CpG Sites In Gene Promoter Research Articles

Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures.

Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.

A preliminary study of endocannabinoid system regulation in psychosis: Distinct alterations of CNR1 promoter DNA methylation in patients with schizophrenia

Compelling evidence supports the involvement of the endocannabinoid system (ECS) in psychosis vulnerability. We here evaluated the transcriptional regulation of ECS components in human peripheral blood mononuclear cells (PBMCs) obtained from subjects suffering from bipolar disorder, major depressive disorder and schizophrenia, focusing in particular on the effects of DNA methylation. We observed selective alterations of DNA methylation at the promoter of CNR1, the gene coding for the type-1 cannabinoid receptor, in schizophrenic patients (N=25) with no changes in any other disorder. We confirmed the regulation of CNR1 in a well-validated animal model of schizophrenia, induced by prenatal methylazoxymethanol (MAM) acetate exposure (N=7 per group) where we found, in the prefrontal cortex, a significant increase in CNR1 expression and a consistent reduction in DNA methylation at specific CpG sites of gene promoter. Overall, our findings suggest a selective dysregulation of ECS in psychosis, and highlight the evaluation of CNR1 DNA methylation levels in PBMCs as a potential biomarker for schizophrenia.

Comparative analysis on content and distribution of CpG sites in milk production traits and mastitis-related genes in dairy cattle

DNA methylation is a major part of epigenetics. DNA methylation on the CpG sites in gene promoter and the first exon often represses gene expression, but demethylation activates gene expression. Previous research has shown that a negative correlation was found between mastitis index (somatic cell count, SCC) and milk production traits in Holsteins. The content and distribution of CpG dinucleotide sites in different regions of the candidate genes related to milk production traits and mastitis were studied in the present study. The regions contained promoter (2000 bp upstream of transcriptional start site), exon 1, and 2000 bp downstream of transcriptional end site. The CpG number of promoter and exon 1 in the mastitis-related genes was significantly less than that of the milk production-associated genes. However, the CpG number of 2000 bp downstream of the genes for the two traits was not significantly different. Two new index quantified CpG characterizations were proposed. One is the CpG distance, which can measure the distribution of CpG. The other is the conditional probability p(G|C), which is used to quantify the probability of CpG in a nucleotide sequence along with C. The two indexes of promoter and exon 1 in the two types of genes and their statistic analysis were carried out. This study sets the basis for DNA methylation regulation of milk production traits- and mastitis-related genes.

Abstract 2006: Genome-wide study of DNA methylation alterations in response to pesticide exposure in in vitro

Abstract Pesticides are widely used in the US and worldwide, and are pervasive in our environment. All pesticides sold in the US have passed the Environmental Protection Agency (EPA) screening procedures for carcinogenicity based on their genotoxicity and mutagenicity. However exposure to pesticides among pesticide applicators and manufacturing workers has repeatedly been shown to increase cancer risk, suggesting that pesticides may cause cancer via alternative mechanisms, such as epigenetic changes. The purpose of the present study is to examine whether exposure to organophosphate pesticides (OPs), a group of the most commonly used pesticides in the US, induces DNA methylation alterations in in-vitro. The K562 progenitor blood cell line was exposed to several OPs (i.e., chlorpyrifos, diazinon, fonofos, malathion, parathion, phorate, and terbufos) at different dosages and time periods. DNA was prepared from samples exposed to ethanol (control) and a range of pesticide concentrations similar to exposure levels experienced by the US licensed pesticide applicators. We conducted genomewide DNA methylation analysis using the Illumina Infinium HumanMethylation27 BeadChip that covers 27,578 individual promoter CpG sites in the entire genome. The relative level of methylation was calculated as the ratio of signal from a methylated probe relative to an unmethylated probe. Bayesian-adjusted t-tests were used to identify differentially methylated sites. A cut-off of False Discovery Rate (FDR)-adjusted p-value (q-value) < 0.05 and fold change > 2 was used to identify candidate CpG sites. We observed significant differences in genomewide DNA methylation patterns in relation to exposure to three pesticides (i.e., fonofos, parathion, and terbufos) that have been associated with cancers in human studies. Out of all genes with differentially methylated CpG site(s) for each of the three pesticides, we identified 712 genes (625 were hypermethylated and 87 were hypomethylated) overlapped for these three pesticides. Gene ontology analysis showed that these hyper- or hypo-methylated genes are implicated in carcinogenesis and related biological process, such as tumor protein p53 inducible protein 11 (TP53I11) (4.0-fold for fonofos, 4.7-fold for parathion, 3.1-fold for terbufos, respectively), growth arrest and DNA-damage-inducible gamma (GADD45G) (25.2-fold for fonofos, 23.1-fold for parathion, 31.2-fold for terbufos, respectively), and interleukin-1 receptor (IL1R1) (−2.2-fold for fonofos, -2.1-fold for parathion, -2.2 fold for terbufos, respectively). Our results provided direct experimental evidence that pesticides can modify DNA methylation in gene promoter CpG sites, which may play pathological role in cancer development. Further studies in other cell types and human samples are required before any firm conclusion could be reached on the significance of pesticide-induced methylation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2006. doi:10.1158/1538-7445.AM2011-2006