Epigenetic Elements Research Articles

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.

Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC) is the most-influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC co-localizes with specific interactors shows that each interaction points to chromatin remodeling, stemness, differentiation, or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs.

Dynamic epigenetic states of maize centromeres.

The centromere is a specialized chromosomal region identified as the major constriction, upon which the kinetochore complex is formed, ensuring accurate chromosome orientation and segregation during cell division. The rapid evolution of centromere DNA sequence and the conserved centromere function are two contradictory aspects of centromere biology. Indeed, the sole presence of genetic sequence is not sufficient for centromere formation. Various dicentric chromosomes with one inactive centromere have been recognized. It has also been found that de novo centromere formation is common on fragments in which centromeric DNA sequences are lost. Epigenetic factors play important roles in centromeric chromatin assembly and maintenance. Non-disjunction of the supernumerary B chromosome centromere is independent of centromere function, but centromere pairing during early prophase of meiosis I requires an active centromere. This review discusses recent studies in maize about genetic and epigenetic elements regulating formation and maintenance of centromere chromatin, as well as centromere behavior in meiosis.

Computational analysis of candidate prion-like proteins in bacteria and their role.

Prion proteins were initially associated with diseases such as Creutzfeldt Jakob and transmissible spongiform encephalopathies. However, deeper research revealed them as versatile tools, exploited by the cells to execute fascinating functions, acting as epigenetic elements or building membrane free compartments in eukaryotes. One of the most intriguing properties of prion proteins is their ability to propagate a conformational assembly, even across species. In this context, it has been observed that bacterial amyloids can trigger the formation of protein aggregates by interacting with host proteins. As our life is closely linked to bacteria, either through a parasitic or symbiotic relationship, prion-like proteins produced by bacterial cells might play a role in this association. Bioinformatics is helping us to understand the factors that determine conformational conversion and infectivity in prion-like proteins. We have used PrionScan to detect prion domains in 839 different bacteria proteomes, detecting 2200 putative prions in these organisms. We studied this set of proteins in order to try to understand their functional role and structural properties. Our results suggest that these bacterial polypeptides are associated to peripheral rearrangement, macromolecular assembly, cell adaptability, and invasion. Overall, these data could reveal new threats and therapeutic targets associated to infectious diseases.

EZH2 dependent epigenetic landscape in adult T cell leukemia and Tax immortalized cells

Epigenetic regulations globally determine gene transcription. Recent studies have revealed that expression changes and genetic mutations of epigenetic factors cause epigenetic imbalance in cancers. We previously reported that aberrant expression of Polycomb repressive complex 2 (PRC2) components causes constitutive NF-κB activation through silencing of miR-31 in ATL cells. However, the underlying mechanisms by which the epigenetic imbalance is induced and maintained remain to be elucidated. Here, we conducted ChIP-on-chip and transcriptome analyses of ATL and normal CD4+ T cells and found that the epigenetic reprogramming closely associates with ATL specific gene expression signature. Leukemic cell-specific silencing of cell cycle regulator, CDNK1A, was correlated with H3K27me3 level. In addition, orchestrated loss of microRNAs and multiple transcription factors appears to be mediated by the epigenetic mechanism. EZH2 upregulation and H3K27me3 accumulation were found in HTLV-1-infected populations derived from ATL patients as well as asymptomatic carriers. Furthermore, EZH2 inhibition blocked Tax-dependent cell growth and its immortalization in vitro. Intriguingly, the Tax-triggered immortalizing cells partially mimicked the methylation pattern observed in ATL cells, suggesting that the epigenetic alterations are closely involved in immortalization of infected cells and disease progression. In parallel, we found that over expression of PRC2 core components was induced by active signaling cascades including NF-κB in ATL cells. Collectively, our results suggest a coherent positive feedback mechanism comprised of PRC2 and NF-κB signaling, which stabilizes the epigenetic rearrangement and phenotypic outcomes in HTLV-1 infected cells. Since pharmacological inhibition of EZH2 selectively killed ATL and HTLV-1 infected cells in ex vivo culture, targeting the epigenetic elements will hold great promise in treatment and prevention of ATL and HTLV-1-related diseases.

Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation.

Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1’s role in gene regulation.

Promoter Hypermethylation and Decreased Expression of Syncytin-1 in Pancreatic Adenocarcinomas.

Syncytin-1 is a member of human endogenous retroviral W gene family (HERVW1). Known to be expressed in human placental trophoblast, syncytin-1 protein mediates the fusion of cytotrophoblasts for the formation of syncytiotrophoblasts, the terminally differentiated form of trophoblast lineage. In addition, in vitro studies indicate that syncytin-1 possessed nonfusogenic functions such as those for immune suppression, cell cycle regulation and anti-apoptotic activities. Overexpression of syncytin-1 has been observed in various malignant tissues including breast, endometrial and ovarian cancers. It was reported that syncytin-1 gene expression is associated with dynamic changes of DNA hypomethylation in the 5’ LTR. In this study, applying the real-time PCR, Western blot analysis and immunohistochemistry methods, we demonstrate a constitutive expression of syncytin-1 in normal pancreas tissues as well as normal tissues adjacent to cancer lesions. Moreover, a reduced expression is found in the pancreatic adenocarcinoma tissues. The expression levels of syncytin-1 are not correlated with the stage, historical grade and gender, but inversely correlated with patients’ age. Furthermore, COBRA and bisulfite sequencing results indicated that the lower expression of syncytin-1 is correlated with the hypermethylation of two CpG dinucleotides in the 5’ LTR of syncytin-1 gene. The nonfusogenic function of syncytin-1 in normal pancreas as well as its role(s) in the pathogenesis and progression of pancreatic cancers remains to be investigated. Identification of the two CpG dinucleotides around transcription start site as key epigenetic elements has provided valuable information for further studies on the epigenetic regulation of syncytin-1 in pancreatic cancer cells.

Molecular Links between Alcohol and Tobacco Induced DNA Damage, Gene Polymorphisms and Patho-physiological Consequences: A Systematic Review of Hepatic Carcinogenesis.

Chronic alcohol and tobacco abuse plays a crucial role in the development of different liver associated disorders. Intake promotes the generation of reactive oxygen species within hepatic cells exposing their DNA to continuous oxidative stress which finally leads to DNA damage. However in response to such damage an entangled protective repair machinery comprising different repair proteins like ATM, ATR, H2AX, MRN complex becomes activated. Under abnormal conditions the excessive reactive oxygen species generation results in genetic predisposition of various genes (as ADH, ALDH, CYP2E1, GSTT1, GSTP1 and GSTM1) involved in xenobiotic metabolic pathways, associated with susceptibility to different liver related diseases such as fibrosis, cirrhosis and hepatocellular carcinoma. There is increasing evidence that the inflammatory process is inherently associated with many different cancer types, including hepatocellular carcinomas. The generated reactive oxygen species can also activate or repress epigenetic elements such as chromatin remodeling, non-coding RNAs (micro-RNAs), DNA (de) methylation and histone modification that affect gene expression, hence leading to various disorders. The present review provides comprehensive knowledge of different molecular mechanisms involved in gene polymorphism and their possible association with alcohol and tobacco consumption. The article also showcases the necessity of identifying novel diagnostic biomarkers for early cancer risk assessment among alcohol and tobacco users.

DNA Methylome Signature in Synoviocytes From Patients With Early Rheumatoid Arthritis Compared to Synoviocytes From Patients With Longstanding Rheumatoid Arthritis.

Epigenetics can contribute to pathogenic mechanisms in autoimmunity. We recently identified an imprinted DNA methylation pattern in rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) involving multiple genes in pathways implicated in cell migration, matrix regulation and immune responses.1,2 To understand when alterations in DNA methylation occur in RA and the specificity of the methylation changes in RA, we compared differentially methylated loci (DMLs) of early RA (ERA), juvenile idiopathic arthritis (JIA) to longstanding RA (LRA) and osteoarthritis (OA). Genomic DNA from fibroblast-like synoviocytes (FLS) was isolated from 4 ERA (1–13 months of symptoms; all female; average age 52) as previously described. 1, 2, 3 All ERA patients were anti-citrullinated peptide antibody positive. Two were treated with methotrexate alone and one was treated with methotrexate and abatacept. One patient was not taking anti-rheumatic drugs. Patients met the 2010 classification criteria for RA and samples were obtained at the time of arthroscopic biopsy.4, 5 FLS from patients with JIA (n=3; 2 female, one male; average age 31) was isolated from synovium obtained at the time of arthroplasty. Previously reported 11 LRA and 11 OA were used as controls.5 DNA methylation level was measured using the Illumina Infinium HumanMethylation450 chip across 485,512 loci and the methylation level at individual locus was reported as β values (see Supplementary Methods). Small but statistically significant global hypomethylation in LRA compared with ERA (average β value per CpG loci = 0.163 in LRA and 0.168 in ERA; p value=0.0046) was detected by summing β values in gene promoter region. Unbiased hierarchical clustering and principal component analysis (PCA) revealed relationships of ERA and JIA to LRA and OA FLS lines (Figure 1A and B, respectively) based on previously identified 15,220 DMLs between 11 LRA and 11 OA2. ERA and JIA clustered with LRA and segregated from OA. ERA and LRA patterns partially overlapped, which could be consistent with a transition of ERA to LRA methylation. FLS from JIA also segregated with the LRA group but formed a separate subgroup. With methylome comparisons between LRA and ERA using Welch’s t-test, we identified 20,776 DMLs (8,059 hypomethylated and 12,717 hypermethylated in LRA compared with ERA) in 5,469 DMGs (average differences of β values > 0.1 and q values < 0.05). Pathway enrichment analysis evaluated by Ingenuity pathway analysis (IPA) identified five potentially enriched pathways (Wnt/β-catenin signaling, enrichment ratio (ER) = 0.249; Integrin signaling, ER = 0.233; RAR activation, ER = 0.233; PDGF signaling, ER = 0.286; Superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism, ER = 0.417) with hypomethylated DMGs in LRA (BH-adjusted p values < 0.1). In addition, 340 CpG loci that most distinguished ERA from LRA were identified by comparing the entire methylation datasets by random forest method and confirmed that ERA and LRA could be distinguished from each other (Supplementary Figure 1). Figure 1 Analysis of DNA methylation patterns in early and longstanding rheumatoid arthritis. (A) Hierarchical clustering of longstanding RA, (LRA), early RA (ERA), juvenile idiopathic arthritis (JIA) and osteoarthritis (OA) based on differentially methylated ... Inflammatory arthritis genome-wide DNA methylation patterns differed from OA and clustered together, suggesting that there are common epigenetic elements of these diseases. However, the FLS formed subgroups implying that the variations are disease specific. Of interest, the methylome of ERA demonstrated a distinctive pattern compared with long-standing disease. These data indicate that differential methylation of RA FLS might occur early and evolve over time. Differentially methylated pathways between ERA and LRA involved cell migration, differentiation, and adhesion, which raises the intriguing possibility that the transition to chronic RA involves epigenetic changes that alter synoviocyte hyperplasia and aggressive behavior. One obvious limitation of the study is that the number of samples is small, in part because obtaining cell lines from ERA biopsies is challenging. Despite that, these unique marks can potentially provide information on mechanisms of disease and how RA evolves over time as well as identifying therapeutic targets based on the duration and type of synovitis.

Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters.

Histone modifications contribute to gene regulation in eukaryotes. We analyzed genome-wide histone H3 Lysine (Lys) 4 trimethylation and histone H3 Lys 9 acetylation (two modifications typically associated with active genes) in meristematic cells at the base and expanded cells in the blade of the maize (Zea mays) leaf. These data were compared with transcript levels of associated genes. For individual genes, regulations (fold changes) of histone modifications and transcript levels were much better correlated than absolute intensities. When focusing on regulated histone modification sites, we identified highly regulated secondary H3 Lys 9 acetylation peaks on upstream promoters (regulated secondary upstream peaks [R-SUPs]) on 10% of all genes. R-SUPs were more often found on genes that were up-regulated toward the blade than on down-regulated genes and specifically, photosynthetic genes. Among those genes, we identified six genes encoding enzymes of the C4 cycle and a significant enrichment of genes associated with the C4 trait derived from transcriptomic studies. On the DNA level, R-SUPs are frequently associated with ethylene-responsive elements. Based on these data, we suggest coevolution of epigenetic promoter elements during the establishment of C4 photosynthesis.

Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells.

Successful generation of high producing cell lines requires the generation of cell clones expressing the recombinant protein at high levels and the characterization of the clones' ability to maintain stable expression levels. The use of cis-acting epigenetic regulatory elements that improve this otherwise long and uncertain process has revolutionized recombinant protein production. Here we review and discuss new insights into the molecular mode of action of the matrix attachment regions (MARs) and ubiquitously-acting chromatin opening elements (UCOEs), i.e. cis-acting elements, and how these elements are being used to improve recombinant protein production. These elements can help maintain the chromatin environment of the transgene genomic integration locus in a transcriptionally favorable state, which increases the numbers of positive clones and the transgene expression levels. Moreover, the high producing clones tend to be more stable in long-term cultures even in the absence of selection pressure. Therefore, by increasing the probability of isolating a high producing clone, as well as by increasing transcription efficiency and stability, these elements can significantly reduce the time and cost required for producing large quantities of recombinant proteins.

It's Time for An Epigenomics Roadmap of Heart Failure.

The post-genomic era has completed its first decade. During this time, we have seen an attempt to understand life not just through the study of individual isolated processes, but through the appreciation of the amalgam of complex networks, within which each process can influence others. Greatly benefiting this view has been the study of the epigenome, the set of DNA and histone protein modifications that regulate gene expression and the function of regulatory non-coding RNAs without altering the DNA sequence itself. Indeed, the availability of reference genome assemblies of many species has led to the development of methodologies such as ChIP-Seq and RNA-Seq that have allowed us to define with high resolution the genomic distribution of several epigenetic elements and to better comprehend how they are interconnected for the regulation of gene expression. In the last few years, the use of these methodologies in the cardiovascular field has contributed to our understanding of the importance of epigenetics in heart diseases, giving new input to this area of research. Here, we review recently acquired knowledge on the role of the epigenome in heart failure, and discuss the need of an epigenomics roadmap for cardiovascular disease.

T cells in the control of organ-specific autoimmunity.

Immune tolerance is critical to the avoidance of unwarranted immune responses against self antigens. Multiple, non-redundant checkpoints are in place to prevent such potentially deleterious autoimmune responses while preserving immunity integral to the fight against foreign pathogens. Nevertheless, a large and growing segment of the population is developing autoimmune diseases. Deciphering cellular and molecular pathways of immune tolerance is an important goal, with the expectation that understanding these pathways will lead to new clinical advances in the treatment of these devastating diseases. The vast majority of autoimmune diseases develop as a consequence of complex mechanisms that depend on genetic, epigenetic, molecular, cellular, and environmental elements and result in alterations in many different checkpoints of tolerance and ultimately in the breakdown of immune tolerance. The manifestations of this breakdown are harmful inflammatory responses in peripheral tissues driven by innate immunity and self antigen-specific pathogenic T and B cells. T cells play a central role in the regulation and initiation of these responses. In this Review we summarize our current understanding of the mechanisms involved in these fundamental checkpoints, the pathways that are defective in autoimmune diseases, and the therapeutic strategies being developed with the goal of restoring immune tolerance.

Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types.

DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their relationships among different genomic regions in human embryonic stem cells (H1), H1-derived neuronal progenitor cultured cells (NPC), and foetal fibroblasts (IMR90) using the Random forests classifier. Histone modifications achieved high accuracy in modelling DNA methylation patterns on a genome scale in the three cell types. The inclusion of sequence features helped improve accuracy only in non-promoter regions of IMR90. Furthermore, the top six feature combinations obtained by mean decrease Gini were important indicators of different DNA methylation patterns, suggesting that H3K4me2 and H3K4me3 are important indicators that are independent of genomic regions and cell types. H3K9me3 was IMR90-specific and exhibited a genomic region-specific correlation with DNA methylation. Variations of essential chromatin modification signals may effectively discriminate changes of DNA methylation between H1 and IMR90. Genes with different co-variations of epigenetic marks exhibited genomic region-specific biological relevance. This study provides an integrated strategy to identify systematically essential epigenetic and genetic elements of genomic region-specific and cell type-specific DNA methylation patterns.

The Screening of Epigenetic Regulatory Elements of IGFBP2 and Impact on the Survival of Colonal Cancer

IGFBP2 (insulin-like growth factor binding protein 2), is overexpressed in a wide spectrum of cancers, and plays a role through regulating the concentration of IGF and promotes the development of neoplasm. The role of IGFBP2 in cancer is unclear, while in general it is considered to be oncogenic. In addition, IGFBP2 is closely connected with the level and prognosis of neoplasm. Large studies have been contributed to the relationship between IGFBP2 and cancer, but few are in the epigenetic field. In this study, we filtered differentially methylated sites in the cis regulatory region of IGFBP2, and found 25 and 9 sites in high and low expression groups. In the following survival analysis, we found two sites could distinguish the samples of long survival time from the short ones. This study filtered several epigenetic elements that regulate the expression of IGFBP2. They can be considered for the drug targets for regulating the expression of IGFBP2 and improving the therapeutic effect in cancer.

Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG>200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG<40), and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P<0.0001) and SCAs (P<0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility.

An epigenetic regulatory element of the Nodal gene in the mouse and human genomes

Nodal signaling plays critical roles during embryonic development. The Nodal gene is not expressed in adult tissues but is frequently activated in cancer cells, contributing to progression toward malignancy. Although several regulatory elements of the Nodal gene have been identified, the epigenetic mechanisms by which Nodal expression is regulated over the long term remain unclear. We found a region exhibiting dynamic changes in DNA methylation at approximately −3.0 kb to −0.4 kb upstream from the transcriptional start site (TSS) that we termed the epigenetic regulatory element (ERE). The ERE was unmethylated in mouse embryonic stem cells (mESCs) but became increasingly methylated in differentiated cells and tissues, concomitant with the downregulation of Nodal mRNA expression. In vitro reporter assays identified an Oct3/4 binding motif within the ERE, indicating that the ERE is responsible for the activation of Nodal in mESCs. Furthermore, the ERE was a target of differentiation-associated Polycomb silencing, and the chromatin condensed when mESCs differentiated to embryoid bodies (EBs). Pharmacological inhibition of PRC2 led to the reactivation of Nodal expression in EBs and mouse embryonic fibroblasts (MEFs). The ERE was also targeted by PRC2 in normal human cells. In NODAL-expressing human cancer cells, accumulation of EZH2 and trimethylation of H3K27 at the ERE were diminished. In conclusion, Nodal is epigenetically controlled through the ERE in the mouse embryo and human cells.

EPIGENETIC MODIFICATIONS ASSOCIATED WITH DYSLIPIDEMIA AMONG OBESE CHILDREN AND ADOLESCENTS

BackgroundThe mechanisms why certain obese adolescents are more susceptible to developing dyslipidemia are not completely understood. Epigenetic elements, such as DNA methylation, may play a significant role in lipid traits.MethodsWe studied a prospectively enrolled cohort of overweight and obese children and adolescents recruited from obesity-related clinics at the Boston Children’s Hospital with body composition measures (air displacement plethysmograph) and fasting cholesterol samples. A nested case-control pilot study was conducted and 12 participants were selected based on extremes of obesity-related lipid traits. Whole blood DNA methylation was interrogated using the Illumina HumanMethylation450 microarray with normalization and adjustment for cell-count. Age and sex adjusted multiple linear regression models were run assessing HDL-C, triglycerides, and case-control status, controlled for multiple testing. Primary models assessed DNA methylation within candidate loci and secondary analysis examined genome-wide sites.ResultsAmong the 12 participants, the 6 with the most abnormal obesity-related traits were slightly older (13 vs. 11 years) but had similar BMI (Z-score 2.3 vs. 2.2) and % body fat (39% vs. 38%). Among the candidate regions, triglycerides were associated with differential methylation at cg20809737, intronic to the fatty acid oxidation enzyme carnitine palmitoyltransferase 1A, CPT1A (p=0.006).ConclusionWe demonstrate an association between differential methylation of CPT1A and triglycerides in children, supporting similar findings from adult studies. Epigenetic mechanisms may confer increased susceptibility to developing obesity-related dyslipidemia via alterations in DNA methylation. BackgroundThe mechanisms why certain obese adolescents are more susceptible to developing dyslipidemia are not completely understood. Epigenetic elements, such as DNA methylation, may play a significant role in lipid traits. The mechanisms why certain obese adolescents are more susceptible to developing dyslipidemia are not completely understood. Epigenetic elements, such as DNA methylation, may play a significant role in lipid traits. MethodsWe studied a prospectively enrolled cohort of overweight and obese children and adolescents recruited from obesity-related clinics at the Boston Children’s Hospital with body composition measures (air displacement plethysmograph) and fasting cholesterol samples. A nested case-control pilot study was conducted and 12 participants were selected based on extremes of obesity-related lipid traits. Whole blood DNA methylation was interrogated using the Illumina HumanMethylation450 microarray with normalization and adjustment for cell-count. Age and sex adjusted multiple linear regression models were run assessing HDL-C, triglycerides, and case-control status, controlled for multiple testing. Primary models assessed DNA methylation within candidate loci and secondary analysis examined genome-wide sites. We studied a prospectively enrolled cohort of overweight and obese children and adolescents recruited from obesity-related clinics at the Boston Children’s Hospital with body composition measures (air displacement plethysmograph) and fasting cholesterol samples. A nested case-control pilot study was conducted and 12 participants were selected based on extremes of obesity-related lipid traits. Whole blood DNA methylation was interrogated using the Illumina HumanMethylation450 microarray with normalization and adjustment for cell-count. Age and sex adjusted multiple linear regression models were run assessing HDL-C, triglycerides, and case-control status, controlled for multiple testing. Primary models assessed DNA methylation within candidate loci and secondary analysis examined genome-wide sites. ResultsAmong the 12 participants, the 6 with the most abnormal obesity-related traits were slightly older (13 vs. 11 years) but had similar BMI (Z-score 2.3 vs. 2.2) and % body fat (39% vs. 38%). Among the candidate regions, triglycerides were associated with differential methylation at cg20809737, intronic to the fatty acid oxidation enzyme carnitine palmitoyltransferase 1A, CPT1A (p=0.006). Among the 12 participants, the 6 with the most abnormal obesity-related traits were slightly older (13 vs. 11 years) but had similar BMI (Z-score 2.3 vs. 2.2) and % body fat (39% vs. 38%). Among the candidate regions, triglycerides were associated with differential methylation at cg20809737, intronic to the fatty acid oxidation enzyme carnitine palmitoyltransferase 1A, CPT1A (p=0.006). ConclusionWe demonstrate an association between differential methylation of CPT1A and triglycerides in children, supporting similar findings from adult studies. Epigenetic mechanisms may confer increased susceptibility to developing obesity-related dyslipidemia via alterations in DNA methylation. We demonstrate an association between differential methylation of CPT1A and triglycerides in children, supporting similar findings from adult studies. Epigenetic mechanisms may confer increased susceptibility to developing obesity-related dyslipidemia via alterations in DNA methylation.

Alterations of epigenetics and microRNAs in cancer and cancer stem cell.

ALTERATIONS OF DNA METHYLATION AND HISTONE MODIFICATION IN CANCER Epigenetics is an acquired modification of methylation and/or acetylation of chromatin DNA or histone proteins, which regulates downstream gene expression. Epigenetic alterations can be induced by aging, chronic inflammation and viral infection. Aberrant DNA methylation and/or histone modification at the CpG island promoter may induce inactivation of tumor suppressor genes and play critical roles in the initiation and progression of human cancer. In silico analysis is essential to investigate putative genetic and epigenetic elements of tumor suppressor genes such as Rb1 gene. This may contribute genetic and epigenetic information modulating tissue-specific transcripts and expression levels of genes (Hajjari et al., 2014). Genome-wide analysis of DNA methylation by BeadChip assay is quite useful to identify aberrantly methylated genes in human cancers. HIST1H3J, POU4F2, SHOX2, PHKG2, TLX3, and HOXA7 were identified as aberrantly methylated genes in human papillary thyroid cancers by genome-wide analysis of DNA methylation. In addition, papillary thyroid cancers with preferential methylation were significantly associated with mutations of the BRAF/RAS oncogenes. These hypermethylated genes may constitute potential biomarkers for papillary thyroid cancer (Kikuchi et al., 2013). In 2010, the International Human Epigenome Consortium (IHEC) was established to coordinate the production of reference maps of human epigenomes for key cellular states (http:// www.ihec-epigenomes.net/). In order to gain substantial coverage of the human epigenome, the IHEC is planning to decipher at least 1000 epigenomes. These multilayer-omics analyses including genome, epigenome, transcriptome, proteome and metabolome are important for elucidating the molecular carcinogenesis and for exploring biomarkers and therapeutic targets for human cancers (Kanai and Arai, 2014).

An Evolutionarily Conserved Prion-like Element Converts Wild Fungi from Metabolic Specialists to Generalists

[GAR(+)] is a protein-based element of inheritance that allows yeast (Saccharomyces cerevisiae) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [GAR(+)] allows cells to circumvent this "glucose repression." [GAR(+)] is induced in yeast by a factor secreted by bacteria inhabiting their environment. We report that de novo rates of [GAR(+)] appearance correlate with the yeast's ecological niche. Evolutionarily distant fungi possess similar epigenetic elements that are also induced by bacteria. As expected for a mechanism whose adaptive value originates from the selective pressures of life in biological communities, the ability of bacteria to induce [GAR(+)] and the ability of yeast to respond to bacterial signals have been extinguished repeatedly during the extended monoculture of domestication. Thus, [GAR(+)] is a broadly conserved adaptive strategy that links environmental and social cues to heritable changes in metabolism.

Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism

In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR(+)], a protein-based epigenetic element, allows yeast to circumvent this "glucose repression" and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR(+)]. [GAR(+)] is advantageous to bacteria because yeast cells make less ethanol and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR(+)] presents a unique example of Lamarckian inheritance.