanjan, Iran.

Abstract

Objective Since nutrition affects all the interactions of the body, especially the genome as well as the expression of genes, and all organisms are always feeding, and without feeding life is not possible. Therefore, the aim of this study was to review the role of nutrition in gene expression, DNA replication, prevention of DNA damage and DNA repair. Materials and methods In this study, the keywords such as cancer, ribonuclease, ribonuclease inhibitor and RNA were used to search in databases including Scopus, SID, IranDoc, PubMed, Google Scholar, Web of Science and IranMedex. In order to select the documents used, all articles published in non-English and Persian languages, duplicate articles, articles that could not be accessed to the full text, as well as articles that were presented as abstracts were removed. Finally, the selected cases were thoroughly studied and summarized in order to prepare the current review. Results Regulation of gene expression is essential to life and health and is sensitive to endogenous and dietary and other environmental factors that exert their action at multiple levels and by multiple mechanisms. There are important and intimate links between diet/nutrition, metabolic status, signaling pathways, and gene regulation. Postgenomic technologies including microarray hybridization and massive next-generation sequencing (RNA-Seq) enable nowadays highthroughput analysis, at genome-wide level, of the transcriptome and its dynamics (presence and quantity of RNAs, RNA expression patterns). Further, changes induced by dietary or other factors in TF binding site occupancy, chromatin features, global patterns of transcript decay, and translational profiling can also be studied nowadays at a genome-wide level. There is overwhelming evidence that a large number of micronutrients (vitamins and minerals) are required as cofactors for enzymes or as part of the structure of proteins (metalloenzymes) involved in DNA repair, prevention of oxidative damage to DNA, as well as maintenance and methylation of DNA. The role of micronutrients in the maintenance of genome stability has been extensively reviewed. Some of micronutrients involved in various genome stability processes. There are various mechanisms by which micronutrient deficiency could cause DNA damage, accelerate senescence and chromosomal instability. Conclusion Integration of results from these varied technologies will ultimately allow a comprehensive, system-wide understanding of gene expression control and of diet-gene-health relationships in modern nutrition science.

Keywords


Ames BN (2006) Low micronutrient intake may accelerate the degenerative diseases of aging through allocation of scarce micronutrients by triage. Proc Natl Acad Sci U S A 103 (47), 17589e17594.
Armendares S, Salamanca F, Frenk S (1971) Chromosome abnormalities in severe protein calorie malnutrition. Nature 232, 271e273.
Bailey, L.B., Stover, P.J., McNulty, H., et al. (2015) Biomarkers of nutrition for development-folate review. J Nutr 145 (7), 1636Se1680S.
Barazandeh A, Mohammadabadi MR, Ghaderi M, Nezamabadipour H (2016a) Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features. Czech J Anim Sci 61, e487.
Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M, Nezamabadipour H (2016b) Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm. Iran J Appl Anim Sci 6 (3), 571-579.
Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M, Rafeied F, Imumorin IG 2019 Whole genome comparative analysis of CpG islands in camelid and other mammalian genomes. Mammal Biol 98, 73-79.
Danino YM, Even D, Ideses D, Juven-Gershon T (2015) The core promoter: at the heart of gene expression. Biochim Biophys Acta 1849, 1116e1131.
Fenech M (2012) Folate (vitamin B9) and vitamin B12 and their function in the maintenance of nuclear and mitochondrial genome integrity. Mutat Res 733 (1e2), 21e33.
Fenech M, Baghurst P, Luderer W, et al. (2005) Low intake of calcium, folate, nicotinic acid, vitamin E, retinol, beta-carotene and high intake of pantothenic acid, biotin and riboflavin are significantly associated with increased genome instability -results from a dietary intake and micronucleus index survey in South Australia. Carcinogenesis 26 (5), 991e999.
Fenech MF (2010) Dietary reference values of individual micronutrients and nutriomes for genome damage prevention: current status and a road map to the future. Am J Clin Nutr 91 (5), 1438Se1454S.
Fenech MF (2014) Nutriomes and personalised nutrition for DNA damage prevention, telomere integrity maintenance and cancer growth control. Cancer Treat Res 159, 427e441.
Ferguson LR, Philpott M (2008) Nutrition and mutagenesis. Annu Rev Nutr 28, 313e329.
Fuss JO, Tsai CL, Ishida JP, Tainer JA (2015) Emerging critical roles of Fe-S clusters in DNA replication and repair. Biochim Biophys Acta 1853 (6), 1253e1271.
Grimaldi KA, van Ommen B, Ordovas JM, et al. (2017) Proposed guidelines to evaluate scientific validity and evidence for genotype-based dietary advice. Genes Nutr 12 (35), eCollection 2017.
Hartwig A (2001) Role of magnesium in genomic stability. Mutat Res 475 (1e2), 113e121.
Kim S, Sung J, Foo M, Jin YS, Kim PJ (2015) Uncovering the nutritional landscape of food. PLoS One 10 (3), e0118697.
Lamprecht SA, Lipkin M (2003) Chemoprevention of colon cancer by calcium, vitamin D and folate: molecular mechanisms. Nat Rev Cancer 3, 601e614.
Lane AN, Fan TW (2015) Regulation of mammalian nucleotide metabolism and biosynthesis. Nucleic Acids Res 43 (4), 2466e2485.
Li X, Egervari G, Wang Y, Berger SL, Lu Z (2018) Regulation of chromatin and gene expression by metabolic enzymes and metabolites. Nat Rev Mol Cell Biol 19, 563e578.
Masoudzadeh SH, Mohammadabadi M, Khezri A, et al. (2020a) Effects of diets with different levels of fennel (Foeniculum vulgare) seed powder on DLK1 gene expression in brain, adipose tissue, femur muscle and rumen of Kermani lambs. Small Rumin Res 193, e106276.
Reynes B, Priego T, Cifre M, Oliver P, Palou A (2018) Peripheral blood cells, a transcriptomic tool in nutrigenomic and obesity Studies: current state of the art. Compr Rev Food Sci Food Saf 17, 1006e1020.
Ross SA, Davis CD (2014) The emerging role of microRNAs and nutrition in modulating health and disease. Annu Rev Nutr 34, 305e336.
Roudbar MA, Mohammadabadi MR, Mehrgardi AA, et al. (2020) Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity 124 (5), 658-674.
Scarpato R, Verola C, Fabiani B, Bianchi V, Saggese G, Federico G (2011) Nuclear damage in peripheral lymphocytes of obese and overweight Italian children as evaluated by the gamma-H2AX focus assay and micronucleus test. FASEB J 25 (2), 685e693.
Schmidt DR, Mangelsdorf DJ (2008) Nuclear receptors of the enteric tract: guarding the frontier. Nutr Rev 66, S88eS97.
Sharif R, Thomas P, Zalewski P, Fenech M (2012) The role of zinc in genomic stability. Mutat Res 733 (1e2), 111e121.
Stover PJ, James WPT, Krook A, Garza C (2018) Emerging concepts on the role of epigenetics in the relationships between nutrition and health. J Intern Med 284, 37e49.
Weake VM, Workman JL (2010) Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet 11, 426e437.
Wood RD, Mitchell M, Sgouros J, Lindahl T (2001) Human DNA repair genes. Science 291 (5507), 1284e1289.