In this issue of Epigenetics

FTO, RNA Epigenetics and Epilepsy

Numerous microRNAs (miRNAs) are highly expressed in the CNS and are associated with several neurological disorders, including epilepsy. Certain specific miRNAs that are upregulated by neuronal activity and are coupled to epileptogenesis also contain a consensus N⁶-methyladenosine (m⁶A) site that, if methylated, could possibly regulate miRNA processing or function. One endogenous enzyme responsible for demethylating RNA m⁶A—FTO—is highly expressed in the CNS and is likely involved in mRNA metabolism, splicing and other nuclear RNA processing events. In this issue of Epigenetics, Rowles et al. review recent papers that propose a functional association between FTO, RNA epigenetics and epilepsy.

Histone Phosphorylation

Multiple studies have shown that histone phosphorylation plays crucial roles in chromatin remodeling. For example, histone phosphorylation takes place during cellular response to DNA damage, when phosphorylated histone H2A(X) demarcates large chromatin domains around the site of DNA breakage. A review by Rossetto et al. summarizes the current knowledge of histone phosphorylation and describes the many kinases and phosphatases that regulate it. The authors also describe the intricate crosstalk that occurs between phosphorylation and other histone modifications that provides sophisticated control over chromatin remodeling processes.

Posttranscriptional Regulation of GLCE in Breast Cancer Cells

Prudnikova et al. investigated the regulation of tumor-suppressor gene D-glucuronyl C5-epimerase (GLCE) by miRNA-218. The authors showed that, in primary breast tumors, miRNA-218 expression is significantly downregulated. Notably, exogenous miRNA-218/anti-miRNA-218 did not affect GLCE mRNA but regulated GLCE protein level in MCF7 breast carcinoma cells in vitro. These findings support a direct involvement of miRNA-218 in the posttranscriptional regulation of GLCE in human breast tissue.

Imprinting Defects in Sperm and Assisted Reproduction

Whether imprinting defects present in the sperm of infertile patients could interfere with fertility treatment outcomes is still unknown. In this issue of Epigenetics, Camprubí et al. analyzed sperm DNA methylation profiles of H19-ICR, KvDMR, SNRPN-ICR, IG-DMR and MEG3-DMR in infertile and fertile men. Individuals included in normal and abnormal methylation clusters were compared according to seminal parameters as well as to the outcome of assisted reproduction.

IGF2 DNA Methylation and Fetal Growth and Development

The insulin-like growth factor 2 (IGF2) gene encodes a fetal and placental growth factor affecting birth weight. Now, St-Pierre et al. have studied IGF2/H19 DNA methylation and IGF2 circulating levels in placenta biopsies. The authors showed that IGF2/H19 epigenotype and genotype independently account for 31% of the newborn’s weight variance, finding no association with maternal diabetic status, glucose concentrations or prenatal maternal body mass index. Therefore, DNA methylation at the IGF2/H19 genes locus may act as a modulator of newborn’s fetal growth and development within normal range. IGF2/H19 DNA methylation could represent a cornerstone in linking birth weight and fetal metabolic programming of late onset obesity.

Micronutrients and Global DNA Methylation

Aberrations in global LINE-1 DNA methylation have been related to risk of cancer and cardiovascular disease. Micronutrients including methyl-donors and retinoids are involved in DNA methylation pathways. Perng et al. investigated associations of LINE-1 methylation and micronutrient status, including erythrocyte folate, plasma vitamin B12, vitamin A ferritin (an indicator of iron status) and serum zinc concentrations, in a cross-sectional study of school-age children from Bogotá, Colombia. Among their results, the authors found that LINE-1 methylation was inversely related to plasma vitamin A and that children with retinol levels higher than or equal to 1.05 µmol/L showed lower LINE-1 methylation than children with retinol levels lower than 0.70 µmol/L. LINE-1 methylation was also inversely associated with C-reactive protein, a marker of chronic inflammation, and female sex. They also identified positive associations of maternal body mass index and socioeconomic status with LINE-1 methylation.

Paternal Uniparental Disomy 14: Analyzing the Placenta

Paternal uniparental disomy 14 [upd(14)pat] affects chromosome 14q32.2 imprinted region and depends on underlying epigenetic factors that are involved in the development of the corresponding associated phenotype. It is thought that markedly increased RTL1 expression is the major underlying factor for the development of the upd(14)pat-like phenotype. Now, Kagami et al. performed molecular studies on fresh placental samples from two patients with the disorder. The authors found that RTL1 expression level was about five times higher in the placental samples of the two patients than in control placental samples, whereas DIO3 expression level was similar between the placental samples of the two patients and the control placental samples. These results suggest that RTL1as-encoded miRNA functions as a repressor of RTL1 expression, and argue against DIO3 being a paternally expressed gene.

Methylation of the MAOA Gene as Predictor of MAOA Enzyme Activity

The levels of monoamine oxidase A (MAOA)—an enzyme metabolizing neurotransmitters—vary widely between healthy men. This variability is not explained by the MAOA genotype, suggesting that environmental factors, through epigenetic modifications, may mediate it. Shumay et al. analyzed MAOA methylation in white blood cells and measured brain MAOA levels in healthy non-smoking male volunteers. The authors found significant interindividual differences in methylation status and patterns at the MAOA promoter. The genotype did not influence the methylation status of the gene nor did it affect the activity of MAOA in the brain. In contrast, regional and CpG site-specific methylation of the MAOA promoter was robustly associated with brain MAOA levels, suggesting that the methylation status of the MAOA promoter (detected in white blood cells) can reliably predict the brain endophenotype.

Drug Combinatorial Regimens in Non-Small Cell Lung Cancer Cells

The use of epigenomic modifiers as monotherapy for lung cancer is not very efficient. Therefore, the development of safe and effective drug combinatorial regimens has the promise to reverse epigenetic modifications while exhibiting profound anticancer activity. Mateen et al. have evaluated the efficacy of a novel combinatorial regimen of histone deacetylase inhibitors (HDACi)—TSA and SAHA—with silibinin (a compound with established pre-clinical anti-lung cancer efficacy) against non-small cell lung cancer. Combinations of HDCAi with silibinin synergistically augmented the cytotoxic effects of these single agents, which were associated with a dramatic increase in p21 (Cdkn1a) transcription. In addition, the authors showed increased acetylated histone H3 and H4 levels on the p21 promoter. Enhanced p21 levels promoted proteasomal degradation of cyclin B1, causing cells to arrest in stage in G₂/M and follow an apoptotic cell death. Similar epigenetic modulations were observed in vivo, together with a marked reduction in xenograft growth.

Measuring the Methylome: Comparing Methodologies

The Infinium Human Methylation450 BeadChip Array^TM (Infinium 450K) offers a high-throughput, low-cost alternative to more comprehensive sequencing-based methodologies used to analyze the methylome. Pan et al. now compared data generated by interrogation of the same seven clinical samples by Infinium 450K and reduced representation bisulfite sequencing (RRBS) and showed good agreement between the two methodologies. A read depth of four or more reads in the RRBS data was sufficient to achieve good agreement with Infinium 450K. However, the authors observed that intermediate methylation values (20–80%) were more variable between technologies than values at the extremes of the bimodal methylation distribution.

Human-Specific CpG “Beacons” = Human-Specific Traits and Disease

Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. In this issue of Epigenetics, Bell et al. suggest that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. The authors report non-polymorphic species-specific CpG dinucleotides (termed “CpG beacons”) as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. By mapping into both the genomic and epigenomic space, the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred.

Maternal Nutrition and Developmental Programming

Epigenetic marks, such as DNA methylation or histone tail modifications, could provide a persistent memory of earlier nutritional states and influence the risk of late-onset chronic diseases. This phenomenon is known as developmental programming. Now, Ivanova et al. have used an established model of developmental programming—isocaloric protein restriction to female mice during gestation or lactation—to examine whether there are effects on expression and DNA methylation of imprinted genes in the offspring. The authors found that although expression of some imprinted genes in the liver of offspring is robustly and sustainably changed, methylation of the differentially methylated regions (DMRs) that control their monoallelic expression remains mostly unaltered. Therefore, regulation of imprinting through a general effect on DMR methylation is unlikely to be a common factor in developmental programming.

Meeting Report

In this issue of Epigenetics, Sascha Duttke summarizes the highlights from the 10th EMBL Conference on Transcription and Chromatin held at the EMBL Advanced Training Centre in Heidelberg, Germany, last August. Superbly organized by Henk Stunnenberg, Eileen Furlong, Ali Shilatifard and Marc Timmers, the main topics of the conference included DNA, RNA and histone modifications, pluripotency and cellular reprogramming and transcriptional regulation, as well as chromatin dynamics and the effect of chromatin on gene regulation.