DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Congenital Heart Diseases

Aims:Multiple genes and environmental factors are known to be involved in congenital heart disease(CHD),but epigenetic variation has received little attention.Monozygotic(MZ)twins with CHD provide a unique model for exploring this phenomenon.In order to investigate the potential role of Deoxyribonucleic Acid(DNA)methyla-tion in CHD pathogenesis,the present study examined DNA methylation variation in MZ twins discordant for CHD,especially ventricular septal defect(VSD).Methods and Results:Using genome-wide DNA methylation profiles,we identified 4004 differentially methylated regions(DMRs)in 18 MZ twin pairs discordant for CHD,and 2826 genes were identified.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis revealed a list of CHD-associated pathways.To further investigate the role of DNA methylation in VSD,data from 7 pairs of MZ twins with VSD were analyzed.We identified 1614 DMRs corresponding to 1443 genes associated with arrhythmogenic right ventricular cardiomyopathy,cyclic guanosine monopho-sphate-protein kinase G(cGMP-PKG)signaling pathway by KEGG analysis,and cell-cell adhesion,calcium ion transmembrane transport by GO analysis.A proportion of DMR-associated genes were involved in calcium signaling pathways.The methylation changes of calcium signaling genes might be related to VSD pathogenesis.Conclusion:CHD is associated with differential DNA methylation in MZ twins.CHD may be etiologically linked to DNA methylation,and methylation of calcium signaling genes may be involved in the development of VSD.

Bivalent histone modifications during tooth development

Histone methylation is one of the most widely studied post-transcriptional modifications. It is thought to be an important epigenetic event that is closely associated with cell fate determination and differentiation. To explore the spatiotemporal expression of histone H3 lysine 4trimethylation（H3K4me3） and histone H3 lysine 27 trimethylation（H3K27me3） epigenetic marks and methylation or demethylation transferases in tooth organ development, we measured the expression of SET7, EZH2, KDM5 B and JMJD3 via immunohistochemistry and quantitative polymerase chain reaction（qP CR） analysis in the first molar of BALB/c mice embryos at E13.5, E15.5, E17.5, P0 and P3, respectively. We also measured the expression of H3K4me3 and H3K27me3 with immunofluorescence staining. During murine tooth germ development, methylation or demethylation transferases were expressed in a spatial–temporal manner. The bivalent modification characterized by H3K4me3 and H3K27me3 can be found during the tooth germ development, as shown by immunofluorescence. The expression of SET7, EZH2 as methylation transferases and KDM5 B and JMJD3 as demethylation transferases indicated accordingly with the expression of H3K4me3 and H3K27me3 respectively to some extent. The bivalent histone may play a critical role in tooth organ development via the regulation of cell differentiation.

Curcumin Interferes with TGF-β1-Induced Fibrosis in NRK-49F Cells by Reversing ADAMTS18 Gene Methylation

Objective To explore the molecular mechanism by which curcumin affects renal interstitial fibrosis(RIF)progression by regulating ADAM metallopeptidase with thrombospondin type 1 motif 18(ADAMTS18)methylation.Methods NRK-49F cells RIF model were induced with transforming growth factorβ1(TGF-β1).Effects of different concentrations of curcumin(0,10,20,and 30μmol/L)on cell proliferation,cell cycle,cell apoptosis as well as cyclin D1 expression were analyzed by cell counting kit-8,flow cytometry and Western blot,respectively.ADAMTS18 methylation levels were determined by methylation-specific polymerase chain reaction.ADAMTS18,fibronectin(FN),type I collagen(Col-I)and alpha-smooth muscle actin(α-SMA)mRNA and protein expressions were analyzed by real-time PCR(RT-PCR)and Western blot,respectively.Meanwhile,cells were treated with 50 mmol/L 5-aza-2′-deoxycytidine(5-aza-dC,demethylation agent)for 72 h.Effect of curcumin on extracellular matrix(ECM)deposition was evaluated by immunochemical staining and Western blot.NRK-49F cells were transfected with ADAMTS18 small interfering RNA and grouped into a normal control,ADAMTS18-knock-out(KO),and ADAMTS18-KO+30μmol/L curcumin groups,and whether curcumin can reverse the effect of ADAMTS18 knockdown on RIF was evaluated.Results Compared with the control group,TGF-β1 significantly inhibited the proliferation of NRK-49F cells,blocked the G1/G0 phase,promoted cell apoptosis and inhibited cyclin D1 expression(P<0.01).Among the different concentrations of curcumin,30μmol/L curcumin significantly reversed these processes(P<0.01).Immunochemical staining and Western blot results showed that curcumin significantly inhibited the deposition of FN,Col-I andα-SMA(P<0.01).Curcumin and 5-zaz-dC had synergistic effects,promoting ADAMTS18 expression,removing ADAMTS18 methylation,and reducing ECM deposition.ADAMTS18 knockdown promoted ECM accumulation,and curcumin reversed this process(P<0.01).Conclusion TGF-β1-induced fibrosis in NRK-49F cells.Curcumin promoted ADAMTS18 expression,reduced ECM accumulation,and alleviated RIF progression by inhibiting ADAMTS18 methylation.

Wnt5a Plays Controversial Roles in Cancer Progression

WntSa is a representative Wnt ligand that regulates multiple cellular functions through the Wnt5a nonclassical pathway.Although Wnt5a has been implicated in various pathological conditions,its role in cancer is ambiguous and might involve methyl modifications,distinct mRNA isofbrms,as well as different downstream pathways.Therefore,it is an essential factor in cancers'progression(invasion,migration,proliferation,and epithelial-mesenchymal transition),and a potential biomarker for prognosis and treatment.

Epigenetic Alterations in Depression and Treatment Perspectives

The global incidence of depression is progressively on the rise and tends to occur more in younger generations,however the pathogenesis of the disease is unclear.Meanwhile,epigenetics is a modification which produces heritable alterations in the DNA sequence,which ultimately manifest in phenotypic differences.It has been suggested that the onset and development of depression can be tentatively explained by the combination of epigenetic and environmental factors.This paper reviews epigenetic changes in depression in the context of environmental factors,including DNA methylation modifications,histone modifications,and non-coding RNA regulation.An epigenetic-based therapeutic outlook was also proposed in this paper,which initially elucidates the epigenetic mechanisms underlying the pathogenesis of depressions and provides a theoretical basis for the treatment of depression.

Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis

Dynamic regulation and packaging of genetic information is achieved by the organization of DNA into chromatin. Nucleosomal core histones, which form the basic repeating unit of chromatin, are subject to various post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitinylation. These modifications have effects on chromatin structure and, along with DNA methylation, regulate gene transcription.The goal of this study was to determine if patterns in modifications were related to different categories of genomic features, and, if so, if the patterns had predictive value. In this study, we used publically available data（ChIP-chip）for different types of histone modifications（methylation and acetylation） and for DNA methylation for Arabidopsis thaliana and then applied a machine learning based approach（a support vector machine） to demonstrate that patterns of these modifications are very different among different kinds of genomic feature categories（protein, RNA,pseudogene, and transposon elements）. These patterns can be used to distinguish the types of genomic features.DNA methylation and H3K4me3 methylation emerged as features with most discriminative power. From our analysis on Arabidopsis, we were able to predict 33 novel genomic features, whose existence was also supported by analysis of RNA-seq experiments. In summary, we present a novel approach which can be used to discriminate/detect different categories of genomic features based upon their patterns of chromatin modification and DNA methylation.

EARLY FLOWERING IN SHORT DAYS(EFS) regulates the seed size in Arabidopsis

Post-transcriptional modifications,including histone modifications and DNA methylation,alter the chromatin landscape to regulate gene expression,thus control various cellular processes in plants.EARLY FLOWERING IN SHORT DAYS(EFS)is the major contributor for H3K36 methylation in Arabidopsis and is important for plant development.Here,we find that EFS is expressed in different stages of embryo morphogenesis,and the efs mutant produces larger embryo that results in enlarged seeds.Further analysis reveals that an imprinted gene MOP9.5 is hypomethylated at the promoter region and its expression is derepressed in efs mutant.MOP9.5 promoter is marked by various epigenetic modifications,and we find that following the increase of H3K36me3,H3K27me3 and H3K9me2 levels are reduced in efs mutant.This data indicates an antagonistic regulation between H3K36me3 and DNA methylation,and/or H3K27me3 at MOP9.5.Our results further show that both maternal and paternal EFS alleles are responsible for the seed size regulation,which unraveled a novel function of EFS in plant development.

Expression Profiles of SIRT1 and APP Genes in Human Neuroblastoma SK-N-SH Cells Treated with Two Epigenetic Agents

In our previous studies, significant hypermethylation of the sirtuin 1（SIRT1） gene and demethylation of the b-amyloid precursor protein（APP） gene were found in patients with Alzheimer＇s disease（AD） compared with the normal population. Moreover, the expression of SIRT1 was significantly decreased while that of APP was increased in AD patients. These results indicated a correlation of DNA methylation with gene expression levels in AD patients. To further investigate the epigenetic mechanism of gene modulation in AD, we used two epigenetic drugs, the DNA methylation inhibitor 5-aza-20-deoxycytidine（DAC） and the histone deacetylase inhibitor trichostatin A（TSA）, to treat human neuroblastoma SK-N-SH cells in the presence of amyloid b-peptide Ab25-35（Ab25-35）. We found that DAC and TSA had different effects on the expression trends of SIRT1 and APP in the cell model of amyloid toxicity. Although other genes, such as microtubule-associated protein s, presenilin 1, presenilin 2, and apolipoprotein E, were up-regulated after Ab25-35treatment, no significant differences were found after DAC and/or TSA treatment. These results support the evidence in AD patients and reveal a strong correlation of SIRT1/APP expression with DNA methylation and/or histone modification, which may help understand the pathogenesis of AD.