Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response

Vernalization, the cold-induced acceleration of flowering, involves the epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC). We investigated the molecular basis for variation in vernalization in Arabidopsis natural accessions adapted to different climates. A major variable was the degree to which different periods of cold caused stable FLC silencing. In accessions requiring long vernalization, FLC expression was reactivated following nonsaturating vernalization, but this reactivation was progressively attenuated with increasing cold exposure. This response was correlated with the rate of accumulation of FLC histone H3 Lys 27 trimethylation (H3K27me3). Thus, variation in epigenetic silencing of FLC appears to have contributed to Arabidopsis adaptation.     

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer

Increasing evidence indicates the high heterogeneity of cancer cells. Recent studies have revealed distinct subtypes of DNA methylation in colorectal cancer (CRC); however, the mechanism of heterogeneous methylation remains poorly understood. Gene expression is a natural, intermediate quantitative trait that bridges genotypic and phenotypic features. In this work, we studied the role of heterogeneous DNA methylation in tumorigenesis via gene expression analyses. Specifically, we integrated methylation and expression data in normal and tumor tissues, and examined the perturbations in coexpression patterns. We found that the heterogeneity of methylation leads to significant loss of coexpression connectivity in CRC; this finding was validated in an independent cohort. Functional analyses showed that the lost coexpression partners participate in important cancer‐related pathways/networks, such as ErbB and mitogen‐activated protein kinase (MAPK) signaling pathways. Our analyses suggest that the loss of coexpression connectivity induced by methylation heterogeneity might play an important role in CRC. To our knowledge, this is the first study to interpret methylation heterogeneity in cancer from the perspective of coexpression perturbation. Our results provide new perspectives in tumor biology and may facilitate the identification of potential biomedical therapies for cancer treatment. © 2014 Wiley Periodicals, Inc.     

DNA methylation patterns in human tripronucleate zygotes

In mammals, the dynamic reprogramming of DNA methylation begins during gametogenesis and continues through embryogenesis. Recently, immunofluorescence staining with an antibody against 5-methylcytosine (anti-5-MeC) has revealed active demethylation of the male pronucleus in zygotes beginning at 4-6 h after fertilization. In this study, we characterized the DNA methylation patterns in mouse zygotes and in human tripronucleate (3 PN) zygotes discarded after conventional fertilization or following ICSI. Pronuclei were subjected to fluorescence in-situ hybridization to identify the X and/or Y chromosomes and then stained with anti-5-MeC. In diandric 3 PN zygotes from conventional IVF, we consistently observed one strongly and two weakly stained pronuclei. In contrast, the majority of 3 PN ICSI zygotes, mainly digynic zygotes, displayed two strongly and one weakly stained pronuclei. Two zygotes from ICSI failed to show any staining difference among the three pronuclei. Our results indicate that the active demethylation of male pronuclei occurs in both mouse and human zygotes. It is possible that the abnormal methylation patterns resulting from a dysfunctional cytoplasm may occur in a small number of oocytes and may affect embryonic viability.     

Prediction of methylation CpGs and their methylation degrees in human DNA sequences

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. The detections of DNA methylation have been determined mostly by experimental methods, which were time-consuming and expensive, difficult to meet the requirements of modern large-scale sequencing technology. Accordingly, it is necessary to develop automatic, reliable prediction methods for DNA methylation. In this study, the trinucleotide composition, a 64-dimensional feature vector of the occurrence frequency of 64 trinucleotides in the DNA sequence, was utilized to model SVM for the prediction of CpG methylation degrees in humans. The model was evaluated by jackknife validation and the correlation coefficient (R) and root-mean-square error (RMSE) were 0.8223 and 0.2042, respectively. The proposed method was also used to predict methylation sites, the model was evaluated by jackknife validation and the Matthews correlation coefficient (MCC) and accuracy (ACC) were 0.6263 and 0.8133, respectively. The good results indicated that the proposed method was a useful tool for the investigation of DNA methylation prediction research.     

Analysis of DNA methylation in human BK virus

Human BK virus may cause nephropathy due to viral replication in patients who have undergone renal transplantation. However, the mechanism regulating replication of BKV is still not clear. Previous studies have suggested that epigenetic modifications may play a crucial role in virus replication. In this study, the DNA methylation profiles of five CpG sites located within the promoter/enhancer regions and nine CpG sites located within the early and late coding regions of the replicating BKV genome were investigated. BKV genomic DNA from mature virions and from the early and late phases of replicating BKV were examined for DNA methylation by bisulfite sequencing that covered 14 CpG sites. Our results showed that none of the examined BKV DNA from the various different stages of replication was methylated. This is the first report to analyze the methylation of BKV genomic DNA during viral replication. The results seem to indicate that methylation is not involved in regulation of BKV replication.     

Somatic mosaicism contributes to phenotypic variation in Timothy syndrome

Timothy syndrome type 1 (TS-1) is a rare disorder that affects multiple organ systems and has a high incidence of sudden death due to profound QT prolongation and resultant ventricular arrhythmias. All previously described cases of TS-1 are the result of a missense mutation in exon 8A (p.G406R), an alternatively spliced variant of the L-type calcium channel gene (Ca(v)1.2, CACNA1C). Most patients reported in the literature represent highly affected individuals who present early in life with severe cardiac and neurological manifestations. Here, we describe somatic mosaicism in TS-1 patients with less severe manifestations than the typical TS-1 patient. These findings suggest that the TS prognosis may not be as dismal as previously reported. Moreover, our findings have implications for genetic counseling in that previously described de novo TS mutations may represent cases of parental mosaicism and warrant careful genotyping of parental tissue other than peripheral blood lymphocytes.     

Extensive variation and low heritability of DNA methylation identified in a twin study

Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we performed bisulfite sequencing of 1760 CpG sites in 186 regions in the human major histocompatibility complex (MHC) in CD4+ lymphocytes from 49 monozygotic (MZ) and 40 dizygotic (DZ) twin pairs. Individuals show extensive variation in DNA methylation both between and within regions. In addition, many regions also have a complex pattern of variation. Globally, there appears to be a bimodal distribution of DNA methylation in the regions, but a significant fraction of the CpG sites are also heterogeneously methylated. Classification of regions into CpG islands (intragenic and intergenic), 5' end of genes not associated with a defined CpG island, conserved noncoding regions, and random CpG sites shows region-type differences in variation and heritability. Analyses revealed slightly lower intra-pair differences among MZ than among DZ pairs, suggesting some genetic influences on DNA methylation variation, with most of the variance attributed to nongenetic factors. Overall, heritability estimates of DNA methylation were low. Our heritability estimates are, however, somewhat deflated due to the presence of batch effects that artificially inflate the estimates of shared environment.     

Stability of DNA methylation of the human hypoxanthine phosphoribosyltransferase gene

Methylation sensitive restriction enzymes were used to evaluate the methylation level of several restriction sites near human hypoxanthine phosphoribosyltransferase (HPRT) genes on active and inactive X chromosomes. DNA samples from leukocytes, from clonally derived fibroblasts, and from independent mouse-human hybrid lines isolated from the fusion of A-9 cells and these clonally derived human cells were studied. Comparison of the methylation patterns shows that restriction sites may show variable or constant methylation among tissues and clones, and heritability of methylation is also different among restriction sites. Methylation is more stable at sites whose methylation status correlate well with HPRT activity. Our results suggest that the methylation of certain cytosine residues may critically affect gene activity and that the methylation pattern of these sites is stably inherited.     

Frontal cortex contributes to human memory formation

The contribution of medial temporal lobe structures to memory is well established. However recent brain-imaging studies have indicated that frontal cortex may also be involved in human memory formation. Specific frontal areas are recruited during a variety of procedures that promote memory formation, and the laterality of these areas is influenced by the type of information contained in the memory. Imaging methods that capture momentary changes in brain activity have further shown that the likelihood of memory formation correlates with the level of activity in these areas. These results, taken in the context of other studies, suggest that memory formation depends on joint participation of frontal and medial temporal lobe structures.     

Alterations of DNA methylation and clinicopathological diversity of human cancers

Alterations of DNA methylation can account for the histological heterogeneity, reflected in the stepwise progression and complex biological characteristics of human cancers, that genetic alterations alone cannot explain. Analysis of DNA methylation status in tissue samples can be an aid to understanding the molecular mechanisms of multistage carcinogenesis. Human cancer cells show a drastic change in DNA methylation status, that is, overall DNA hypomethylation and regional DNA hypermethylation, which results in chromosomal instability and silencing of tumor-suppressor genes. Overexpression of DNA methyltransferase (DNMT) 1 is not a secondary result of increased cell proliferative activity but may underline the CpG island methylator phenotype of cancers. Splicing alteration of DNMT3B may result in chromosomal instability through DNA hypomethylation of pericentromeric satellite regions. Alterations of DNA methylation are observed even in the precancerous stage frequently associated with chronic inflammation and/or persistent viral infection or with cigarette smoking. Precancerous conditions showing alterations of DNA methylation may generate more malignant cancers. Aberrant DNA methylation is significantly associated with aggressiveness of cancers and poorer outcome of cancer patients. Genome-wide analysis of DNA methylation status based on array-based technology may identify DNA methylation profiles that can be used as appropriate indicators for carcinogenetic risk estimation and prognostication.     

DNA methylation profiles of human active and inactive X chromosomes

X-chromosome inactivation (XCI) is a dosage compensation mechanism that silences the majority of genes on one X chromosome in each female cell. To characterize epigenetic changes that accompany this process, we measured DNA methylation levels in 45,X patients carrying a single active X chromosome (X(a)), and in normal females, who carry one X(a) and one inactive X (X(i)). Methylated DNA was immunoprecipitated and hybridized to high-density oligonucleotide arrays covering the X chromosome, generating epigenetic profiles of active and inactive X chromosomes. We observed that XCI is accompanied by changes in DNA methylation specifically at CpG islands (CGIs). While the majority of CGIs show increased methylation levels on the X(i), XCI actually results in significant reductions in methylation at 7% of CGIs. Both intra- and inter-genic CGIs undergo epigenetic modification, with the biggest increase in methylation occurring at the promoters of genes silenced by XCI. In contrast, genes escaping XCI generally have low levels of promoter methylation, while genes that show inter-individual variation in silencing show intermediate increases in methylation. Thus, promoter methylation and susceptibility to XCI are correlated. We also observed a global correlation between CGI methylation and the evolutionary age of X-chromosome strata, and that genes escaping XCI show increased methylation within gene bodies. We used our epigenetic map to predict 26 novel genes escaping XCI, and searched for parent-of-origin-specific methylation differences, but found no evidence to support imprinting on the human X chromosome. Our study provides a detailed analysis of the epigenetic profile of active and inactive X chromosomes.     

Hyperoxia-induced DNA damage causes decreased DNA methylation in human lung epithelial-like A549 cells

The effect of hyperoxia on levels of DNA damage and global DNA methylation was examined in lung epithelial-like A549 cells. DNA damage was assessed by the single-cell gel electrophoresis (comet assay) and DNA methylation status by the cytosine extension assays. Cells exposed to ionizing radiation (0, 1, 2, 4, or 8 Gy) showed increasing rates of percentage of DNA in the tail and tail length with increasing radiation dose. When cells were exposed to room air (normoxia) for 1 day and 95% O2 (hyperoxia) for 1, 2, 3, 4, and 5 days, data indicated that hyperoxia caused time-dependent increases in levels of (a) single strand breaks, (b) double strand breaks, and (c) 8-oxoguanine. Decreased DNA methylation also was observed at day 5 of hyperoxic exposure, suggesting that hyperoxia-induced DNA damage can influence patterns of DNA methylation in a lung-derived cell line.     

Season of birth contributes to variation in university examination outcomes.

Epidemiological studies show that birth season influences a wide range of biological parameters such as growth, reproduction, mental illnesses, dyslexia, personality, and success in school. The present study is aimed at examining birth season's relationship to examination marks achieved at a university in a very large contemporary sample of male and female undergraduate students. We find that female university students born in spring and summer achieve better marks than those born in autumn and winter. Male students born in spring receive worse marks than those born in other seasons of the year. Furthermore, we find a birth-week periodicity in examination results of female students, with highest examination results for those born in May. We suppose that biological mechanisms might explain part of the observed effects.