Inflammatory bowel diseases (IBD) are chronic relapsing-remitting inflammatory disorders of the gastrointestinal tract encompassing two main phenotypes: Crohn’s disease (CD) and ulcerative colitis (UC). The pathogenesis of IBD is not fully understood to date, but the most commonly accepted hypothesis is an inappropriate gut mucosal immune response towards the constituents of the gut microbiota, which cross an impaired epithelial barrier, in genetically predisposed individuals and under the influence of environmental factors [1]. Epidemiological studies (such as those carried out on monozygotic twins [2] and immigrants [3]), as well as the increase over time of the CD and UC incidence and prevalence (while the human gene pool is the same as before) [4], are all arguments that emphasize the importance of environmental factors in the occurrence of these inflammatory diseases. Epigenetics is a branch of life science that studies mechanisms regulating DNA-dependent processes (e.g., transcription, replication, recombination, repair, etc.) without primarily involving the nucleotide sequence of the DNA but, rather, the structure of how DNA is packed in the cell nucleus (chromatin structure), which can be inherited by daughter cells after cell division. Epigenetic mechanisms, including DNA methylation, post-translational histones modifications and non-coding ribonucleic acids (ncRNAs) [5]^, [6], regulating gene expression provide plausible explanations for the influence of the environment on gene expression profiles that favor intestinal inflammation [7]. Supporting this line of ideas, DNA methylation profiles observed in older monozygous twins with different environmental histories shows that epigenetic imprinting occurs mainly during crucial periods of development, whereas epigenomic changes can also occur day after day and accumulate over time in response to the exposome ^[8][9][10][8,9,10].

The term exposome has been proposed to encompass all environmental influences over the life course, from conception to death, that may influence disease emergence and clinical outcomes ^[11][12][11,12]. External environmental factors influencing the occurrence of IBD include the maternal lifestyle and in utero events [13], breastfeeding [14], diet [7], smoking habits ^[15][16][15,16], drugs ^[16][17][18][16,17,18], physical activity [16], stress [19], appendicectomy [16], vitamin D/UV exposure [16], infections [20] and hygiene [21]. While it is possible that these different factors directly induce epigenetic changes in the host, it is also possible that they influence the microbiome, an internal component of the exposome, and contribute to the occurrence of IBD through the exposome–microbiome–epigenome axis [22].

2. Epigenetics in IBD

Epigenetic mechanisms of gene expressions are involved in the intestinal epithelium homeostasis and in the development and differentiation of the immune cells, as well as in the modulation of responses generated by the immune system to defend against potential pathogens [23]. These epigenetic changes are reversible [24]. The genomic DNA in the eukaryotic cell nucleus is organized into chromatin. Chromatin consists of nucleic acids (genomic DNA and different types of RNAs); histone proteins (H2A, H2B, H3, H4 and H1) and non-histone chromatin-associated proteins ^[5][25][26][5,25,26]. Nucleosomes constitute the functional and structural units of chromatin. A nucleosome is built by around 146 bp of genomic DNA surrounding a histone octamer, which consists of two H2A–H2B dimers and one (H3–H4)2 tetramer ^[27][28][27,28]. In other words, chromatin is the physiological template for all DNA-dependent biological processes, including transcription. This fact increases the complexity of transcription regulation, since it implies that the chromatin structure has to be dynamic to grant or block access of transcription regulators to their respective binding elements on the DNA and to the transcription machinery to the genomic information in the nucleotide sequence. The epigenetic mechanisms of transcriptional regulation involve DNA methylation, histone modifications, nucleosome remodeling, interaction with the nuclear matrix and regulation via long non-coding RNAs (lncRNAs) and micro RNAs (miR) ^{[26][29][30][31]}[26,29,30,31]. These mechanisms of transcription regulation establish cell-specific, heritable patterns of differential gene expression and silencing from the same genome and allow the cells to change these gene expression signatures in response to stimuli, such as changing conditions due to their environment ^[32][33][32,33]. DNA methylation in eukaryotes refers to the covalent transfer of a methyl group (-CH3) to the carbon atom at position 5 of cytosine forming 5-methylcytosine (5mC), most frequently at the dinucleotide sequence CG (mCG) ^{[31][34][35][36][37]}[31,34,35,36,37]. DNA regions that are ≥200 bp long and show a CG:GC ratio ≥ 0.6 are defined as a CpG island [38]. The presence of DNA methylation prevents transcription factors from reaching gene promoters and generally leads to gene silencing ^[39][40][39,40]. DNA methylation in eukaryotes is catalyzed by DNA methyltransferases (DNMTs): DNMT1, which maintains DNA methylation patterns (during DNA replication and cell division), and DNMT3A/3B, which are responsible for de novo methylating DNMTs (during development or differentiation) ^[41][42][43][41,42,43]. These enzymes transfer methyl groups from S-adenosyl-L-methionine (SAM) to the cytosine residues in DNA [44]. On the contrary, DNA demethylation is mediated by the ten-eleven translocation (TET) enzymes, which add a hydroxyl group onto the methyl group of 5mC to form 5hmC (5-hydroxymethyl cytosine) [45]. Compared to healthy subjects, IBD patients show DNA methylation changes both at the cell (mainly immune) level and at the tissue level ^{[46][47][48][49][50][51][52]}[46,47,48,49,50,51,52]. These changes also differ between UC and CD patients and involve several loci responsible for the regulation of immune responses ^{[46][47][48][49][50][51][52]}[46,47,48,49,50,51,52]. Another epigenetic mechanism of transcriptional regulation involves post-translational modifications of histone proteins (further referred to as histone modifications). Histone proteins (H1, H2A, H2B H3 and H4) are relatively small and basic proteins that are abundant in the cell nucleus and are an essential part of the nucleosome, as described above. Due to structural characteristics of the nucleosome, histone proteins can undergo post-translational modifications at their N-terminal tails, which include acetylation, methylation, phosphorylation, ubiquitination and sumoylation, among others ^{[53][54][55][56]}[53,54,55,56]. While DNA methylation is relatively stable in somatic cells, histone modifications are more diverse and dynamic, changing rapidly during the course of the cell cycle ^{[6][30][53][54]}[6,30,53,54]. Acetylation at specific amino acids of histones (e.g., histone 3 lysine 9 acetylation; H3K9Ac) is generally associated with active chromatin and is mediated by histone acetyltransferases (HAT) and removed by histone deacetylases (HDAC). Histone methylation also occurs at specific amino acids of histone proteins and can be associated with both the repression (e.g., H3 lysine 27 trimethylation; H3K27me3) and activation (e.g., H3 lysine 4 trimethylation; H3K4me3) of gene expressions. There is a variety of enzymes mediating histone methylation (histone methyltransferases; HMT) and histone demethylation ^[57][58][57,58]. Similarly, the reactions leading to other histone modifications are catalyzed by a broad spectrum of enzymes in a regulated manner. Several environmental agents induce changes in histone modifications, thereby leading to changes in gene expression signatures. In addition to these mechanisms, epigenetic regulation can also involve ncRNA, which are RNAs not translated into proteins, including miRs and lncRNAs. If miRs have a length of 18–25 nucleotides, lncRNAs are over 200 bases long [59]. These nucleic acid molecules can regulate gene expressions by interfering with messenger RNA (mRNA) translations by degrading them or through interactions with protein complexes involved in the regulation of gene expression ^[59][60][59,60]. The ncRNAs are differentially expressed between the control and IBD subjects, and there is also a difference in expression between CD and UC patients ^[61][62][63][61,62,63]. In IBD, miRs are involved in the regulation of the intestinal mucosal barrier, T-cell differentiation, the Th17 signaling pathway and autophagy [63]. In UC patients, miR-21, miR-16 and let-7 expressions are significantly increased in inflamed mucosa, while miR-192, miR-375 and miR-422b expressions are significantly reduced [61]. In CD patients, miR-23b, miR-106 and miR-191 are significantly increased in the inflamed mucosa, while miR-19b and miR-629 expressions are significantly decreased [61]. All these epigenetic mechanisms contribute to the development, progression and maintenance of IBD. They are usually triggered by a range of environmental factors. Some authors have mentioned three critical periods during which the environment can favor the onset of the disease: (1) during the prenatal period (in response to the maternal lifestyle), (2) in the early postnatal period (during gut microbiota colonization) and (3) just before the disease onset [64].