Bridging Epigenetics and Metabolism
Chromatin-modifying enzymes regulate gene expression in response to changes in the cellular microenvironment, which are manifested by fluctuations of specific metabolites, including S-adenosylmethionine, acetyl-CoA, alphaketoglutarate and NAD+. In an enlightening Point-of-View in this issue of Epigenetics, Phang et al. review how these metabolites are produced by metabolic pathways other than those involving glucose, and discuss the coupling of these pathways to the intermediates affecting epigenetic regulation. The authors explain how pathways involving non-essential amino acids may also play important roles, especially in cancer. Examples include metabolic pathways for glutamine, serine and glycine.
The Epigenetics of Estrogen Signaling in Breast Cancer
In hormone-dependent breast cancer, estrogen signaling is mediated by estrogen receptors ERα and ERβ. The role of epigenetic pathways in breast cancer tumorigenesis has been extensively studied. In this issue of Epigenetics, Hervouet et al. reviews the epigenetic-mediated estrogen signaling, controlling both ER level and ER-targeted gene expression in breast cancer.
Epigenetic Signature in Rett Syndrome Patients
Rett syndrome (RTT), a neurodevelopmental condition associated with motor disorders and mental retardation, is in most cases caused by mutations in the DNA binding protein MeCP2. In mice, deletion of the MeCP2 gene results in genome-wide increased histone acetylation. Transcriptional regulation of neurotrophic factor BDNF and transcription factor DLX5, which are essential for proper neurogenesis, is further altered in MeCP2-deleted animals. In this issue of Epigenetics, Lilja et al. investigated the chromatin environment of MeCP2 target genes BDNF and DLX5 in lymphocytes from RTT patients and analyzed the density of histones H3, H2B and H1, as well as the levels of methylation and acetylation on selected lysines of histone H3. Their results reveal an unexpected alteration of the chromatin state of established MeCP2 target genes in lymphocytes of human subjects with RTT.
Distinguishing RCC Histological Subtypes by DNA Methylation Profiling
Renal cell carcinoma (RCC) can be divided into several subtypes, of which chromophobe RCC comprises 5% of all RCC cases and renal oncocytoma (a benign tumor) accounts for another 5%. Slater et al. have now studied the DNA methylation profiles of chromophobe RCC and renal oncocytomas utilizing the Infinium HumanMethylation450 BeadChips in order to identify differentially methylated genes between the two subtypes. The study provides valuable insight into the pathology of RCC subtypes and the classification of renal tumors.
Epigenetic Repression of LEDGF during UVB Exposure
Expression level of lens epithelial derived growth factor (LEDGF) is vital for LEDGF-mediated cell survival and cytoprotection against proapoptotic stimuli. LEDGF is transcriptionally regulated by Sp1-responsive elements within a CpG island in its promoter. Bhargavan et al. now report on the existence of epigenetic signaling involved in the repression of LEDGF transcription in lens epithelial cells (LECs) facing UVB exposure. Exposure of LECs to UVB stress altered LEDGF protein and mRNA expression as well as promoter activity, while failing to methylate the CpG island. These events were correlated with increased reactive oxygen species (ROS) and increased cell death.
Epigenetic Changes in In Vitro Bovine Blastocysts
In this issue of Epigenetics, Herrmann et al. investigated gene-specific histone modifications in in vitro produced bovine blastocysts. The authors focused on the two cell compartments of the blastocyst, the inner cell mass (ICM) and the trophectoderm (TE), and investigated several modifications of histone H3 in relation to mRNA expression profiles in selected genes thought to be critical for bovine preimplantation development. They show that gene expression patterns in the ICM and TE of the bovine blastocyst are consistent with histone modification patterns on the promoter of the corresponding genes, displaying a complex epigenetic pattern of promoter occupancy by transcriptionally permissive and repressive H3 modifications. These results are crucial to gain a better understanding of the epigenetic changes frequently observed after the use of assisted reproductive technologies.
In Silico Neuronal Profiling from DNA Methylation Data
Brain cellular heterogeneity may bias cell type-specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. In order to identify DNA methylation associations with specific cell types, Guintivano et al. have now performed FACS of neuronal nuclei followed by DNA methylation profiling in post mortem frontal cortex of major depression and matched controls. The authors identified genomic features and ontologies enriched for cell type-specific epigenetic variation. They generated a publically available R package, called “CETS,” capable of quantifying neuronal proportions and generating in silico neuronal profiles from DNA methylation data. The authors argue that CETS-based control of cellular heterogeneity will enable more robust hypothesis testing in the brain.
Epigenetic Alterations in Folate Transport Genes in Neural Tube Defect Infants
In order to identify tissue-specific differentially methylated regions (T-DMRs) in the folate transport genes in placental tissue from infants with or without neural tube defects (NTD), Farkas et al. have developed methylation assays for the CpG islands and shore regions of the folate receptor α (FOLR1), proton-coupled folate transporter (PCFT) and reduced folate carrier 1 (RFC1) genes. A higher T-DMR methylated fraction was associated with a lower mRNA level of the FOLR1 and RFC1 genes. Methylation fractions differed according to RFC1 genotype in the neural tube defect cases and in leukocytes from subjects with high total plasma homocysteine. The authors found no differences in the methylated fraction of folate transporter genes between NTD cases and controls. These results suggest that T-DMRs participate in the regulation of expression of the FOLR1 and RFC1 genes, with RFC1 polymorphism exerting a gene-nutrition interaction on DNA methylation in the RFC1 gene, an interaction that appears to be most prominent in NTD-affected births and in subjects with high total plasma homocysteine concentrations.
Looking at DNA Methylation in the Muscle Lineage
Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. Tsumagari et al. report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. non-muscle samples, using reduced representation bisulfite sequencing. Their findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.
Evaluating Analysis Pipelines for the Illumina 450K Array
The design of an appropriate pipeline for the analysis of Illumina HumanMethylation450 BeadChip DNA methylation data are challenging due to the complexity of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. To date, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. In a much needed study, Marabita et al. have performed a comparative analysis that targets the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. The authors present a useful comparative analysis and suggest an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays.