Nutrients can interact directly with the genome and indirectly through modulation of mechanisms, including DNA methylation, histone modification and non-coding RNA expression, in particular the miRNAs. Vitamins and minerals can induce the expression of miRNAs through the activation of transcription factors, which regulate the gene expression by induction of messenger RNA (mRNA) degradation or inhibit their translation. They can also modify the expression of DNA methyltransferases (DNMT) and different enzymes such as histone deacetylase and histone acetyltransferase that are involved in several processes such as transcription activation, gene silencing, DNA repair and cell cycle progression [
44]. DNMT would appear to prevent demethylation in postmitotic neurons, which together with DNA methylation provides an epigenetic mechanism of gene regulation in neural development, function and disorders [
45]. The modulation of the activity of these enzymes leads to changes in the methylation state of DNA as well as the histones, which in turn modulate the expression of some genes, including the miRNAs themselves [
6]. Among the micronutrients, vitamin D plays a key role in promoting bone mineralization [
5], facilitating the intestinal absorption of phosphorus and calcium intake with the diet that is involved in bone calcification. Vitamin D is a member of the steroid hormones families with nuclear steroid receptors (NR) signalling function and is involved in the biogenesis and regulation of miRNAs expression [
5,
6]. It is already known that estrogens have fundamental anticatabolic and anabolic effects on bones; therefore, the lack of estrogen plays a central role in the development of osteoporosis [
46,
47]. The active form, 1,25 dihydroxy vitamin D (1,25(OH)2 D), can regulate the expression of osteoblastic mineralization factors by affecting the expression of some specific miRNAs like miR-637 and miR-1228. The miR-637 would seem to act by degrading the mRNA of Collagen Type IV Alpha 1 Chain (COL4A1), whose expression, during osteoblastic differentiation, inhibits matrix mineralization; while miR-1228, is a mirtron, an alternative precursor for microRNA biogenesis that was recently described in invertebrates, that uses a different mechanism of action than classical miRNAs, as they bypass the cleavage of enzyme DROSHA, is exported out of the nucleus, split by endoribonuclease Dicer and incorporated into the RISC [
48]. The miR-1228 reduces the expression of the Bone Morphogenetic Protein 2 (BMP2K) inducible kinase, a protein potentially implicated in cellular endocytosis and differentiation, but its molecular functions have remained unknown; it seems to be a potent inducer of bone formation through its stimulation of osteoblast differentiation [
5]. Given the importance of vitamin D, it is therefore very important to guarantee high levels which can be achieved through diet, such as cholecalciferol, thanks to animal foods intake such as salmon and blue fish or mackerel or cod liver oil consumed mainly as a supplement. Another source of vitamin D is vitamin D2 or ergocalciferol which is a bit less active but of which plant-based food is rich, for example, mushrooms. In any case, 80% of the vitamin D needed is guaranteed by sun exposition. Therefore the best practice to increase vitamin D levels is to carry out physical exercise outdoors to guarantee good production and positive action also on bone metabolism [
9,
24]. Even vitamin C plays a positive role in bone health; in fact, it is a cofactor in multiple biological processes such as collagen synthesis and antioxidant capability, regulating stem cell differentiation and improving osteoblast activity [
6,
8,
49] Clinical studies performed in humans and animals have shown that a deficiency of vitamin C leads to musculoskeletal alterations; noteworthy, the results showed that 100 mM of vitamin C effectively activates genes related to the musculoskeletal system in BMSCs, whilst lower doses, 25 mM, didn’t induce any effect. Similar results have also been observed for the regulation of vitamin C-dependent miRNAs production [
50,
51]. There is a possibility that vitamin C treatments regulate miR-29b-1 and miR-589-5p expression by promoting Octamer-binding transcription factor ¾ (Oct3/4), Nanog, sex-determining region Y-box 2 (SOX2) and Mitogen-Activated Protein Kinase Kinase Kinase 8 (MAP3K8) expressions in BMSCs contributing to cell proliferation and differentiation. In addition, it increases the expression of miR-371b-5p, miR-181a and miR-215 in BMSCs. The study hypothesis would be that these miRNAs respectively promote cell proliferation and differentiation of these cells [
51,
52,
53]. Among the various micronutrients that contribute to bone health, is also orthosilicic acid (OSA) which stimulates osteoblastic differentiation. Studies on ovariectomized rats orthosilicic acid fed compared to other deprived rats, showed a higher Bone Mineral Density (BMD) and trabecular thickness. Recently it has been discovered that miR-130b plays a role in cell proliferation, differentiation, and apoptosis; its expression increased during the osteogenic differentiation of multipotent mesenchymal stem cells of the human bone marrow. The study provided by Yunhao You et al. found an increase in his level during osteogenesis in response to 20 mM of orthosilicic acid and suggested that overexpression of miR-130b promoted osteogenic differentiation. However, the mechanisms of action which promote his transcription, have yet to be explored. Nutrition can contribute to the intake of OSA. Indeed its absorption is more effective if taken from the liquid phase in which it is dissolved and easily assimilated not having to undergo major changes [
11]. Regular mineral water contains about 6.8 mg per litre but there are some water whose silicon content can range from 14.4 mg up to 60 mg per litre. In food it is mainly contained in the leathery parts of vegetables; for this reason, it is important to consume vegetables and fruits with peel and legumes and prefer foods that have undergone few industrial processes to preserve their structure and content. Recent studies suggest that other micronutrients, such as natural phenolic acids, usually found in plants that are commonly intake by diet, may have an important bone anti-resorption activity [
4,
54,
55]. One of these compounds is syringic acid, 3,5-dimethoxy-4-hydroxybenzoic acid (SA), a phenolic acid acts on mouse mesenchymal stem cells (mMSC) cells inducing the differentiation of osteoblasts. It increases miR-21 expression which reduces Smad7 activity by targeting the TGF-b/BMP signalling pathway, resulting in increased RUNX2 expression, thus leading to the expression of osteoblast differentiation markers genes such as alkaline phosphatase (ALP), Collagen Type I Alpha 1 (Col-I) and osteocalcin (OCN) in BMSCs [
56]. Also, isoflavones i.e. syringe, genistein, laminarin, hesperetin and sulphurin, promote osteoblast differentiation through activation of the BMP2/SMAD5/Akt/RUNX2 pathway [
57]. Deep SA has several positive effects on bone health due to its strong antioxidant activity and also through antihypertensive, antiproliferative, antiendotoxic, antitumor, hepatoprotective and antihyperglycemic effects. It is mainly present in olives, walnuts and dates but also in blue-coloured fruits and berries where it is formed by the decomposition of lenin, an anthocyanin, and its aglycone, malvidin [
58]. This justifies its presence in red wine (0.27 mg/100 mL) and red vinegar (0.30 mg/100 mL) whilst in dried fruits such as walnuts or peanuts as well as in olives, cocoa pulp, pumpkin, durum wheat and in smaller quantities in peas and cauliflower, the concentration can reach 33mg/100g [
11].