Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.

Wetlands are of a considerable environmental value as they provide food and habitat for plants and animals. Several important chemical transformations take place in wetland media, including the conversion of inorganic mercury (Hg) to monomethylmercury (MeHg), a toxic compound with a strong tendency for bioconcentration. Considering the fact that wetlands are hotspots for Hg methylation, we investigated, for the first time, Hg methylation and demethylation rates in an old growth cypress wetland at Sky Lake in the Mississippi Delta. The Sky Lake ecosystem undergoes large-scale water level fluctuations causing alternating periods of oxic and anoxic conditions in the sediment. These oscillating redox conditions, in turn, can influence the transformation, speciation, and bioavailability of Hg. In the present study, sediment cores from the wetland and Sky Lake itself were spiked with enriched stable isotope tracers of inorganic Hg and MeHg and allowed to incubate (in-situ) before freezing, sectioning, and analysis. Methylation rates (day−1) ranged from 0.012 ± 0.003 to 0.054 ± 0.019, with the lowest rate in the winter and the highest in the summer. Demethylation rates were about two orders of magnitude higher, and also greater in the warmer seasons (e.g., 1.84 ± 0.78 and 4.63 ± 0.51 for wetland sediment in the winter and summer, respectively). Methylation rates were generally higher in the open water sediment compared to wetland sediment, with the latter shaded and cooler. Both methylation (r = 0.76, p = 0.034) and demethylation (0.97, p = 0.016) rates (day−1) were positively correlated with temperature, but not with most other water quality parameters. MeHg concentration in the water was correlated with pH (r = 0.80, p < 0.05), but methylation rates were only marginally correlated (r = 0.71). Environmental factors driving microbial production of MeHg in the system include warm temperatures, high levels of labile natural organic matter, and to a lesser extent the relatively low pH and the residence time of the water. This study also provides baseline data that can be used to quantify the impacts of modifying the natural flow of water to the system on Hg methylation and demethylation rates.

Specific rates of mercury methylation and demethylation were determined for water and surficial sediment samples taken from several lakes located in the Experimental Lakes Area, northwestern Ontario. Specific rates of mercury methylation were found to increase with decreasing pH in epilimnetic water samples in which pH was adjusted prior to incubation and in epilimnetic water samples taken from lakes of different pH. Reduction of pH also increased methyl mercury production at the sediment surface. Both increases and decreases in pH reduced specific rates of mercury demethylation. However, these changes were smaller than for methylation. Proportionally, specific rates of methylation increased faster than increasing concentrations of Hg2+, while specific rates of mercury demethylation increased linearly with increasing concentrations of methyl mercury. Overall, this study predicts that the net rate of methyl mercury production in the water column and at the sediment–water surface will increase as a result of lake acidification, and this may at least partially explain why the mercury concentration of fish appears to increase during lake acidification.

ABSTRACTPeriphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10−3 day−1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day−1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.

Aberrant Methylation of Multiple Tumor Suppressor genes and Expression Level of DNA Methyl Transferases(DNMT1, 3A, 3B) in Acute Myeloid Leukemia.

Mercury methylation and demethylation rates were measured in periphyton biofilms growing on submerged plants from a shallow fluvial lake located along the St. Lawrence River (Quebec, Canada). Incubations were performed in situ within macrophytes beds using low-level spikes of (199)HgO and Me(200)Hg stable isotopes as tracers. To determine which microbial guilds are playing a role in these processes, methylation/demethylation experiments were performed in the absence and presence of different metabolic inhibitors: chloramphenicol (general bacteriostatic inhibitor), molybdate (sodium molybdate, a sulfate reduction inhibitor), BESA (2-bromoethane sulfonic acid, a methanogenesis inhibitor), and DCMU (3-(3,4-dichlorophenyl)-1,1 dimethyl urea, a photosynthesis inhibitor). Active microbes of the periphytic consortium were also characterized using 16S rRNA gene sequencing. Methylation rates in the absence of inhibitors varied from 0.0015 to 0.0180 d(-1) while demethylation rates ranged from 0.083 to 0.217 d(-1), which corresponds to a net methylmercury balance of -0.51 to 1.28 ng gDW periphyton(-1) d(-1). Methylation rates were significantly decreased by half by DCMU and chloramphenicol, totally inhibited by BESA, and were highly stimulated by molybdate. This suggests that methanogens rather than sulfate reducing bacteria were likely the primary methylators in the periphyton of a temperate fluvial lake, a conclusion supported by the detection of 16S rRNA gene sequences that were closely related to those of methanogens. This first clear demonstration of methanogens' role in mercury methylation in environmental periphyton samples expands the known diversity of microbial guilds that contribute to the formation of the neurotoxic substance methylmercury.

Gene silencing associated with aberrant methylation of promoter region CpG islands is an acquired epigenetic alteration. It serves as an alternative to genetic defects in the inactivation of tumor suppressor and other genes in human cancers. Several genes have been shown to be epigenetically inactivated in a wide range of tumors and most neoplasms show hypermethylation of one or more genes. Concurrent methylation status of the CpG islands of 24 genes were determined in 40 PTC cases and in a panel of PTC cell lines, using methylation specific PCR. Seven genes demonstrated a relatively high frequency of aberrant methylation: RASF1 (95%), HIC1 (55%), GSTP1 (26%), P14 (25%), TMS1 (24%), DCR1 (17%) and SERF (15%). Five genes (BRACA1, P15INK4B, MGMT, BLU and APC) showed a low frequency (2-6%) of methylation, and no methylation was detected for the remaining twelve genes (P16INK4A, APAF1, FANCF, FAS, MINT25, P73, MLH1, DAPK, RARB, CASP8, E-Cadherin and SOC1. Statistical analysis demonstrated that frequency of methylated and unmethylated HIC1 was significant (p &amp;lt;0.05). Further clinical analysis demonstrated significant association of only HIC1 methylation with: age of patients, stage of disease and expression of HIC1 IHC data (p = &amp;lt;0.0001, &amp;lt;0.0173 and &amp;lt; 0.0448; respectively). HIC1 has been shown to be hypermethylated in different cancers and confers bad prognosis. HIC1 is a tumor suppressor gene which encodes a transcriptional repressor with five Kruppel-like Cys2-His2 zinc fingers in the C terminus and a protein-protein interaction domain called the BTB/POZ domain at the N terminus. Analysis of BCPAP-1 and TPC1 (papillary thyroid cell lines) revealed that they are completely methylated for HIC1 gene. Treatment of methylated thyroid cell line with the methyltransferase inhibitor, 5-aza-2’deoxy-cytidine, resulted in partial demethylation and re-expression of HIC1 gene, suggesting the role of methylation in silencing of the gene. We further evaluated the role of HIC1 gene after demethylation for apoptosis. After demethylation of HIC1 gene with 5-aza-2’deoxy-cytidine we treated our PTC cell lines with increasing doses of TRAIL and evaluated its response by Annexin/PI dual staining. We found that after demethylation of HIC1 there was increase in percentage apoptosis following increasing doses of TRAIL suggesting that HIC1 gene plays a major role in inducing apoptosis in PTC. In conclusion, HIC1 methylation may be a promising molecular marker to predict patient outcome in PTC, and may be used as therapeutic demethylating target. 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 2017. doi:10.1158/1538-7445.AM2011-2017

Prognostic value of opioid binding protein/cell adhesion molecule-like promoter methylation in bladder carcinoma

The methylation status of 7 genes was examined in four cell lines, 36 samples of benign prostatic hyperplasia (BPH), 20 samples of prostatic intraepithelial neoplasia (PIN) and 109 samples of prostate cancer (PCa), using methylation-specific PCR (MSP): the pi-class glutathione S-transferase (GSTP1), retinoic acid receptor beta 2(RARbeta2), androgen receptor (AR), death-associated protein kinase (DAPK), tissue inhibitor of metalloproteinase-3 (TIMP-3), O(6)-methylguanine DNA methyltransferase (MGMT), and hypermethylated in cancer-1 (HIC-1). The frequencies of methylation in PCa were 88% for GSTP1, 78% for RARbeta2, 36% for DAPK, 15% for AR, 6% for TIMP-3, and 2% for MGMT, whereas the values were 11% for AR and DAPK, 6% for TIMP-3, 3% for GSTP1, and 0 for RARbeta2 and MGMT in BPH. Aberrant methylation of the GSTP1 and RARbeta2 genes was detected in 30% and 20% of PIN, respectively. Most samples of BPH and PCa were positive for HIC-1 methylation. Regarding accumulation of methylated cancer-related genes, there were significant correlations between PCa and BPH as well as PIN and BPH. In the present study, a high frequency of aberrant promoter methylation of the GSTP1 and RARbeta2 genes was noted in PCa. Our findings suggest that methylation of cancer-related genes may be involved in carcinogenesis of the prostate.

Mercury methylation and demethylation by periphyton biofilms and their host in a fluvial wetland of the St. Lawrence River (QC, Canada)

The response of DNA methyltransferase and demethylase genes to abiotic stresses in tomato seedling

CpG Island Methylator Phenotype: The Third Way of Colorectal Carcinogenesis

Transmembrane chemoreceptors of Escherichia coli bind periplasmic ligands and transduce the signal to the flagella motors, thereby adjusting the swimming behaviour of the cell according to the chemical nature of the ligand. Cell movement, directed either towards nutrients or away from toxic compounds, is known as chemotaxis. An important property of the chemotaxis signalling pathway essential for navigation in complex gradients of nutrients is adaptation, mediated by methylation of specific glutamate residues in the chemoreceptors cytoplasmic domain. The aspartate chemoreceptor Tar possesses four such sites, but it is still unclear why several sites of methylation are needed and if a certain hierarchy among these sites exists. In this study, we systematically and quantitatively characterized the efficiency of chemotaxis and the precision of adaptation for cells expressing Tar mutated at one or more modification sites as the only chemoreceptor. Therefore, we constructed Tar chemoreceptors with all possible combinations of alanine substitutions at the methylation sites to specifically render them non-methylatable. These Tar mutants were then tested for their ability to mediate chemotaxis on soft agar plates. Furthermore, adaptation kinetics of Tar mutants were analyzed by in vivo FRET microscopy and wild-type Tar was investigated by mass spectrometrical analysis, which allows to follow the order and kinetics of methylation at individual modification sites during the adaptation process. We found that the receptor methylation rate following addition of attractant differs for the individual methylation sites with methylation site 2 being fastest, followed by sites 1 and 3, and site 4 having the slowest rate of methylation. Demethylation upon removal of attractant occurs first at methylation site 3, followed by sites 2 and 1. Furthermore, we discovered that specific methylation sites are responsible for different features of chemotaxis and adaptation. Methylation site 1 mainly contributes to the adaptation precision and the methylation rate, whereas methylation site 2 is important for the methylation rate as well as for the demethylation rate. Methylation site 3 is responsible for the chemotaxis and the demethylation rate and methylation site 4 mainly contributes to the methylation rate. In summary, the results of the present study provide new insights into the molecular details of the adaptation process in E. coli chemotaxis and the subtle interplay of individual methylation sites in the regulation of chemotactic behavior.

The entomopathogenic fungus (EPF), Beauveria bassiana, is an important and commonly used EPF for microbial control. However, the role of DNA methylation has not been thoroughly studied. Therefore, the whole genomic DNA methylome of one promising EPF isolate, B. bassiana NCHU-157 (Bb-NCHU-157), was investigated by Oxford Nanopore Technologies (ONT). First, the whole genome of Bb-NCHU-157 was sequenced by next-generation sequencing (NGS) and ONT. The genome of Bb-NCHU-157 contains 16 contigs with 34.19Mb and 50% GC content, which are composed of 10,848 putative protein-coding genes. Two putative DNA methyltransferases (DNMTs) were found, including Dim-2 and C-5 cytosine-specific DNA methylases. Both DNMTs showed higher expression levels in the mycelium stage than in the conidia stage, indicating that development of DNA methylation in Bb-NCHU-157 might occur in the mycelium stage. The global methylation level of the mycelium stage (5mC = 4.56%, CG = 3.33%, CHG = 0.74%, CHH = 0.49%) was higher than that of the conidial stage (5mC = 2.99%, CG = 1.99%, CHG = 0.63%, CHH = 0.37%) in both the gene and transposable element (TE) regions. Furthermore, the TE regions showed higher methylation frequencies than the gene regions, especially for CHH site methylation, suggesting regulation of genomic stabilization during mycelium development. In the gene regions, high methylation frequencies were found around the transcription start site (TSS) and transcription end site (TES). Moreover, CG and CHG methylation mainly occur in the promoter and intergenic regions, while CHH methylation occurs in the TE region. Among the methylated regions, 371, 661, and 756 differentially DNA methylated regions (DMRs) were hypermethylated in the mycelium in CG, CHG, and CHH, while only 13 and 7 DMRs were hypomethylated in the mycelium in CHG, and CHH, respectively. Genes located in the DMR shared the GO terms, DNA binding (GO: 0003677), and sequence-specific DNA binding (GO: 0043565) for hypermethylation in the mycelium, suggesting that methylation might regulate gene expression from the initial process. Evaluation of the DNA methylome in Bb-NCHU-157 by ONT provided new insight into this field. These data will be further validated, and epigenetic regulation during the development of B. bassiana will be explored.

Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size (N(e)). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N(e) is often substantial, however, and must be accounted for in analyses of molecular evolution.

Episodic evolution of RNA viruses.