Environmental factors contribute to autoimmune disease manifestation, and as regarded today, AhR has become an important factor in studies of immunomodulation. Besides immunological aspects, AhR also plays a role in pharmacological, toxicological and many other physiological processes such as adaptive metabolism. In recent years, epigenetic mechanisms have provided new insight into gene regulation and reveal a new contribution to autoimmune disease pathogenesis. DNA methylation, histone modifications, chromatin alterations, microRNA and consequently non-genetic changes in phenotypes connect with environmental factors. Increasing data reveals AhR cross-roads with the most significant in immunology pathways. Although study on epigenetic modulations in autoimmune diseases is still not well understood, therefore future research will help us understand their pathophysiology and help to find new therapeutic strategies. Present literature review sheds the light on the common ground between remodeling chromatin compounds and autoimmune antibodies used in diagnostics. In the proposed review we summarize recent findings that describe epigenetic factors which regulate AhR activity and impact diverse immunological responses and pathological changes. Heredity is only the sum of all past environment—this famous statement published in 1906 in the article “The Training of the Human Plant” in Century magazine by Luther Burbank . EpigeneIt has been estimated that autoimmune diseases (ADs) represent a family of at least 80 illnesses that share common pathogenesis . It is nConsidering the particular role of AhR in immune responses, increasing data reveals its cross-roads on the other significant in immunology pathways such as NF-κB , TGFβ/SMAryl Hydrocarbon Receptor (AhR) is one of the transcription factors that has been extensively studied in the context of cellular responses to environmental toxins and also plays an important physiological role in T cell immune responses and T cell differentiation  68]. To. To68]. AhR, a basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) transcription factor ,77, is bIn the absence of a ligand, AhR is localized in the cytoplasm of the cell and associated with a dimer of Hsp90 and other proteins such as p23, immunophilin-like AhR interacting protein AIP  or cytosolic proteins such as kinome chaperone Cdc37 and the non-receptor tyrosine kinase Src ,77,84. LAhR activity may be regulated via a few different mechanisms. One of them is degradation by the proteasome. Binding Ahr with ligand induces ubiquitination and subsequent degradation. Another is the auto-regulatory feedback loop. AhR activation induces the expression of negative regulators, which prevent excessive AhR activation. For example, a repressor of AhR–AhRR through competition with AhR-ARNT complex downregulates the expression of AhR dependent genes ; or few It should be mentioned that AhR activation and its target gene networks may be caused not only by agonist or antagonist but also by factors that do not fit well into the AhR ligand-binding domain (LBD) and by numerous stress factors like oxidative stress, shear stress that do not bind at all with the LBD . NeverthIn general, according to chemical structure, AhR ligands may be categorized into two major classes. The first one, which was mentioned above, contains aromatic hydrocarbons, which are derived mainly from environmental toxins  or also Another class of AhR ligands is composed of tryptophan-based molecules that can be derived from the diet or endogenously produced by the host organism  such as Among endogenous AhR ligands such as bilirubin and biliverdin, prostaglandin G2, indirubin and lipoxin A4 have been identified. In the case of endogenous ligands, rapid metabolism is very often observed, also as a negative feedback loop mechanism. For example, anti-inflammatory lipoxin A4 is degraded by Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) and bilirubin via UDP glucuronosyltransferase family 1 member A1 (UGT1A1), whose expression is induced by AhR . As it wDNA methylation was the first described covalent DNA modification. In this process methyl group onto the 5’ carbon position of cytosine in CpG islands is added and in consequence access to DNA for transcription factors and RNA polymerases is reduced and transcription is repressed . DNA metFundulus heteroclitus) that adapted to survive in PCB-contaminated water, revealed an evolved genetic mechanism where methylation status of promoter regions may control the tissue-specific expression of AhR genes. PCB-resistant and PCB-sensitive populations of killifish respectively, exhibit different patterns of DNA methylation in the promoters of AhR genes [Research conducted on Atlantic Killifish  expression, crucial for efficient antibody response [AhR also plays a role in B cell differentiation. Recently, it has been proved that in induce arthritis in mice model, AhR promoter is methylated in B cell and its demethylation by 5’-azacytidine decrease IgG antibody production. Another consequence of reactivation of AhR is the suppression of response . Overproresponse . It has response . Howeverresponse ,118. Chromatin remodeling and histone modification are interrelated processes. Regulation of gene expression is strongly associated with the state of chromatin—1) euchromatin-relaxed with active genes and 2) packed, transcriptionally inactive heterochromatin . The basIn the present review, we focused particularly on methylation and acetylation as they have been mostly studied in the aspect of AhR and immune regulations. Histone methylation affects lysine (K) and arginine (R) residues. Lysine can be methylated with one to three methyl groups, while arginine can be methylated with only one methyl group. Histone methylation correlates with gene activation and repression. An active form of chromatin consists with for example, H3K4me; H3K36me, H3K79me while H3K9me2 and H3K27me3 occur in condensed chromatin and silence the activity of genes. Histone methylation is conducted by the histone methyltransferases HKMT and PRMT whereas demethylation by histone demethylases (HDM) ,124,125.However, epigenetic mechanisms of AhR and the role of this transcription factor in epigenetic modifications are not fully explored. For example, Joshi et al.  showed tGlobal hypermethylation (except H3K4 methylation) and also novel methylation marks have been observed in a lupus-prone mouse study . HypermeP300, one of the major HAT proteins, has an impact on STAT3 expression and consequently IL10 production and B cell activity, and production of specific autoantibodies in SLE . In T ceIn the histone acetylation process, the electrostatic interaction between histones and DNA is diminished. Consequently, the chromatin structure is decondensed which provides access to the transcription initiation . It appeIt has been established that in human T cells, HAT and HADC enzymes co-occupy active and aligned genomic loci to maintain proper transcription regulation and uncontrolled binding of RNA polymerase II . Hyperacetylation has been reported in RA patients, which is related to HATs and HDACs disbalance . High acBased on the earlier study, it seems that HDAC inhibitors may be used in successful autoimmune diseases therapy. It has been shown that the HDAC inhibitors  cause changes in T cells and reduces the activity of SLE . Also stDepending on the AhR ligand, a different response might be observed. Joshi et al.  revealedChromatin remodeling is usually initiated by posttranslational modification of the amino acids that make up the histone proteins, but also through the methylation of neighboring DNA. Additionally, proper heterochromatin formation in certain regions of the mammalian genome requires Dicer- an enzyme involved in microRNA maturation . One of Chromatin remodeling is a process in which a cascade of protein complexes, transcription factors, coactivators participate and together with RNA polymerase II (Pol II) enables transcription initiation. So-called “bridge model” connects Mediator, large multisubunit polypeptides with the transcription factors and Pol II. Mediator complex might be a master in epigenetic regulation, but also a “coordinator” in non-coding RNA activation or super-enhancer formation . It has Another complex of proteins SWI/SNF  complexes) with other histone-modifying enzymes may independently or cooperatively mediate remodeling of targeted chromatin structures . NowadayAhR activity is tissue-specific, which might depend on chromatin-accessible regions. Moreover, AhR may regulate its own locus chromatin accessibility . On the Another transcriptional factor that has an impact on chromatin architecture is growth factor independence (GFI1). It has been shown that GFI1 mediates transcriptional repression mainly by recruiting histone-modifying enzymes such as histone deacetylases (HDAC-1–3), histone methyltransferases (EHMT2) or histone demethylases (KDM1A/LSD1/) . GFI1 prMicroRNAa (miRNA) are short/small, non-coding RNAs of 19–25 nucleotides long that regulate expression of many genes by the inhibition of translation after complementary base pairing or mRNA degradation after imperfect complementary base pairing with 3’ untranslated regions (3’UTR) of target mRNA . http://mirbase.org/), human genome encodes over 2600 miRNAs (miRbase v.22) that are involved in post-transcriptional regulation of thousands of protein-coding genes. One miRNA may regulate the expression of several genes and a group of miRNAs may interact with the expression of one gene. Since miRNA controls the expression of variate of genes, they are involved in important life processes including immune cell differentiation, maturation and function [According to the primary public repository and online source for microRNA , almost a hundred miRNAs are potentially involved in post-transcriptional regulation of AhR. However to date, in the aspect of autoimmune diseases, there is still a paucity data regarding the regulation of AhR by miRNA. AhR regulates the differentiation of Th17 and Treg cells; therefore, the difference in its expression shifts the balance between these two T cell subtypes and may contribute to the pathogenesis, among others, of Crohn’s diseases (CD). Zhao et al.  showed aRecent study conducted by Lu et al.  showed tin silico analysis of the interaction between miRNAs and their potential targets become a popular tool in molecular biology studies. Based on this approach Ogando et al. [There is a lot of evidence that AhR plays an important role in rheumatoid arthritis (RA) pathogenesis. In human synoviocytes, AhR ligands upregulate IL-1β whereas in macrophages upregulation of AhR inhibits expression of cytokines TNF-α, IL-1β and IL-6 . Recentlo et al.  indicateo et al. . On the o et al. . TherefoAnother example of possible therapy with miRNA activity was miR-155 in systemic sclerosis treatment. It appeared that the expression of miR-155 in skin of SSc patients is upregulated, therefore, Yan et al.  suggesteBased on in silico analyzes, Ushakov et al. , selecteEpigenetic mechanisms of AhR and the role of this transcription factor in epigenetic modifications have not been fully explored. Based on the above literature, we can see that it may be implicated into epigenetic processes which are significant in immunomodulation. Although it seems that inhibitors of DNA methylation have a therapeutic significance, in the case of variable autoimmune entities like in lupus treatment, this strategy might be more complicated and needs further research.AhR regulates the differentiation of Th17 and Treg cells, therefore, the difference in its expression shifts the balance between these two T cell subtypes and may contribute to their pathogenesis of autoimmune diseases. Increasing data reveals AhR cross-roads with the most significant in immunology pathways and probably many of other inter-reaction is still unknown. Therefore, AhR is considered a potential target for new therapeutic strategies in autoimmune diseases. Nevertheless, it has to be considered that the implementation of AhR as a therapeutic target might be very complex and many factors, such as type of ligand and its pharmacokinetics, cell type and cell environment  should be taken into account. Another important aspect of effective treatment using AhR as a therapeutic target is drug interactions through activation of CYP1 or phase II enzymes , as well as different genetic variants of this transcription factor which can affect drug metabolism by enzymes that are regulated by AhR . In general, implications of AhR in therapy may be directed into its inhibition as well as activation.Studies on cancer cell lines revealed upregulated AhR levels . Higher Recent identification of structurally-diverse AhR ligands that include salutary phytochemicals and microbial metabolites has changed the course of underlying clinical trials. Nowadays, there is a trend in research on the importance of gut microbiota, their metabolites (including AhR ligands) and various diseases such as MS, nonalcoholic fatty liver disease. The role of diet particularly dietary tryptophan on AhR activation is also comprehensively studied. In the aspect of autoimmune diseases, AhR upregulation and modulation toward increased Treg cell ratio seems to ameliorate of inflammation and inhibit autoimmune response. Particularly in barrier organs regulation of AhR activity reveals high potential of effective therapy. AhR ligands, such as coal tar, FICZ and tapinarof via the AhR pathway, restore barrier dysfunction and have been implicated into atopic dermatitis or psoriasis therapy ,249,250.Moreover, in the present article, the association between AhR pathway and autoantibodies against complexes such as ACPA or anti-CarP has been described. These autoantibodies are involved in epigenetic modulation and are used in contemporary diagnostic for autoimmune diseases. Noteworthy is that today, in the diagnostics of autoimmune diseases there is a need for more specific and sensitive biomarkers.


The growth of expertise in molecular techniques, their application to clinical evaluations, and the establishment of databases with molecular genetic information has led to greater insights into the roles of molecular processes related to gene expression in neurodevelopment and functioning. The goal of this review is to examine new insights into messenger RNA transcription, translation, and cellular protein synthesis and the relevance of genetically determined alterations in these processes in neurodevelopmental, cognitive, and behavioral disorders. Precise stimuli for gene expression in neurons remain to be elucidated. Early studies revealed that neurotransmitter activation of receptors triggered intracellular signaling. Abundant evidence of the importance of epigenetic factors and chromatin modifiers in gene expression in brain development and function can be derived from data on the high frequency of mutations in chromatin modifiers in neurodevelopmental, neurocognitive, and neurobehavioral disorders , 2.The transcription start site was noted to be embedded in the core promoter, and the core promoter was defined as including sequence approximately 50 bp upstream and 50 bp downstream of the transcription start site.Sequence elements in the promoter region act as binding sites for transcription factors, including general transcription factors and transcription cofactors, sequence elements for enhancer binding and the promoter region forms an anchoring site for RNA polymerase II.Specific sequence elements occur in some, but not all, promoters; these included the TATA box and a sequence element defined as the initiator motif. Specific features of promoter-associated chromatin have been defined that are strongly associated with transcription; these include H3K4me3 and H3K27ac. Transcription initiation at core promoters is defined as a stepwise process that includes recruitment to the promoter of general transcription factors TFIID, TFIIA, TFIIB, and RNA polymerase II, followed by recruitment of general transcription factors TFIIE and TFII H.Specific histone methyl transferases and histone demethylase interact with enhancers. Enhancer activation was considered to be a stepwise process, and active enhancers could be transcribed by RNA polymerase II to yield enhancer RNA (eRNA) transcripts. The eRNA level indicated the degree of activation of the enhancer. The eRNA then interacted with the gene promoter, and this interaction was mediated by cohesin and mediator complexes. Highly active enhancers were sometimes referred to as super-enhancers, and these were often several kilobases in length.In It is important to note that enhancers may also function in trans relative to the genes they regulate. Enhancers that function in cis relative to the genes they regulate may employ chromatin looping in gene interactions.There is now evidence that a large proportion of the human genome is transcribed, and increasingly, long non-coding RNAs are identified. Linc RNAs were reported to be primarily present in the nucleus, and their functions were reported to be regulating chromatin topology and formation of scaffolds for binding of proteins. Linc RNAs were reported to stabilize chromatin and to also play roles in chromatin looping.Specific architectural proteins including CTCF CCCTC-binding factor, YY1 (transcription factor), and cohesin complex subunits were reported to be anchors of chromatin loops.1.Chromatin loops were shown to be important features of the vertebrate genome and to serve to bring enhancers into contact with promoters. The importance of this process was demonstrated in erythroid cells, and a specific upstream locus control region was brought into contact with the beta globin gene locus . ImportaCore elements of the cohesin complex are presented in Mutations in SMC1, SMC3, RAD21, and NIPBL have been reported to lead to Cornelia de Lange syndrome associated with developmental defects in a number of systems .Topologically associated domains (TADS) were defined as sub-megabase-sized domains in which preferential intra-domain interactions occurred, indicating that DNA elements within the TADS interact . GenomicSpecific architectural proteins including CTCF CCCTC-binding factor, YY1 (transcription factor), and cohesin complex subunits were reported to be anchors of chromatin loops.Developmental defects can also result from structural chromosome changes that disrupt TADS.There is evidence that chromatin loop formation organized by cohesin and CCCTC binding factor (CTCF) plays important roles in the regulation of gene transcription and in the organization of the 3-dimensional genome. Chromosomes, chromatin, chromatin regulators, and architectural proteins were reported to be involved in the formation of the 3-dimensional genome that has been shown to play an important role in gene expression.Other factors that promote the cohesion of sister chromatids include ESCO 1, ESCO2 establishment of sister chromatid cohesion N-acetyltransferase 1 and 2, PDS5 cohesin associated factor B, and Sororin also known as CDCA5 cell cycle division-associated 5.The length of the 3′UTR region upstream of the polyadenylation site utilized influences availability of sites for binding of microRNAs and for binding of other RNA-binding proteins.Factors in the polyadenylation complex were also noted to be more abundant in proliferating stem cells and in pluripotent stem cells.Use of proximal polyadenylation sites was also noted when neuronal cells were activated by membrane depolarization. Activation of mammalian target of rapamycin (mTOR) signaling was also reported to lead to the generation of transcripts with shorter 3′-UTRs.Core splicing elements were noted to include 5′ and 3′ splice sites at exon intron junctions, branch points, and polypyrimidine tracts within introns. In addition, splicing is influenced by enhancers and silencers, nucleotide elements that can have trans effects in splicing machinery. Splicing is also dependent on appropriate function of components of the spliceosome.Genome-wide association studies in autism demonstrated an autism spectrum disorder-associated variant in PTBP2 polypyrimidine tract binding protein 2 that binds to intronic polypyrimidine clusters in pre-mRNA molecules and is implicated in controlling the assembly of other splicing-regulatory proteins.The composition of the highly dynamic spliceosome was reviewed by The spliceosome is described as a multi-megadalton ribonucleoprotein complex. It contains small nuclear ribonucleoproteins (snRNPs) and many other proteins. Core elements recognized by the spliceosome include the 5′ donor site GU dinucleotides, the branch point followed by the polypyrimidine tract and subsequently the AG dinucleotide at 3′ splice acceptor site.Alternative splicing was reported to be highly regulated and to be responsive to developmental and environmental stimuli . AlternaSNRPN gene located in chromosome 15q11.2 in the region involved in Prader–Willi syndrome is reported to encode a component of the snRNP complex, expressed from the paternally derived chromosome. It functions in pre-mRNA processing and may contribute to tissue-specific alternative splicing.The Numerous studies in humans with autism have revealed altered neuronal excitation–inhibition ratios resulting from altered neuronal activity and synaptic function. Many different gene defects have been reported to be associated with autism manifestations. In addition, microarray analyses and RNA sequence analyses have revealed altered patterns of gene expression. Misregulation and reduced transcription of the RBFOX family of RNA-binding splice regulators were reported by The specific nSR100 defects investigated by The activity of nSR100 was shown to be important in the inclusion of microexons in the transcripts of EIF4G component of the transcription initiation complex, in MEF2C transcription factor transcripts, and in transcripts shown to be aberrant in autism including ANK2, NBEA (neurobeachin), NRXN2 (neurexin 2), and in SHANK 1 (SH3 and multiple ankyrin repeat domains 1).Importantly, they postulated that nSR100.SRRM4 could potentially be a target for diagnostics and therapeutic intervention in autism.Early-switch exons were reported to be enriched in the transcripts of genes that encoded ion channels and in genes that encoded products related to transmembrane transport and synaptic transmission. Late-switch exons were enriched in transcripts of genes involved in cytoskeletal remodeling and in the formation of synaptic connections.In mouse brain, Posttranscriptional mechanisms, including alternative splicing, in neural developments, maturation, and plasticity, were reviewed by Information on the functional roles of alternative splicing in particular genes has sometimes been derived from information on pathology and disease manifestation that result from splicing mutations in specific genes.Insights into splice regulation have also been obtained through studies on specific nucleotide elements that interact with RNA-binding proteins and the precise positions of these binding elements relative to alternate exons.They noted that the presence of cell type heterogeneity in tissues complicates alternative splicing studies. In recent years, transcription studies are increasingly carried out on single cell or on samples with a uniform cell population.Another important factor to consider is that specific RNA-binding proteins require modifications, and changes in these modifications can impact their binding properties.Drosophila and studies of the transmembrane receptor Dscam1. Evidence was obtained indicating that extensive alternative splicing of Dscam 1 occurred, leading to the generation of products with different numbers of Ig domain inclusions. There was evidence that in dendrite arbor formation, neurites expressing the same number of repeat containing Dscam1 molecules formed connections with each other while dendrites each expressing different Dscam1 isoforms that differed in the number of Ig repeat domain repulse each other and failed to connect. The Dscam1 gene in Drosophila is the paralog of a human gene DSCAM that is impacted in Down syndrome.They considered whether transcript splicing patterns impacted circuit wiring in the brain and noted that there was evidence that alternate splicing of specific transcripts impacts axonal guidance and synapse formation. This information was derived primarily from studies in The DCC guidance receptor, also known as DCC netrin receptor, was shown to undergo alternate splicing events in mice, and the specific isoform expressed impacted axon guidance and interaction.Transcripts of neurexin, the synaptic adhesion molecule, were reported to exhibit significant differences based on splice site usage differences.Transcripts of KCNMA1, the potassium calcium-activated channel, were also reported to exhibit splicing differences, leading to protein products that differentially influence neuronal excitability.Mutations in genes that encode sodium ion channels are important causes of epilepsy. Mutations in the SCNA genes are reported to be associated with Dravet syndrome, an autosomal dominant disorder associated with encephalopathy, epilepsy, and developmental delay.Through studies in autism and developmental disabilities, they provided evidence that putative loss of function variants in weakly expressed exons in neuronal cell types has the same level of significance as synonymous variants.They noted that no information tools currently exist for incorporation of transcript analysis into variant interpretation.MRNA degradation processes include mechanisms involved in degradation of normal MRNA and also additional processes involved in degradation of mutant MRNA. Degradation processes include endonucleolytic cleavage, exonucleolytic cleavage, de-adenylation, and exosome activity. Particular processes are involved in the degradation of mRNA forms with premature termination codons.Exosomes are involved in trimming and degradation of mRNAs. The presence of AU-rich elements in the 3′-UTR of mRNA facilitates binding to exosomes. Importantly, mutations in specific exosome component EXOSC3 were reported to be associated with the neurodevelopmental disorder pontocerebellar hypoplasia. Mutations in the exosome component EXOSC8 was associated with a disorder in children in which cerebellar hypoplasia, hypomyelination, and spinal muscular atrophy occurred.There is evidence that exosome activity occurs in the nucleus and in the cytoplasm. MRNA to be degraded is reported to be guided to the exosome in the nucleus by a complex referred to as the TRAMP complex. In the cytoplasm, the SKI complex guides MRNA for degradation to the exosome. The MTR4 (MTREX) helicase complex was reported to be important for mRNA degradation in humans.Long non-coding RNAs were postulated by MRNA passes from nucleus to cytoplasm through nuclear pore complexes. This complex is composed of multiple proteins including nucleoporins, and energy for transport through nuclear pores is dependent on guanine triphosphate. Exportin proteins also facilitate transport out of the nucleus. In recent years, there are reports of nucleoporin defects in specific neurodevelopmental disorders. RANBP2 is a large protein that localizes to the nuclear pore complex. Defects in RANBP2 have been reported to predispose to familial encephalopathy . FichtmaThe preinitiation complex refers to a complex that includes guanosine triphosphate (GTP) bound to eIF2 and methionyl initiator tRNA, eIF3, eIF5, eIF1, eIF1A 40S ribosome subunit. The PIC complex was reported to scan mRNA until the AUG initiation codon was encountered. Subsequently, hydrolysis of the eIF2-bound GTP occurs, leading to the release of many of the bound initiation factors. This facilitates recruitment of GTP-bound eIF5B and the 80S binding, and the remaining bound eIF factors are released. The aminoacyl-tRNA-binding site on ribosomes is exposed, allowing translation extension to occur.Another important factor involved in controlling the degree of cellular protein synthesis is the integrated stress response .Specific translation initiation complex subunits that recognize the 3-end of the mRNA include eif4G and eif4E. Additional initiation factors that serve to bring the mRNA to the ribosome include eiF4E, eiF4G, eiF4A, and eif4b, and eiF4G was reported to also interact with eiF3.Following this binding, the 40S ribosome subunit with bound eif5 and initiator methionyl tRNA scans the mRNA for the AUG initiator codon. Hydrolysis of GTP on eif2 occurs through the activity of eiF5; the eiF2 is then released, and the 60s subunit of the ribosome joins the 40s ribosomal subunit and translation can then begin.In 2012, Microsatellite nucleotide repeat expansions were reported to be associated with more than 49 different diseases that impact the central and peripheral nervous systems. There is growing evidence that the repeat sequence regions can be transcribed and translated, giving rise to aberrant peptides and proteins. The first RAN translation process was recognized in spin cerebellar ataxia cases associated with a CAG repeat expansion. There is some evidence that aberrant dipeptides and short proteins derived from aberrant translation can accumulate in inclusions.Translation involves aminoacyl tRNAs being escorted to ribosomes by the GTP-bound elongation factors, e.g., eEf1, eEf1a. On recognition of the cognate nucleotide codon in the mRNA, the specific aminoacyl-tRNA interacts with the ribosome and polypeptide, and the GTP on the elongation factor is hydrolyzed. The elongation process involves movement of the ribosomes along three nucleotides of the mRNA with each addition of an amino acid. Elongation proceeds until a termination codon is encountered in the mRNA transcript.Each aminoacyl-tRNA synthetase couples a specific amino acid. MRI abnormalities, psychomotor retardation, microcephaly, hypotonia, seizures, and encephalopathy were frequently encountered. Failure to thrive was a commonly encountered early manifestation in children. Other manifestations that were encountered in some patients included liver, bone marrow, and gastrointestinal defects.They defined tRNAs as adaptors in the translation process. Multistep maturation processes are required for tRNAs to be functional. In addition, there is evidence that TRNAs have other functions.In reviewing the tRNA life cycle, In the mitochondria, 22 tRNA genes were reported to be active. Products for modifying mitochondrial tRNAs were reported to be encoded in the nucleus and to require transport into mitochondria. Following modification, TRNAs occur in the cytoplasm, mitochondria, and endoplasmic reticulum. Specific transporters of TRNAs included exportin 7 encoded by the XPO7 gene.Twenty different aminoacyl tRNA synthetases occur, each recognizing a specific amino acid.Childhood neurological disorders associated with impaired biogenesis of nuclear TRNAs are noted to lead to hypomyelinating leukodystrophies and pontocerebellar hypoplasia. Leukodystrophies have also been reported to result from POLR3A or POLR3B defects. POLR3A and POLR3B encode the component of RNA polymerase III that is involved in the transcription of tRNA genes.Pontocerebellar hypoplasia can result from defects in functions of the products of the TSEN genes including TSEN2, TSEN15, TSEN34, and TSEN54 that encode tRNA splicing endonucleases.Neurological disorders can also result from defective functions of enzymes that charge tRNAs, namely, TRNA synthetases. Specific syndromic disorders due to defects in aminoacyl-tRNA synthetases include forms of Charcot–Marie–Tooth disease that is characterized by impaired peripheral nerve functions primarily in axons that often first present with abnormalities in the legs. Defects in any one of more than 70 different genes have been reported to lead to this disorder. The PMP2 gene that encodes peripheral myelin protein 22 is the most commonly involved. Defects leading to Charcot–Marie–Tooth disease have been identified in six different aminoacyl-tRNA synthetases, alanyl-t-RNA synthetase 1 (AARS1), methionyl-tRNA synthetase 1 (MARS1), histidyl-tRNA synthetase 1 (HARS1), tyrosyl-tRNA synthetase 1 (YARS), lysyl-tRNA synthetase 1 (KARS), and glycyl-tRNA synthetase 1 (GARS).This combined phenotype can also arise due to a defective function of mitochondrial methionyl-tRNA transformylase (MTFmt) that is required for initiation of translation in the mitochondria.Microcephaly with cerebellar atrophy was reported to result from defects in glutaminyl-tRNA synthetase 1 (QARS1) or defects in seryl-tRNA synthetase 1 (SARS1).Premature termination codons in mRNA elicit a mechanism referred to as nonsense-mediated decay that involves a surveillance complex composed of RENT1 also referred to as UPF1 RNA helicase and ATPase and peptide release factor also known as ERF3A.The proteins eEF1A1 and eEF1A2 were noted to constitute central components of the complex with eEF1A2 occurring primarily in neurons and eEF1A1 widely present. The EEF1A gene was reported to be mutated in specific cases of autism. The eEF1A complex was reported to function to deliver aminoacyl-associated tRNAs to the ribosome to generate the polypeptide chain. Energy for this process is provided by GTP.Deletion of an exon in the EEF1B2 gene was reported to be present in three siblings with intellectual disability in one family. EEF1D mutations have been reported to be associated with intellectual disability in members of one family. Different VARS gene mutations were reported to occur in two different families with intellectual disability.They noted that advances in molecular techniques have expanded insights into factors involved in translation and its termination. One of these techniques includes ribosome profiling. This technique is designed to determine quantitative measures of protein synthesis. A specific aminoacyl-tRNA synthetase must select the correct amino acid, and it must select the correct tRNA from the TRNA pool. Specific editing processes take place. In pretransfer editing, an incorrectly bound amino acid can be removed from the aminoacyl-tRNA synthetase by hydrolysis. Mischarged tRNAs can also be edited. These pre- and posttranslation editing processes require the existence of proofreading mechanisms .Translation Elongation factor mutations in EEF1A2 were reported in cases of epilepsy, ataxia, intellectual disability, and autistic behavior by Translation termination factors were designated eRF, and genes were designated ERF or ETF1. Termination proteins included eRF1, eTF1 (eRF3); a gene encoding etf3 was not found in the human gene database. It is important to note that nomenclature for translation factors remains complex.A specific process referred to as ribosome quality control (RQC) is initiated when a ribosome stalls during the process of translation. When ribosomes stall, the aberrant or shortened polypeptide chain undergoes proteosomal degradation. in vitro studies to study the effects of regulatory regions and target genes.Their study focused on analyses of haplotypes of defined regulatory regions that were located in cis to the target gene. They also utilized The study was based on the hypothesis that nucleotide variants, the haplotype, in regulatory regions impact penetrance; specific haplotypes reduced penetrance, while other haplotypes were disadvantageous and increased penetrance, while other haplotypes were advantageous and individuals with the advantageous haplotype showed few manifestations of the disease despite the presence of deleterious mutations in the target gene. They also postulated that the deleterious haplotypes were rare in the general population. Patients with manifestations of the disease caused by deleterious mutations in a specific disease would have an overrepresentation of specific regulatory haplotypes relative to the frequency of those haplotypes in the general population.Among the results of their study was evidence for a regulatory region haplotype that modified the phenotype of Birt–Hogg–Dubé syndrome. This syndrome was reported by It is however important to note that there are many other factors that can influence the clinical expressivity and penetrance of a specific deleterious variant. In a review in 2013, Posttranslational modifications are often important in regulating protein functions and in determining the locations of specific proteins in specific subcellular organelles. In addition, specific factors influence the correct three-dimensional folding of proteins that may be required for their function.SCN1B played roles in epilepsy. Sodium ion channel proteins occur in neuronal soma and in dendrites and to have high density in the axon initial segment and in the myelinated node of Ranvier. Sodium ion channels are reported to initiate electrical neuronal action potentials.Five different genes that encode alpha subunits of sodium ion channels have been reported to have mutations that lead to epilepsy; these include SCN1A, SCN2A, SCN3A, SCN8A, and SCN9A, and epilepsy-inducing mutations have also been reported in SCN1B.In addition, posttranslational modifications are required for the sodium ion channel functions. The extent to which specific amino acid residues are involved in posttranslational modifications needs to be considered in analyses of the impact of specific mutations on function.The subunit interactions are also impacted by the degree to which posttranslational modifications impact the subunit interactions and protein functions.MS reviewed literature and generated the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Escherichia coli, has up until recently been that RNA functions mainly as an information intermediate between a DNA sequence (gene), localized in the cell nucleus, serving as a template for the transcription of messenger RNAs, which in turn translocate into the cytoplasm and act as blueprints for the translation of their encoded proteins. There are a number of classes of non-protein coding RNAs (ncRNAs) which are essential for gene expression to function. The specific number of ncRNAs within the human genome is unknown. ncRNAs are classified on the basis of their size. Transcripts shorter than 200 nucleotides, referred to as ncRNAs, which group includes miRNAs, siRNAs, piRNAs, etc, have been extensively studied. Whilst transcripts with a length ranging between 200 nt up to 100 kilobases, referred to as lncRNAs, make up the second group, and are recently receiving growing concerns. LncRNAs play important roles in a variety of biological processes, regulating physiological functions of organisms, including epigenetic control of gene regulation, transcription and post-transcription, affecting various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. LncRNAs are also capable of tuning gene expression and impact cellular signalling cascades, play crucial roles in promoter-specific gene regulation, and X-chromosome inactivation. Furthermore, it has been reported that lncRNAs interact with DNA, RNA, and/or protein molecules, and regulate chromatin organisation, transcriptional and post-transcriptional regulation. Consequently, they are differentially expressed in tumours, and they are directly linked to the transformation of healthy cells into tumour cells. As a result of their key functions in a wide range of biological processes, lncRNAs are becoming rising stars in biology and medicine, possessing potential active roles in various oncologic diseases, representing a gold mine of potential new biomarkers and drug targets.The central dogma of molecular biology, developed from the study of simple organisms such as  There are a number of classes of non-protein coding RNAs (ncRNAs) which are essential for gene expression to function. These include small nuclear RNAs (snRNAs), mainly involved in mRNAs splicing events; transfer RNAs (tRNAs) which are responsible for specifically recognising three-nucleotide sequences of mRNAs, decoding the mRNA sequence into peptide or protein, and recruiting amino acids into ribosomes in the correct order. The most abundant cellular RNA molecules are represented by ribosomal RNAs (rRNAs), forming the framework of ribosomes. snRNAs, tRNAs, rRNAs are referred to as housekeeping RNAs and are constitutively expressed and are essential for normal cellular function .Next generation sequencing methods and progress in transcriptome analysis have led to the discovery that up to 70% of the human genome is transcribed into RNA, however, only up to 2% of this serves as blueprints for proteins . MoreoveThe term ncRNA is commonly used to refer to RNA which does not encode a protein. However, this does not imply that such RNA molecules do not contain any information and serve no function. Traditionally, it has been assumed that most genetic information is transacted by proteins. Recent evidence through the development of new techniques have revolutionised the molecular world and have shown that the majority of the mammalian and other complex organisms’ genomes is in fact transcribed into ncRNAs, which appear to comprise a hidden layer of internal signals controlling various levels of gene expression in physiology and development, including chromatin structure, epigenetic memory, transcription, RNA splicing, editing, translation and turnover .2The specific number of ncRNAs within the human genome is unknown. ncRNAs are classified on the basis of their size. Transcripts shorter than 200 nucleotides, referred to as ncRNAs, which group includes miRNAs, siRNAs, piRNAs, etc, have been extensively studied. Whilst transcripts with a length ranging between 200 nt up to 100 kilobases, referred to as lncRNAs, make up the second group, and are recently receiving growing concerns. The latter transcripts lack a significant open reading frame ,7,12.BC1 and snaR in the lncRNA database, even though these are less than or close to 200 nt in length [Long non-coding RNAs (lncRNAs), encompassing nearly 30,000 different transcripts in humans, represent the most prevalent and functionally diverse class of ncRNAs . There in length .LncRNas are observed in a large diversity of species, including animals , plants LncRNAs play important roles in a variety of biological processes, regulating physiological functions of organisms, including epigenetic control of gene regulation, transcription and post-transcription ,6, affecResearch is also showing that lncRNAs are deregulated in a number of human cancers, and their aberrant expression leads to cell proliferation, tumour initiation, growth and metastasis of cancer cells . More sp2.1A broad definition of cancer, also referred to as malignancy, is an abnormal and uncontrolled growth of cells, with the potential of invading or spreading of the affected cells to other parts of the body . Cancer Several studies, particularly with the recent application of next-generation sequencing to a growing number of cancer transcriptomes, comparing malignant cells with their corresponding normal cells have revealed that many transcription factors, post-transcriptional regulators such as RNA binding proteins, microRNAs, and lncRNAs are crucial regulators for promoting or inhibiting tumour development ,12,29. L reported have repin vivo [Moreover ,12, have2.2i.Facilitating combinatorial actions of different transcription factorsii.Removing transcription factors and other regulatory protein from chromatiniii.cis and trans genesRecruiting chromatin modifiers in iv.acting as scaffolds bringing multiple proteins together, forming ribonucleoprotein complexes inducing histone modificationv.cis and trans genesInteract with DNA methyltransferase enzymes through other protein mediators, regulating DA methylation in both A number of studies using next generation sequencing have revealed that a significant portion of the mutation associated with cancer development lies within the non-coding region of the human genome, which mutation has a particular effect on the expression of lncRNAs, which in turn may regulate various cancer phenotypes by interacting with DNA, RNA, and proteins . ResearcMoreover, lncRNAs are significantly associated with the growth, survival, migration, and angiogenesis of a number of cancer cell types by transcriptionally or posttranscriptionally regulating the epigenetic regulators/modifiers ,55. The Furthermore, Pei-fen  have rep2.3LncRNAs can also act as tumour suppressors. Genome-wide studies have revealed that transcription factors, such as p53 ,56, MYC  have rep3Given the important of lncRNAs in controlling important cellular processes, it is sound to say that similar to protein-coding regions of the human genome, genetic regions encoding lncRNAs play equally important roles in regulating the malignant transformation and progression. With the improvement of research methods such as the development of gene array technologies and high-throughput sequencing technologies, more categories of lncRNAs are expected to be discovered, which technologies will allow for the effective understanding of their complex mechanism/s of action, and eventually using recent CRISPR/CAS gene editing technologies to play certain roles in developing lncRNAs as tumour suppressor therapies, delivering novel and alternative treatment strategies for targeting cancer associated lncRNAs.


Efficient osteogenic differentiation of mesenchymal stem cells (MSCs) is a critical step in the treatment of bone defects and skeletal disorders, which present challenges for cell-based therapy and regenerative medicine. Thus, it is necessary to understand the regulatory agents involved in osteogenesis. Epigenetic mechanisms are considered to be the primary mediators that regulate gene expression during MSC differentiation. In recent years, epigenetic enzyme inhibitors have been used as epidrugs in cancer therapy. A number of studies mentioned the role of epigenetic inhibitors in the regulation of gene expression patterns related to osteogenic differentiation. This review attempts to provide an overview of the key regulatory agents of osteogenesis: transcription factors, signaling pathways, and, especially, epigenetic mechanisms. In addition, we propose to introduce epigenetic enzyme inhibitors (epidrugs) and their applications as future therapeutic approaches for bone defect regeneration. Mesenchymal stem cells (MSCs) are considered to be potent tools for regenerative medicine, tissue engineering, and cell-based therapy because of their tri-lineage differentiation, self-renewal potential, low immunogenicity, decreased risk for tumorigenicity, capability for expansion, and ease of accessibility . During Osteoblastogenesis has three important phases that are characterized by sequential expression of specific osteoblastic markers: proliferation, matrix maturation, and mineralization. Major genes involved in the osteoblast differentiation process include alkaline phosphatase (ALP), type 1 collagen (COL1A1), osteopontin (OPN), bone sialoprotein (BSP), and osteocalcin (OCN) . ALP, BSRunx2, the most important transcription factor, is essential for bone formation and activation of osteogenic genes . Runx2 aIn addition to specific genes in the osteogenesis process, there are several known signaling pathways that play critical roles during osteoblast differentiation. MSCs proliferate and differentiate in response to these signaling pathways during different stages of osteogenesis. Activation of specific genes mediated by molecular signaling pathways regulates MSC differentiation . HedgehoHh, an important secreted molecule of the hedgehog family, regulates cell functions during bone formation. The Hh receptor is expressed on the surface of osteoblasts. Shh, Ihh, and Dhh are members of the Hh family in mammals, and Shh and Ihh are vital for bone development. Family members of the Hh protein bind to its receptor, Ptc, which inhibits Smo, a key transducer in Hh signaling, and leads to activation of the GLI family Gli1-3) transcription factors. Gli translocate into the nucleus and activate a series of Hh target genes  signaling pathway. Subsequently, PKA phosphorylates CREB, which regulates transcription of PTH target genes during osteogenesis Fig. d. PTH maThe TGF-β superfamily consists of over 40 members, including TGF-βs, Activins, Nodal, bone morphogenetic proteins (BMPs), and growth differentiation factors (GDFs). TGF-β and BMP signaling are of utmost importance in both bone formation during skeletal development and maintenance of postnatal bone . BMP famThe interplay of molecular signals and genes enables MSCs to begin the differentiation process. The role of epigenetic modification in precise control of specific transcriptional programs and signaling pathways in the osteogenesis process has been less explored.Epigenetics are heritable changes in the patterns of gene expression that do not directly alter DNA nucleotide sequences. Epigenetic marks include DNA methylation, histone modifications, microRNA (miRNA), and chromatin remodeling in diverse biological processes. The results from a growing number of studies have indicated that these mechanisms participate in all aspects of osteogenesis . Below, DNA methylation is an epigenetic process that causes changes to chromatin that are associated with gene repression. In DNA methylation, a methyl group is added to the 5′ position of cytosine in a CpG dinucleotide . MethylaDNA methylation associated with transcriptional silencing participates in biological processes such as imprinting of specific genes, X chromosome inactivation, and cell type-specific gene expressions . AccordiHistone modifications are covalent post-translational modifications on the histone proteins. These modifications change the architecture of chromatin, which generally occurs at chemically unstable residues  on the histone tail regions. Histone tails are modified by acetylation, methylation, ubiquitination, phosphorylation, sumoylation, and ADP-ribosylation , 45. AmoHistone acetylation is mediated by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). Acetylation of lysine residues on histones neutralizes the partial electric charge of lysine, which relaxes the chromatin structure that correlates with transcriptional activation. In contrast, histone deacetylation compacts the chromatin structure and induces transcriptional repression .Many studies have reported that histone acetylation regulates expression of osteo-specific genes. According to Shen et al., H3 and H4 acetylation was associated with fluctuations of OCN gene expression during osteogenesis. In the proliferative phase, acetylation of H3 and H4 decreased, which resulted in inactivation of OCN. In contrast, OCN was active in mature osteoblasts with increasing H4 acetylation . AnotherHistone methylation is another histone modification that regulates gene expression during osteogenesis. Histone methyltransferases (HMTs) transfer up to three methyl groups to histone proteins, commonly at lysine residues, in contrast to histone demethylases (HDMs) that remove the methyl groups. These modifications activate or repress transcription depending on the location of the methylation . The impZhang et al. demonstrated that JMJD3 (KDM6B), an H3K27me3 demethylase, was necessary for both intramembranous and endochondral ossification. JMJD3 might act as a co-activator of Runx2, and their cooperation promoted osteoblast differentiation and bone formation in mice .EZH2 in MSC stimulates adipogenesis in vitro and inhibits the osteogenic differentiation potential both in vitro and in vivo, whereas KDM6A acts in the opposite manner [H3K27me3 (repressive mark) has an important function in osteogenesis regulation. This epigenetic mark is stimulated by enhancer of zeste homology 2 (EZH2), an HMT, and is removed by lysine demethylase 6A (KDM6A). Ye et al. reported that the HDMs, KDM4B and KDM6B, regulated DLX and HOX gene expressions by removing H3K9me3 and H3K27me3, respectively, which indicated their pivotal role in osteogenic commitment of MSCs . EZH2 ane manner . TherefoChromatin remodeling is the dynamic modification of chromatin by which nucleosomes move to a new location on the genomic DNA, which induces chromatin reconstruction to access DNA and control gene expression . ReconstATP-dependent chromatin remodelers are categorized into four distinct families: switch/sucrose-non-fermenting (SWI/SNF), imitation switch (ISWI), chromodomain-helicase-DNA-binding (CHD), and inositol requiring 80 (INO80) . Other mmiRNAs are endogenous small non-coding RNAs ~ 20 nucleotides long that post-transcriptionally regulate gene expression. miRNAs perform their actions through interaction with sites of antisense complementarity in 3′ untranslated regions (UTRs) of specific target mRNAs. They cause degradation of the target mRNAs or translational suppression depending on the degree of miRNA-mRNA complementarity , 64. In Collectively, the abovementioned studies illustrated that epigenetic factors regulate genes, transcription factors, and signaling pathways. Precise knowledge of epigenetic patterns in MSCs before and after differentiation is necessary to improve efficient differentiation of MSCs. These findings enable us to discover regulation of osteogenesis via epigenetic modifications. In addition, they provide clues to discover novel treatments for bone defects by targeting specific regulators involved in osteogenesis and can help us to better control the fate of MSCs in cell-based therapy and advances in regenerative medicine and tissue engineering.The results of various experiments show that growth factors, peptides, small molecule, and epidrugs, as chemical compounds, play important roles in targeted osteogenesis. These compounds affect genes and transcription factors, and can induce MSC differentiation to osteoblasts. Some have been assessed in the in vitro studies and in vivo . However, only a few of these components have reached the clinical trial stage . Table 2Epigenetics is defined as reversible heritable changes in gene expression without concomitant changes to the genomic sequence that engages in the biological process of mammalian development, and cellular differentiation and maintenance of tissue- and cell type-specific functions . ExtensiHDACs modulate gene expression. Histone deacetylase inhibitors (HDACi) alter gene expression and are being considered as favorable drugs for the treatment of malignancy. HDACi are divided into several classes: hydroxamic acids, cyclic peptides, short-chain fatty acids, and epoxides. These inhibitors arrest cell growth and induce differentiation or apoptosis of cancer cells both in vitro and in vivo . SeveralmiRNAs are another important aspect of epigenetic regulation in cancers. The expression profiles of miRNAs deregulate during oncogenesis. Hence, Epi-miRs open up new horizons for novel cancer therapies . The resDespite promising reports on the potential application of epidrugs as therapeutic strategies, there is significant concern that surrounds the unwanted adverse and off-target effects. Hematologic complications, such as bleeding and anemia, can occur following treatment with DNMTi . In mousIn order to reduce the unwanted adverse effects, it is necessary to precisely recognize epidrug targets in order to design selective and class or isoform-specific enzyme inhibitors for specific cells. Also, the use of a suitable drug delivery system with controlled local, sustained release and evaluation of the lowest effective dose might overcome this issue.MSCs are of tremendous interest to stem cell-based transplantation therapy; newly emerging research has implicated the important role of epigenetic mechanisms in regulating mesodermal lineage determination and differentiation. Evidence indicates that the induction of MSC differentiation toward osteoblasts is supported by epigenetic regulations .There is growing evidence that pertains to the effect of epidrugs on bone formation as well as cancer clinical therapy. A number of studies have highlighted the role of DNMTi during osteogenesis. Chen et al. reported the role of 5-Aza-dC as a lineage determinator between adipogenesis and osteoblastogenesis. They found that it promotes osteoblastogenesis by demethylation and upregulation of the Wnt10a gene and osteoblastogenic markers ALP, OSX, Twist1, and Dlx5 in 3T3-L1 preadipocytes and the ST2 MSC line . Lee et In addition to DNMTi, some studies have focused on HDACi and their role during differentiation of MSCs to an osteoblast lineage. VPA is a short-chain branched fatty acid prescribed for treatment of epilepsy and neurological disorders. Cho et al. reported that treatment of human adipose tissue-derived stromal cells (hADSCs) with VPA as an HDAC inhibitor increased the expressions of OSX, OPN, Runx2, and BMP2 during osteogenesis, which indicates a positive role for VPA in osteogenesis . Paino eSAHA is another HDACi that is clinically used to treat cancer. In a study, the treatment of C57BL/6J mice with SAHA caused decreased mineralization and OPN, COL1A1, and OCN gene expression, and eventually led to bone loss in rodents . In contTrichostatin A (TSA), a widely applied HDACi, has been assessed in bone studies. Boer et al. reported that ALP expression and bone formation were dramatically enhanced by TSA-treated human MSCs in an ex vivo cultured mouse calvaria but implantation of these cells into immune-deficient mice did not show any significant results . TSA alsSodium butyrate (NaBu) is a short-chain fatty acid that plays a critical function in the homeostasis of the gastrointestinal tract; NaBu inhibits HDACs. It has been shown that NaBu modulates osteogenic differentiation in hMSCs by an ERK-dependent Runx2 activation . NaBu, bBesides the effect of HDACi during osteoblast differentiation, several studies were conducted to assess inhibition of the EZH2 epigenetic factor, a novel therapeutic target for improvement of bone formation. Inhibition of EZH2-mediated 3-deazaneplanocin A (DZNep) promoted osteoblast differentiation of hMSCs . Jing etThe survival of MSCs is a significant point to be made about the use of epidrugs in promotion of MSC differentiation. The results of studies have shown that the viability of MSCs was affected by various doses of epidrugs; increased doses had a negative impact on MSC survival , 132. AnMSC characteristics include their ability to be isolated from various sources, multipotent properties, immunosuppressive capacity, no risk of tumorigenesis, and easy expansion in vitro. These characteristics make them ideal candidates for regenerative medicine and tissue engineering. However, the use of these cells for stem cell-based therapy still requires a rigorous understanding of the mechanisms that occur during in vitro and in vivo MSC differentiation. Osteogenesis is controlled by numerous genes, transcription factors, signaling pathways, and epigenetic mechanisms. Nevertheless, detailed knowledge of epigenetic regulation of osteoblast differentiation is obscure. Hence, a novel insight into prevention and treatment of disease-associated epigenetic defects such as cancer would include the identification and targeting of epigenetic modification enzymes by epidrugs. Recently, the use of epidrugs to treat various cancers has been studied. Some have been approved by the FDA, and several are in phase I/II studies. The role of some epigenetic enzyme inhibitors has been addressed in osteoblast differentiation of MSCs, and the results have shown that some of these epidrugs improve osteogenesis and bone formation via alterations in epigenetic arrangements. According to the emerging knowledge on the role of these epigenetic modifiers in osteogenesis, epidrugs can be potentially used to improve in vitro and in vivo osteogenic differentiation with the goal to enhance the capability of MSCs to be used in tissue engineering and regenerative medicine. Epidrugs have the ability to be used as treatment for metabolic bone disorders such as osteoarthritis and osteoporosis; however, cytotoxicity is the main problem for their clinical use. In order to overcome the adverse effects of an epidrug, the first step would be to identify which epigenetic marker should be targeted in a certain disease and use its class or isoform-specific enzyme inhibitors. Furthermore, additional research is needed to determine the optimal dose and discover the appropriate epidrug transfer systems prior to their clinical applications in bone tissue engineering. Currently, a gap exists between our knowledge and clinical applications, and a more thorough investigation in this context would be essential prior to the use of epidrugs as therapy. It is, therefore, necessary that further research should be conducted to fully understand the epigenetic changes that occur with bone disorders and to recognize epigenetic patterns in genes responsible for their repair and rejuvenation.


FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing promoters. In humans, FENDRR is located on chromosome 16q24.1, and is positively regulated both by the FOXF1 distant lung-specific cis-acting enhancer and by trans-acting FOXF1. Fendrr has been shown to function as a competing endogenous RNA, sponging microRNAs and protein factors that control stability of mRNAs, and as an epigenetic modifier of chromatin structure around gene promoters and other regulatory sites, targeting them with histone methyltrasferase complexes. In mice, Fendrr is essential for development of the heart, lungs, and gastrointestinal system; its homozygous loss causes embryonic or perinatal lethality. Importantly, deregulation of FENDRR expression has been causatively linked also to tumorigenesis, resistance to chemotherapy, fibrosis, and inflammatory diseases. Here, we review the current knowledge on the FENDRR structure, expression, and involvement in development and tissue maintenance.The  Nearly the entire human genome is transcribed; however, only approximately 2% of the transcriptome becomes translated into polypeptides longer than 100 amino acids ,4.RNF157-AS1 and FOXJ1, FOXC2-AS1 and FOXC2, ZCCHC14-DT and ZCCHC14). In other cases, like lncRNA gene FENDRR  and the transcription factor (TF)-coding FOXF1, they share a genomic region containing promoters. The symbol FENDRR is an acronym for the Fetal-lethal Non-coding Developmental Regulatory RNA and reflects the significance of this lncRNA in early embryonic development [FENDRR was referred to as FOXF1-AS1, lincFOXF1, onco-lncRNA-21, or TCONS_00024240. FENDRR was identified in the studies that expanded the catalog of human lncRNAs to over 3000 based on their (i) distinctive histone 3 (H3)-based chromatin signature (H3K4me3-H3K36me3) that marks transcribed genes and (ii) limited protein coding potential [A subset of anti-sense lncRNAs have their 5′ ends located in proximity to the 5′ ends of the protein-coding genes transcribed in the opposite direction. In some cases, those divergent genes may overlap  and alternative splicing, the combined genomic region coding for all FENDRR transcripts is actually larger, ~37 kb in size, mapping between chr16:86,473,637 for the 3′ end of the FENDRR:25 transcript and chr16:86,510,615 for the 5′ end of the HSALNT0234884 transcript  relatively short exons, FENDRR isoforms are only ~0.4–4 kb in size after splicing. LncBook, a curated database of human lncRNAs, incorporated in a non-coding RNA database RNAcentral, lists 50 FENDRR transcripts , PhyloCSF score (=65.5245), CPAT coding probability (=28.39%), and Ribosome-profiling: Lee translation initiation sites (=0) and Bazzini small ORFs (=0) predictions (LNCipedia: http://lncipedia.org). In contrast to evolutionary conservation of FOXF1, the orthologs of human FENDRR are best conserved among higher primates and have not been identified in animals other than mammals (http://genome.ucsc.edu/ENCODE).FENDRR transcription can start from at least three promoters. The majority of the FENDRR isoforms are transcribed from the intergenic promoter P1, annotated in the Eukaryotic promoter database  mapping at chr16:86,508,968–86,509,250  originates possibly from this promoter in the direction opposite to the FENDRR transcription , is located within FENDRR intron 1 and may initiate FENDRR-202, FENDRR:10 to 12, 26, 27, and 29 transcripts , begins with a cCRE  overlapping the 5′ end of the non-coding portion of the FOXF1 exon 1  a nucleosome-free region around and upstream of a transcription start site (TSS), (ii) a peak of RNA polymerase II binding slightly downstream of TSS and usually overlapping with the TF binding sites, and (iii) several H3K4me3-marked nucleosomes especially in the downstream portion of the promoter region . Taking l-it.ch, ) as a pr,509,250 C–F. Thiscription B. The FEnscripts . As in twnstream . Interes1 exon 1 .FOXF1 enhancer is located ~270 kb upstream to the FOXF1 gene [FOXF1 haploinsufficiency [FENDRR-FOXF1 intergenic promoter region. Interestingly, we have found a ~35 kb-large genomic instability hotspot, featuring the evolutionarily young LINE1 elements, L1PA2 and L1PA3 flanking five Alu repeats, located at the distal edge of this enhancer region, and responsible for several pathogenic enhancer deletions of which the distal breakpoints are mapped within the hotspot [Homo-Pan-Gorilla clade.The lung-specific XF1 gene ,19,20,21ficiency . It consficiency , each ovficiency  and 3C a hotspot . The appFOXF1 expression, this enhancer was narrowed to the ~10 kb-large most essential region [Based on the overlap of additional pathogenic CNV deletions causative for ACDMPV and the presence of hypermorphic single nucleotide variants (SNVs) in the undeleted allele of the enhancer that significantly ameliorated the lethal ACDMPV phenotype by increasing l region ,21. Thisl region  based onFENDRR allele, we have found that the FOXF1 enhancer regulates in cis also FENDRR [Fendrr/Foxf1 and other lncRNA/protein-coding divergent gene pairs showing that lncRNAs mimic the expression patterns of their protein-coding neighbors [Recently, through a correlation of the parental origins of chromosome 16, bearing the heterozygous CNV deletions of this enhancer with that of the transcribed o FENDRR   that, based on their H3 chromatin signature and eQTLs (expression quantitative trait loci), may potentially function as FENDRR proximal enhancers or modulators of its tissue specificity. For instance, in mice, a genomic region located ~1 kb downstream of Foxf1 functions as Foxf1 enhancer in foregut mesoderm and mesenchyme of developing liver and lungs [in vivo with Fendrr-Foxf1 intergenic region [Besides the nd lungs . It was c region .FENDRR and FOXF1 expression by the same cis-acting distant enhancer, the involvement in this regulation of the trans-acting TF FOXF1 was unexpected. Depletion of FOXF1 in lung fibroblasts by siRNA or FOXF1 point mutations causative for ACDMPV were found to correlate with a substantial (~50%) decrease in FENDRR levels  [Foxf1 was also shown to likely support Fendrr expression in mice [FOXF1 to the FENDRR promoters or the enhancer has yet to be documented. Interestingly, FENDRR promoters and the enhancer all contain several variants of the FOX TF binding RYAAAYA motif  showed that other members of the FOX TF family, especially FOXA1, bind to the FENDRR major promoter, P1, and the essential region of the enhancer. In addition, FOXF1 might also indirectly regulate FENDRR expression through the control of factors that directly regulate FENDRR. Based on our RNA-seq analyses of the ACDMPV transcriptomes, of about 40 TFs potentially interacting, based on ENCODE’s ChIP-seq data, with the FENDRR primary P1 promoter and the most essential portion of the enhancer, the expression of a histone methyltransferase subunit, ASH2L (binding next to FENDRR P1 promoter’s cCRE), positively correlates with the expression of FOXF1 (reduced by ~40% in ACDMPV cases linked to FOXF1 deficiency) [FENDRR expression by FOXF1.In contrast to the co-regulation of ctively) . Foxf1 w in mice . Howeverimidine; ), suggesiciency) . ASH2L ciciency) , a TrithFENDRR expression is a pro-apoptotic Annexin 2 (ANXA2) [Fendrr promoter, ANXA2 was specifically bound to the Fendrr intergenic promoter, and the increase in Anxa2 expression in caerulein-treated pancreatic cells positively correlated with the increase in the Fendrr level.Another potential regulator of  (ANXA2) . In elecFENDRR was also shown to be positively regulated by EGR2 and TFAP2A [FENDRR primary promoter based on ChIP-seq data from lung fibroblasts (ENCODE).Using a reporter assay in lung cancer cells lines, d TFAP2A . Both thMesp1 during cardiomyocyte differentiation also led to upregulation of several genes including Fendrr [Fendrr can be a downstream effector of MESP1, a TF best known as a master regulator of cardiovascular system development.Interestingly, induced expression of g Fendrr . Thus, FFENDRR, its expression is negatively regulated in the lungs by SMAD3 (but not SMAD2), which is a major signal transducer for cell-membrane Ser/Tyr kinase receptors of TGF-β1 [Regarding suppressors of f TGF-β1 .FENDRR-FOXF1 enhancer, (ii) TBX4 at chr16:86,508,364–86,508,853 next to the FENDRR primary promoter, and (iii) TBX2 at 86,507,893–86,509,510, overlapping the FENDRR primary promoter [Of note, using ChIP-seq for TBX2 and TBX4 in IMR-90 fibroblasts, we have found a specific binding of (i) TBX4 at chr16:86,223,833–86,225,160, largely overlapping the GH16J086219 regulatory element in the essential region of the FENDRR expression can be regulated through the epigenetic modification of its promoter (P1) that overlaps a large CpG island. The hypermethylation of this promoter has been shown to correlate with suppression of FENDRR expression in gastric cancer-associated fibroblasts [FENDRR promoter was also found in 36% of non-small cell lung cancers [Lastly, it has been suggested that roblasts . Hyperme cancers .FENDRR was shown to sequester, by sequence complementarity, at least ten different miRs, resulting in an increase in the expression of genes whose mRNAs were targeted for degradation by those miRs  (The well-known activity exhibited by lncRNAs is to function as a molecular sponge. ose miRs . The majriant 2) A.FENDRR-203, 209, 213 and 214 do not have exons corresponding to the exons 3 and 4 of FENDRR-206 that bind several miRs  of mRNAs. In particular, FENDRR was shown to compete with the Hu/ELAV-like protein 1 (HuR) for binding to the AU-rich elements in the 3′UTR of the multi-drug resistance gene MDR1 (ABCB1) mRNA [MDR1 mRNA 3′UTR, destabilizing MDR1 mRNA. As expected, the overexpression of FENDRR in drug-resistant myeloid leukemia cells specifically decreased expression of MDR1, likely due to a decrease in HuR-bound MDR1 3′UTRs, and improved the responsiveness of those cells to adriamycin [Besides interacting with miRs, B1) mRNA . This inriamycin .FENDRR can specifically interact also with proteins. It was shown that FENDRR sequesters HuR and this interaction has a stabilizing effect on FENDRR, but contributes to the decrease in MDR1 mRNA levels and restoration of drug sensitivity [miR-184 competes with HuR for binding to FENDRR and marks FENDRR for degradation by RISC/Ago [FENDRR is Iron-responsive Element Binding Protein 1 (IRP1), discussed later in the context of lung fibrosis [FENDRR-201 and 205 last exon in the position that corresponds to the intron 3/exon 4 junction of FENDRR-206 or an intron in other isoforms.In its role as a molecular sponge, sitivity ,57. Of nRISC/Ago . Anotherfibrosis . IRP1 biFENDRR was found physically associated with the chromatin modifying histone methyltransferase complexes such as Polycomb Repressive Complex (PRC) 2 [LncRNAs function often as a platform on which certain RNA-binding proteins can be locally increased in abundance and multicomponent complexes assembled to target those ligands to specific genomic locations.  (PRC) 2 ,6, TrxG/ (PRC) 2 ,58, and FENDRR with PRC2 was identified using RIP-ChIP assay in human fibroblasts (HLFs and human foot fibroblasts (HFFs)) with antibodies against two components of PRC2 complex, SUZ12 or EZH2 [FENDRR was also found bound to EZH2 in lung cancer cells CALU1 [Fendrr with PRC2 was confirmed using a similar assay in extracts from embryonic mouse cells [FENDRR resulted in de-repression of the PRC2-regulated genes [FENDRR not only can bind to chromatin-modifying complexes, but also can guide them to specific genomic locations such as promoters or enhancers. This hypothesis was verified in an in vitro mouse system by Grote et al. [Fendrr directs histone methyltransferase complexes to the Foxf1 and Pitx2 promoters, which independently showed a decrease in PRC2 occupancy with loss of Fendrr. A 20 nt-long Fendrr segment, mapping to mouse Fendrr exon 3 was predicted to form a triple-helix with complementary segments of the Foxf1 and Pitx2 promoters [PRC2 primarily trimethylates H3 at Lys27 (H3K27me3), causing transcriptional silencing through chromatin compaction. Association of  or EZH2 . FENDRR ls CALU1 . Associase cells . In addied genes . These re et al. . Using promoters .FENDRR was demonstrated in HLFs and HFFs using RIP-ChIP assay and antibodies against CoREST1 [REST also represses transcription by forming a complex with CoREST1 and recruiting chromatin-modifying proteins, among others, to methylate H3K9 and demethylate H3K4me or H3K4me2, resulting in chromatin condensation . CoREST  CoREST1 .Fendrr was identified using a pool-down assay in the murine embryonic cell extracts with antibodies against a component of this transmethylase complex, WDR5 [In contrast to the repressive PRC2 and CoREST complexes, TrxG/MLL proteins are responsible for transcription-activating methylation of H3, H3K4me3. The physical interaction of TrxG/Mll complex with Fendrr expression in mice is confined to the nascent lateral plate mesoderm. They found expression of Fendrr in cardiac mesoderm progenitor cells at the early midstreak stage E6.5–7. Sauvageau et al. [Fendrr is expressed in the pulmonary mesenchyme surrounding the bronchiolar epithelial cells, in mesenchymal cells of the developing mucosa, in the muscular layer of the gut, and in the lymphoid aggregations within mucosa of the gut. Lai et al. [Fendrr is expressed in the frontonasal process, upper respiratory track, lungs, and the posterior aorta-gonad-mesonephron region.Grote et al.  reportedu et al.  found thi et al.  showed tFendrr was lethal at E13.75 due to heart and omphalocele defects. Sauvageau et al. [Fendrr is lethal although at a later, perinatal stage; Fendrr−/− lungs at the pseudoglandular stage (E14.5) were hypoplastic, had decreased number of pulmonary arteries, and featured general failure of vasculogenesis. At E18.5, Fendrr−/− lungs had fewer and enlarged alveoli. The observed respiratory failure at birth was likely caused by the defects in lung maturation and vascularization. Regarding development of the esophagus and the gut, E18.5 embryos featured thinning of the mesenchymal layer of the mucosa and external smooth muscle layers in the esophagus. Moreover, they featured intraventricular septal heart defects prior to birth. Perinatal lethality in Fendrr−/− mice was also reported by Lai et al. [Fendrr knockout mice described by the three groups may be due to differences in the Fendrr ablation strategies used. While Grote et al. [Fendrr transcription by replacing the 1st exon of Fendrr with multiple transcription terminators, the other two groups [Fendrr gene with the lacZ reporter while retaining the transcription from the endogenous Fendrr promoter.Described by Grote et al. , homozygu et al.  also shoi et al. . E13.5 eo groups ,62 replaFendrr is highly expressed in the lungs and colon, then in the liver, spleen, brain, and testes (http://useast.ensembl.org/Mus_musculus) [FENDRR levels in the bladder, lungs, esophagus, colon, prostate, and small intestine [FENDRR has the highest expression in the lungs, followed by urinary bladder, gall bladder, esophagus, prostate and appendix, and was almost undetectable in the heart, kidney, and liver.In the adult mouse, usculus) . In humantestine . Similarntestine . These sFendrr in mouse lung development and the regulation of FENDRR expression by FOXF1 as well as by the FOXF1 enhancer suggest that FENDRR might be involved in etiology of ACDMPV and/or associated diseases. Point mutations involving FOXF1 and CNV deletions of FOXF1 or its enhancer are causative for ACDMPV in more than 80% of patients.The involvement of FOXF1 through FENDRR, we have performed RNA-seq in FENDRR-depleted (by siRNA or CRISPR/Cas9) IMR-90 cells [FENDRR depletion in IMR-90 cells suggest deregulation of some pathways also affected in the ACDMPV lungs, including those involved in RNA processing, cell cycle regulation, membrane trafficking, VEGFA-VEGFR2 signaling, TGF-β signaling, EGF signaling, β-catenin-independent WNT signaling, G protein signaling, and other processes [FENDRR-depleted fibroblasts, include, e.g., PDGFRA, PLXNC1, or serotonin transporter genes SLC5A1 and SLC6A4 with roles in vascular remodeling [FENDRR-deficient fibroblasts include, e.g., COL6A2 and ELN which might contribute to pulmonary arterial hypertension [To determine whether any genes or pathways affected in ACDMPV lungs could be controlled by 90 cells . Our prerocesses . Genes imodeling . Genes trtension .FENDRR was proposed to have a tumor suppressor role by inhibiting cell proliferation, motility, chemotherapy resistance, or inducing apoptosis. Its expression level was found often significantly reduced in several cancers, including lung adenocarcinoma and squamous cell carcinoma, bladder urothelial carcinoma, or colorectal adenocarcinoma [FENDRR overexpression correlated with a decreased rate of proliferation of cancer cell lines [FENDRR exhibited significantly decreased growth rate of tumor xenograft compared with their controls in vitro. Xu et al. [FENDER over-expression also suppressed migration and invasion of gastric cancer cells.Long non-coding RNAs have been shown to be involved in the pathogenesis of various malignant cancers as tumor suppressors or oncogenes ,67,68. Farcinoma ,55,56,69ll lines ,70, inhill lines . The A54u et al.  have repFENDRR has been proposed to play an inhibitory role in cancer by sponging miRs that target mRNAs of tumor suppressors  sponging fibroblast activating miR-214 , and (ii) reducing iron level through interaction with IRP1 [FENDRR expression and activates expression of collagen and other extracellular matrix protein genes. IRP1 binds, among others, to iron-responsive element of Transferrin Receptor TFRC mRNA  is caused by uncontrolled stimulation of fibroblasts, leading to the accumulation of ACTA2, collagen and fibronectin in the extracellular matrix, resulting in loss of tissue architecture and functioning ,74. The ignaling ,75, and ignaling . FENDRR ith IRP1 . Iron isto cells ), allowiFENDRR can be tissue specific. In a mouse fibrotic heart, Fendrr level rather increased [Fendrr seems to play pro-fibrotic role in the developed heart by sponging miR-106b, which targets pro-fibrotic Smad3 mRNA for degradation.However, the anti-fibrotic functioning of ncreased . Fendrr Macrophage polarization: FENDRR was identified as a positive regulator of pro-inflammatory M1 macrophage polarization via the STAT1-dependent pathway [FENDRR could function in this process as a chromatin modifier, increasing the expression of pro-inflammatory CXCL10 through TrxG/MLL-mediated H3K4me3 methylation, or EZH2-dependent H3K27 methylation that suppresses anti-inflammatory genes. It is also possible that FENDRR reduces iron level in macrophages, leading to activation of STAT1 signaling and M1 macrophage polarization. pathway . Disorde pathway , cancer  pathway , infecti pathway , insulin pathway , atheros pathway , and aut pathway . The exaPancreatitis: In an in vitro rat model of caerulein-induced inflammation of the pancreas, pancreatitis, ANXA2 and FENDRR were found to be increased in pancreatic acinar cells [FENDRR and Anxa2 upregulation correlated with an increase in pro-apoptotic BAX and a decrease in an anti-apoptotic BCL2. FENDRR was also found bound to ANXA2 and this interaction might contribute to apoptosis.ar cells . FENDRR FENDRR was shown to be essential for heart development in mice [FENDRR’s role in cardiovascular development in humans is unknown. FENDRR was suggested to have cardio-protective role based on negative correlation of its levels in peripheral blood mononuclear cells with left ventricular mass index in hypertensive patients [ in mice ,61,62. Hpatients .FENDRR emerges as a significant cell type- and developmental stage-specific regulator of gene expression at transcriptional and post-transcriptional levels. Its own expression involves promoter activation both by a distant tissue-specific enhancer acting in cis, shared with FENDRR-neighboring FOXF1, and by trans-acting FOXF1. This kind of expression control may represent a paradigm for the regulation of other divergent gene pairs. However, the overall current understanding of FENDRR structure and functioning is just the tip of the iceberg. For instance, FENDRR spatial structure is unknown and likely depends on its multiple ligands and local environment. This picture is further complicated by the existence of numerous FENDRR isoforms, whose presence may be tissue- and developmental stage-dependent. In addition, FENDRR subcellular localization requires further clarification. In mouse embryonic lungs, it seems mostly nuclear, whereas in adult human lung fibroblasts, it localizes preferentially to the cytoplasm. Moreover, FENDRR’s known ligands have been identified in in vitro experiments focused rather on testing selected proteins or miRs. However, the current knowledge already points at the importance of FENDRR in development and tissue maintenance. In vitro experiments have shown that increasing FENDRR expression can potentially be of therapeutic significance in many cancers and lung fibrosis. Nevertheless, although targeting cancer cells and fibroblasts with FENDRR can be beneficial, FENDRR overexpression in epithelia may inhibit epithelial cell proliferation and hinder restoration of organ function. Thus, therapeutic manipulation with FENDRR expression would have to be organ/tissue specific. Other challenges faced in FENDRR studies are related to its very nature as a rapidly evolving regulatory molecule or even group of molecules, taking into account all its alternatively spliced isoforms that sometimes may be involved in contradictive biological processes.The lncRNA


Endogenous retroviruses (ERVs) are repetitive sequences in the genome, belonging to the retrotransposon family. During the course of life, ERVs are associated with multiple aspects of chromatin and transcriptional regulation in development and pathological conditions. In mammalian embryos, ERVs are extensively activated in early embryo development, but with a highly restricted spatial-temporal pattern; and they are drastically silenced during differentiation with exceptions in extraembryonic tissue and germlines. The dynamic activation pattern of ERVs raises questions about how ERVs are regulated in the life cycle and whether they are functionally important to cell fate decision during early embryo and somatic cell development. Therefore, in this review, we focus on the pieces of evidence demonstrating regulations and functions of ERVs during stem cell differentiation, which suggests that ERV activation is not a passive result of cell fate transition but the active epigenetic and transcriptional regulation during mammalian development and stem cell differentiation. ERVs belong to a Class family of retrotransposon elements in the genome. Together with DNA transposons, they are known as transposable elements (TEs), which are derived from DNA fragments able to transpose within the genome. Due to their capacities to hop around and copy themselves in the genome, TEs are considered one of the main driving forces in reconstructing the genome during mammalian evolution. To date, TEs have mostly lost the ability to transpose , 2, consGAG, POL, and ENV) in the center. It should be emphasized that LTRs are the regulatory elements of ERVs [Comparing to other repeat element families, such as short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs), ERVs bear more sequence complexities and thus may play more specific regulatory functions in the genome , 3. Alth of ERVs . The LTR of ERVs . Meanwhi of ERVs . Based oThe expression level of ERVs is dynamically regulated in early embryogenesis, differentiated tissues, and germ cells . InteresOver the last 10 years, increasing pieces of evidence are showing that LTRs may play under-recognized regulatory roles in mammalian development and diseases –13. In tIf chromatin regulation is a symphony, then ERV has several instruments to play. ERV recruits transcription factors, works as alternative promoters, encodes long non-coding RNAs (lncRNAs), and produces protein products to mediate cellular function. These abilities could be stemmed from intrinsic functions of ERV or could be coopted during the coevolution with the host genome. Nevertheless, the functions of ERV have become an integral part of the regulatory machinery in the genome and indispensable for the normal development and homeostasis of mammals.In-silico mapping revealed that many ERVs are enriched with transcription factor-binding sites, suggesting ERVs may act as cis-regulatory elements for transcription . PutativAIM2 which senses cytosolic foreign DNA and activates inflammatory responses [Moreover, ERVs can also modulate signaling pathways to coordinate cell fate change. It has been found that ERVs shaped the evolution of the transcription network underlying the interferon response . For insesponses . This suZfp352 has two promoters (P1 and P2) that are active in mouse early embryo and somatic cells, respectively [Zfp352 in early embryos overlaps with MT2B1 repeats, indicating the ERV promoter may be critical for the early activation of Zfp352 [JAZF1 prefers the 3′ full-length promoter (prmtr.40310) in KIRP cancer, whereas in KIRC cancer, a truncated promoter (prmtr.40312) is favored [The LTR elements in ERVs possess the intrinsic promoter activity to drive ERVs expression. LTRs can also function as alternative promoters to drive host ORF expression. It has been estimated that up to 75% of human genes take advantage of alternative promoters to achieve tissue-specific regulation . The empectively –27. Intef Zfp352 –27. A ref Zfp352 . For exa favored .GTSO1, which led to the generation of 15 isoforms of GTSO1 that may function differently under different disease contexts [The presence of alternative promoters not only leads to context-dependent gene activation but also creates alternative splicing variants of the transcripts . Alternacontexts .More importantly, many ERVs can encode for lncRNA. The functions of these lncRNAs can be involved in various processes like recruiting transcription factors, cooperating with epigenetic regulators or modifiers, or interacting with miRNAs –33.in vivo, suggesting that TROJAN promotes cancer invasion and can serve as a potential therapeutic target [A few studies demonstrated that the ERV-derived lncRNAs can participate in signaling transduction by regulating protein recruitment and protein degradation –37. One c target .GAG, POL, and ENV. The functions of these viral proteins are diversified [In addition to RNAs, the proteins translated from ERVs can also perform specific functions under certain contexts. These proteins are derived from the open reading frame of ERV, including ersified –40. For ersified , 42, andersified .Embryonic development is initiated after fertilization, followed by zygote cleavage. In the early embryo cleavage stages, the zygotic genome is activated, accompanied by global remodeling and rewiring of the transcription network. Before the first cell fate segregation in late morula and blastocyst, cells in embryos retain the capacity to give rise to the complete embryo proper and are thus considered totipotent. In blastocyst, cells are committed to the outer layer trophectoderm and inner cell mass which gives rise to the pluripotent epiblast and differentiates into three germ layers and somatic tissues. Numerous genetic and epigenetic programs governing the embryo developmental processes have been revealed, but mostly focusing on the regulation of the coding genome. Non-coding elements such as ERVs are poorly understood in this context but are increasingly gaining attention. ERVs are extensively activated in early embryo development, with a highly restricted spatial-temporal pattern, and are drastically silenced during differentiation with exceptions of extraembryonic tissue and germlines . Here, wZscan4 cluster gene expression in mouse 2C embryo, and the upregulation of Zscan4 can further activate MT2, resulting in DNA demethylation and open chromatin configuration to further activate 2C-specific genes nearby MT2 loci [During both mouse and human embryo development, ERVL subfamily is activated around ZGA but gradually silenced thereafter. It seems that ERVL is predominantly associated with the totipotent state. In mouse, transcripts from MERVL loci occupy 2% of the total mRNA in 2C embryo . More thMT2 loci . InteresMT2 loci , implyinDux in mESCs can activate MERVL and downstream 2C genes. Similarly, human DUX4 over-expression results in HERVL activation and simultaneously upregulation of human 8C-specific genes [Similarly, in human, HERVL expression is also enriched in 8C stage corresponding to the time of human embryo ZGA , 46. Oveic genes , 46.Zfp809 produces two isoforms: a full-length protein and a truncated protein that lacks 50 residues at C-terminus. The full-length protein is selectively stable in ESCs but degraded in other cell types. Whereas the short isoform is constitutively expressed in both ESCs and differentiated cells, but the underlying impact and functional differences between the two differentially expressed isoforms remain unknown [Upon exiting from 2C stage, MERVL is rapidly silenced and its expression falls back to baseline in mouse 8C embryos. The silencing of MERVL is mediated by ZFP809. ZFP809 is a mouse-specific zinc finger protein, containing the KRAB domain at the N-terminus and seven zinc finger domains at the C-terminus . The zin unknown . NeverthUpon exiting from totipotent state, cells take on the first cell fate decision to become extraembryonic trophectoderm or pluripotent epiblast. ERVL is rapidly silenced along with the exit from totipotency, while other sub-families of ERVs are upregulated , 11, 45.HERVH copies are highly enriched with the putative binding sites for pluripotent factors including KLF4, NANOG, and OCT4 . In hESCIn addition, the lncRNAs derived from HERVH also play critical roles in pluripotency regulation. They may function as scaffold units to recruit chromatin modifiers and direct them towards specific locations , 51. In Despite the importance of HERVH, pieces of evidence have been controversial about whether HERVH is required for naïve or primed pluripotency , 52, 53.Research work has shed more light on the roles of ERVs in trophectoderm differentiation since the 1990s . The rolENV gene [the ENV gene of HERVW lacks an immunosuppressive domain compared to full-length ENV protein. It is specifically upregulated in syncytiotrophoblast during implantation [ENV gene can induce cell fusion, which is reversed by neutralizing antibodies against SYNCITIN 1 [Many ERVs have a robust expression in placenta development . Among aENV gene , 57. Theantation , 42. Theantation . EctopicNCITIN 1 . In contNCITIN 1 . SimilarNCITIN 1 . InteresNCITIN 1 , 63. MorNCITIN 1 , 55. DifNCITIN 1 . MoreoveNCITIN 1 .Despite the high activity of ERV and other TE families in early embryos, they are thought to be largely deactivated during the differentiation process. The silencing mechanism involves coevolution between the host transcription regulatory machinery and ERVs to tame ERV expression and limit their transposition. Improper silencing of ERVs is associated with loss of tissue homeostasis and pathological conditions. For example, the ENV protein derived from HERVW is highly expressed in type-1 diabetes and inhibited the secretion of insulin . Transcrin vitro, distinct sets of ERVs are selectively activated in different cell populations. For example, LTR32, MER57A-int, and MER45A are specifically expressed in definitive cardiomyocytes while MLT1H1, HERVIP10B-int, and LTR5A are selectively active in non-contractile cells [In addition to the conventional view that ERV activation in differentiated tissue led to pathological conditions, more and more tissue-specific ERVs were identified, and they are thought to contribute to the cell type-specific differentiation or tissue-specific functions . For insle cells . It is nTaken together, these pieces of evidence demonstrate two fundamental aspects of ERV in differentiation: (1) Various ERVs are now associated with tissue differentiation and specific cell lineage. (2) Aberrant ERV expression in differentiated tissues may be toxic while targeting these ERVs could provide potential therapeutic means to slow down disease progression.Although ERV activity may be largely silenced during differentiation, it is highly expressed and activated during germline formation. The first observation of ERV expression in germline cells can be dated back to 1983 when virus-like “intracisternal A particle (IAP)” was detected in mouse oocytes . Up to nOn the contrary, the progenitors of mouse germline cells, namely primordial germ cells (PGCs), show repressed ERV activity. ERV sequences are enriched with H3K9me3 and H3K27me3 that induce a repressive chromatin configuration . In detaERVs are previously thought to coordinate with the host genome during mammalian evolution, and now they are considered as integral parts to form species and cell type-specific gene regulatory networks. The research of ERVs in stem cell fate decision and differentiation has just been unraveled, and many questions remained to be answered. Given the observed stage-specific expression pattern of ERV , what wi