Establishment Of DNA Methylation Patterns Research Articles

Genome-wide DNA methylation changes in human spermatogenesis.

Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatids/sperm-specific methylome. Hypomethylated regions in spermatids/sperm were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.

DNMT3B PWWP mutations cause hypermethylation of heterochromatin

The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein’s N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.

DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells

The correct establishment of DNA methylation patterns during mouse early development is essential for cell fate specification. However, the molecular targets as well as the mechanisms that determine the specificity of the de novo methylation machinery during differentiation are not completely elucidated. Here we show that the DNMT3B-dependent DNA methylation of key developmental regulatory regions at epiblast-like cells (EpiLCs) provides an epigenetic priming that ensures flawless commitment at later stages. Using in vitro stem cell differentiation and loss of function experiments combined with high-throughput genome-wide bisulfite-, bulk-, and single cell RNA-sequencing we dissected the specific role of DNMT3B in cell fate. We identify DNMT3B-dependent regulatory elements on the genome which, in Dnmt3b knockout (3BKO), impair the differentiation into meso-endodermal (ME) progenitors and redirect EpiLCs towards the neuro-ectodermal lineages. Moreover, ectopic expression of DNMT3B in 3BKO re-establishes the DNA methylation of the master regulator Sox2 super-enhancer, downmodulates its expression, and restores the expression of ME markers. Taken together, our data reveal that DNMT3B-dependent methylation at the epiblast stage is essential for the priming of the meso-endodermal lineages and provide functional characterization of the de novo DNMTs during EpiLCs lineage determination.

P-114 Transgenerational effects of maternal circadian rhythm changes on DNA methylation pattern in the testis of offspring rats

Abstract Study question Does maternal circadian rhythm change during pregnancy and lactation cause transgenerational epigenetic changes on DNA methylation in the gonads of adult male offspring? Summary answer The expression of DNA methyltransferases (DNMTs) is altered in the testis of offspring rats due to maternal circadian rhythm changes during pregnancy and lactation periods. What is known already Epigenetic mechanisms are essential for normal development and maintenance of tissue specific expression in mammals. Key mechanisms involved in epigenetic gene regulation include specifically DNA methylation and histone modifications. DNA methylation is an important regulatory mechanism that plays a role in many cellular processes and it is catalyzed by specific DNMT enzymes. Regulation of the circadian clock is also subject to epigenetic influence. Current evidence increasingly indicates that environmental conditions during pregnancy may have lifelong effects on offspring in both humans and animal models. Study design, size, duration Male offspring from pregnant Wistar rats (n = 60) which were exposed to control (12 h light/12 h dark), short day (SD) (8 hours light/16 hours dark) or long day (LD) periods (16 hours light/8 hours dark) during only pregnancy, only lactation or both periods (n = 15/group) categorized as control (C), SD pregnancy (SD-P), SD lactation (SD-L), SD pregnancy and lactation (SD-P+L), LD pregnancy (LD-P), LD lactation (LD-L), LD pregnancy and lactation (LD-P+L) groups. Participants/materials, setting, methods Maternal body weights were recorded during pregnancy and lactation periods. The global methylation pattern was evaluated with 5-methylcytosine (5-mC) immunostaining in line with histopathological analyzes in the testis tissues. In addition, the expression of three DNMTs, DNMT1, DNMT3A and DNMT3B, were evaluated to analyze the maintenance of DNA methylation and de novo establishment of DNA methylation patterns, respectively. Main results and the role of chance DNMT1 immunolocalization showed a nuclear staining pattern, predominantly in spermatogonia, spermatocytes, round spermatids and Sertoli cells in all experimental groups. A significant increase in DNMT1 expression was determined in SD-P, SD-L, SD-P+L, LD-P and LD-L groups compared to the control group (p < 0.001). On the other hand, DNMT3A was especially expressed in spermatogonia, spermatocytes, and Leydig cells in the interstitial areas. Spermatogonia, round spermatids and the head of elongated spermatids and also in Leydig cells in the interstitial areas were immunopositively stained with DNMT3B and 5-mC. 5-mC expression was also present in spermatocytes. There was a significant increase in DNMT3A, DNMT3B and 5-mC expressions in SD-P, SD-L and SD-P+L groups compared to the control group (p < 0.001). DNMT3B and 5-mC expressions were statistically higher in LD-P than control group (p < 0.001). Limitations, reasons for caution Although using a rat model has several advantages, translating these results to the human setting is a limitation of this study. Wider implications of the findings The recent studies regarding circadian regulation in reproductive tissues suggests that it plays important role in several aspects of fertility. Our study indicates that expression of DNMT proteins alters in testis due to maternal circadian rhythm changes suggesting potential influences on transgenerational reproductive health of offspring. Trial registration number This work was supported by research grants from the Scientific and Technological Research Council of Turkey (TUBITAK) (SBAG 219S636) and Akdeniz University, The Scientific Research Projects Coordination Unit (TYL-2018-3580)

Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases.

In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.

Uterine deficiency of Dnmt3b impairs decidualization and causes consequent embryo implantation defects.

Uterine deficiency of Dnmt3b impairs decidualization and consequent embryo implantation defects. Recent advances in molecular technologies have allowed the unprecedented mapping of epigenetic modifications during embryo implantation. DNA methyltransferase 3a (DNMT3A) and DNMT3B are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. It was reported that conditional knockout of Dnmt3a in the uterus does not markedly affect endometrial function during embryo implantation, but the tissue-specific functions of Dnmt3b in the endometrium during embryo implantation remain poorly understood to investigate the role of Dnmt3b during peri-implantation period. Here, we generated Dnmt3b conditional knockout (Dnmt3bd/d) female mice using progesterone receptor-Cre mice and examined the role of Dnmt3b during embryo implantation. Dnmt3bd/d female mice exhibited compromised fertility, which was associated with defective decidualization, but not endometrial receptivity. Furthermore, results showed loss of Dnmt3b did not lead to altered genomic methylation patterns of the decidual endometrium during early pregnancy. Transcriptome sequencing analysis of uteri from day 6 pregnant mice identified phosphoglycerate kinase 1 (Pgk1) as one of the most variable genes in Dnmt3bd/d decidual endometrium. Potential roles of PGK1 in the decidualization process during early pregnancy were confirmed. Lastly, the compromised decidualization upon the downregulation of Dnmt3b could be reversed by overexpression of Pgk1. Collectively, our findings indicate that uterine deficiency of Dnmt3b impairs decidualization and consequent embryo implantation defects.

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction.

Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.

A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features

BackgroundSpermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis.ResultsThe quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats.ConclusionsThese results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention.

Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation.

SummaryThe establishment of DNA methylation patterns in oocytes is a highly dynamic process marking gene-regulatory events during fertilization, embryonic development, and adulthood. However, after epigenetic reprogramming in primordial germ cells, how and when DNA methylation is re-established in developing human oocytes remains to be characterized. Here, using single-cell whole-genome bisulfite sequencing, we describe DNA methylation patterns in three different maturation stages of human oocytes. We found that while broad-scale patterns of CpG methylation have been largely established by the immature germinal vesicle stage, localized changes continue into later development. Non-CpG methylation, on the other hand, undergoes a large-scale, generalized remodeling through the final stage of maturation, with the net overall result being the accumulation of methylation as oocytes mature. The role of the genome-wide, non-CpG methylation remodeling in the final stage of oocyte maturation deserves further investigation.

Establishment of DNA methylation patterns of the Fibrillin1 (FBN1) gene in porcine embryos and tissues.

DNA methylation in transcriptional regulatory regions is crucial for gene expression. The DNA methylation status of the edges of CpG islands, called CpG island shore, is involved in tissue/cell-type-specific gene expression. Haploinsufficiency diseases are caused by inheritance of one mutated null allele and are classified as autosomal dominant. However, in the same pedigree, phenotypic variances are observed despite the inheritance of the identical mutated null allele, including Fibrillin1 (FBN1), which is responsible for development of the haploinsufficient Marfan disease. In this study, we examined the relationship between gene expression and DNA methylation patterns of the FBN1 CpG island shore focusing on transcriptionally active hypomethylated alleles (Hypo-alleles). No difference in the DNA methylation level of FBN1 CpG island shore was observed in porcine fetal fibroblast (PFF) and the liver, whereas FBN1 expression was higher in PFF than in the liver. However, Hypo-allele ratio of the FBN1 CpG island shore in PFF was higher than that in the liver, indicating that Hypo-allele ratio of the FBN1 CpG island shore likely correlated with FBN1 expression level. In addition, oocyte-derived DNA hypermethylation in preimplantation embryos was erased until the blastocyst stage, and re-methylation of the FBN1 CpG island shore was observed with prolonged in vitro culture of blastocysts. These results suggest that the establishment of the DNA methylation pattern within the FBN1 CpG island shore occurs after the blastocyst stage, likely during organogenesis. In conclusion, Hypo-allele ratios of the FBN1 CpG island shore correlated with FBN1 expression levels in porcine tissues.

Uhrf1 controls the self-renewal versus differentiation of hematopoietic stem cells by epigenetically regulating the cell-division modes

Hematopoietic stem cells (HSCs) are able to both self-renew and differentiate. However, how individual HSC makes the decision between self-renewal and differentiation remains largely unknown. Here we report that ablation of the key epigenetic regulator Uhrf1 in the hematopoietic system depletes the HSC pool, leading to hematopoietic failure and lethality. Uhrf1-deficient HSCs display normal survival and proliferation, yet undergo erythroid-biased differentiation at the expense of self-renewal capacity. Notably, Uhrf1 is required for the establishment of DNA methylation patterns of erythroid-specific genes during HSC division. The expression of these genes is enhanced in the absence of Uhrf1, which disrupts the HSC-division modes by promoting the symmetric differentiation and suppressing the symmetric self-renewal. Moreover, overexpression of one of the up-regulated genes, Gata1, in HSCs is sufficient to phenocopy Uhrf1-deficient HSCs, which show impaired HSC symmetric self-renewal and increased differentiation commitment. Taken together, our findings suggest that Uhrf1 controls the self-renewal versus differentiation of HSC through epigenetically regulating the cell-division modes, thus providing unique insights into the relationship among Uhrf1-mediated DNA methylation, cell-division mode, and HSC fate decision.

Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases.

In mammals, three DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains, and in this chapter, the structures and functions of these domains are described.

P152: Long non-coding RNA HOTAIR affects DNA methylation patterns in gastrointestinal stromal tumours (GIST)

Aberrant alterations of DNA methylation patterns have been recognized as early and common events in oncogenesis emphasizing high therapeutic and preventive potential. Concurrent epigenetic silencing of multiple tumour suppressor genes has been reported in different tumours suggesting the existence of a directed program, whereby groups of genes are regulated by promoter methylation. The molecular bases of such a program remain largely unclear. Certain long non-coding RNAs (lncRNAs) have been recently identified that are responsible for target specificity of the histone modification complexes. It remains incompletely understood, however, if lncRNAs may play a role in patterning DNA methylation. In this study, we asked by using gastrointestinal stromal tumours as a model if an epigenetic related HOX Antisense Intergenic RNA , or HOTAIR , is involved in establishment of DNA methylation patterns. To this end, we first showed high up-regulation of HOTAIR in patient samples of high risk compared to low and intermediate risk groups ( n = 66, p = 6.7 × 10 −6 ), what is supported by the earlier reports on common carcinomas. Highest levels of HOTAIR endogenous expression were next detected also in cell lines GIST T1, GIST48b and GIST882. Stable knockdown of HOTAIR was achieved in GIST T1 and GIST48b cells by RNAi using lentiviral transduction. As expected epigenetic alterations due to HOTAIR knockdown could develop with a delay, genome-wide DNA methylation profiling was performed at passage 12 after the transduction on the Infinium HumanMethylation450 BeadChip platform in triplicates. DNA methylation data were analysed by an R package RnBeads. A total of 218 CpG sites got hypomethylated upon HOTAIR knockdown in GIST T1 and GIST48b cells (Δ β > 0.3, FDR RASSF1 was almost entirely erased upon HOTAIR knockdown in GIST T1 cell line with concomitant up-regulation detected by qRT-PCR. Concordant with earlier reports, HOTAIR knockdown led to reduced migration potential in GIST T1 cells. Taken together, the results suggest that HOTAIR is one of the factors involved in establishment of specific DNA methylation patterns in GIST. While the molecular mechanism remains to be determined, it is plausible to assume a recruitment of DNA methyltransferases by the Polycomb repressive complex 2, which target specificity is determined by HOTAIR . The results further suggest the feasibility of manipulating DNA methylation patterns in a targeted manner and are of potential interest in context of developing epigenetic cancer therapy. The study is supported by the Interdisciplinary Centre for Clinical Research (IZKF) at the University of Erlangen-Nuremberg.

MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation.

SummaryIn developing male germ cells, prospermatogonia, two Piwi proteins, MILI and MIWI2, use Piwi-interacting RNA (piRNA) guides to repress transposable element (TE) expression and ensure genome stability and proper gametogenesis. In addition to their roles in post-transcriptional TE repression, both proteins are required for DNA methylation of TE sequences. Here, we analyzed the effect of Miwi2 deficiency on piRNA biogenesis and transposon repression. Miwi2 deficiency had only a minor impact on piRNA biogenesis; however, the piRNA profile of Miwi2-knockout mice indicated overexpression of several LINE1 TE families that led to activation of the ping-pong piRNA cycle. Furthermore, we found that MILI and MIWI2 have distinct functions in TE repression in the nucleus. MILI is responsible for DNA methylation of a larger subset of TE families than MIWI2 is, suggesting that the proteins have independent roles in establishing DNA methylation patterns.

DNA methylation reprogramming during oogenesis and interference by reproductive technologies: Studies in mouse and bovine models.

The use of assisted reproductive technology (ART) to overcome fertility problems has continued to increase since the birth of the first baby conceived by ART over 30 years ago. Similarly, embryo transfer is widely used as a mechanism to advance genetic gain in livestock. Despite repeated optimisation of ART treatments, pre- and postnatal outcomes remain compromised. Epigenetic mechanisms play a fundamental role in successful gametogenesis and development. The best studied of these is DNA methylation; the appropriate establishment of DNA methylation patterns in gametes and early embryos is essential for healthy development. Superovulation studies in the mouse indicate that specific ARTs are associated with normal imprinting establishment in oocytes, but abnormal imprinting maintenance in embryos. A similar limited impact of ART on oocytes has been reported in cattle, whereas the majority of embryo-focused studies have used cloned embryos, which do exhibit aberrant DNA methylation. The present review discusses the impact of ART on oocyte and embryo DNA methylation with regard to data available from mouse and bovine models.

Abstract 265: Early life exposure to air pollution and promoter methylation in breast tumors in the Western New York Exposures and Breast Cancer Study

Abstract Background: It has been hypothesized that early life exposures are important in establishing DNA methylation patterns and that these changes may be a mechanism for alteration in breast cancer risk. We previously found an association of exposure to total suspended particulates (TSP) in early life and breast cancer risk among post-menopausal women. Particulate matter and secondhand smoke (SHS) have been associated with aberrant DNA methylation. To our knowledge the relation between early life exposure to air pollution via SHS or TSP and aberrant DNA methylation has not been examined in breast cancer tissues. Purpose: We investigated the association between breast tumor DNA methylation in the promoter regions for 11 genes and exposure to TSP at the time of birth and SHS before age 20. We hypothesized that these exposures lead to hypermethylation of tumor suppressor genes in breast cancer tumor tissue in post-menopausal cases. Methods: A case-case study design, utilizing breast cancer cases participating in the WEB Study, a large population-based case-control study, was used to investigate our hypotheses. Five hundred and four archived tumor blocks from breast cancer cases were retrieved, DNA was extracted and methylation of 11 genes (SFN, ESR1, GSTP1, RASSF1, RARB, SYK, SCGB3A1, CDKN2A, CCND2, BRCA1, and FHIT ) was assayed with pyrosequencing. TSP exposure at birth address was estimated with ArcGIS 8.0 (ESRI, Inc., Redlands, CA), based on annual average TSP concentrations (1959-1997). Participants reported household SHS exposure before age 20. Hypermethylation was defined as mean methylation greater than 20%. Unconditional logistic regression was used to compute odds ratios (OR) and 95% confidence intervals, adjusted for age, estrogen receptor status and current smoking status. Results: Exposure to SHS before age 20 was associated with decreased average methylation (OR: 0.83; 95% CI: 0.50, 1.41) as was TSP exposure at birth (OR: 0.56; 95% CI: 0.29, 1.11), although these associations were imprecise. Exposure to SHS before age 20 was associated with decreased FHIT methylation (OR: 0.39; 95% CI: 0.17, 0.89). The other genes assessed showed similar inverse risk estimates and imprecision. Conclusions: While our results are necessarily preliminary, they are not consistent with our hypothesis that TSP or SHS exposure in early life is associated with DNA hypermethylation of promoter regions of genes in breast cancer tumor tissue. Inferences are complicated by several limitations. For instance, air pollution may have a stronger impact on global DNA hypomethylation. However these findings could also be attributed to low variability in exposures, relatively small sample size, or the choice of loci and genes assayed. Citation Format: Catherine Callahan, Matthew Bonner, Peter Shields, Christine Ambrosone, Daikwon Han, Jing Nie, Stephen Edge, Maurizio Trevisan, Jo L. Freudenheim. Early life exposure to air pollution and promoter methylation in breast tumors in the Western New York Exposures and Breast Cancer Study. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 265. doi:10.1158/1538-7445.AM2014-265

DNMT3B promoter polymorphisms and maternal risk of birth of a child with Down syndrome

Are DNMT3B promoter polymorphisms among maternal risk factors for the birth of a child with Down syndrome (DS)? Present results suggest that combinations of functional DNMT3B promoter polymorphisms might modulate maternal risk of birth of a child with DS. The DNMT3B gene codes for DNA methyltransferase 3b (DNMT3b), a protein required for genome-wide de novo methylation, for the establishment of DNA methylation patterns during development and for regulating the histone code and DNA methylation at centromeric regions. Two common functional DNMT3B promoter polymorphisms, namely -149 C > T (rs2424913) and -579 G > T (rs1569686), have been extensively investigated in cancer genetic association studies but less is known about their role in non-cancer diseases. Early in 1999, it was supposed that impaired DNA methylation of pericentromeric regions might represent a maternal risk factor for having a baby with DS. We aimed to investigate DNMT3B -149 C > T and -579 G > T polymorphisms as maternal risk factors for the birth of a child with DS. The study was performed on DNA samples from 172 mothers of DS individuals (135 aged <35 years when they conceived) and 157 age-matched mothers of unaffected individuals. Genotyping was performed by means of the PCR-RFLP technique. The DNMT3B -579T allele [odds ratio (OR) = 0.68; 95% confidence interval (CI) = 0.48-0.94, P = 0.02], the DNMT3B -579 GT genotype (OR = 0.55; 95% CI = 0.35-0.87 , P = 0.01) and the combined DNMT3B -579 GT + TT genotype (OR = 0.55; 95% CI = 0.36-0.86 , P = 0.008) were associated with reduced risk of birth of a child with DS. A joint effect of the two polymorphisms was observed and the combined -579 GT/-149 CC genotype resulted in decreased DS risk (OR = 0.22; 95% CI = 0.08-0.64, P = 0.003). The effect remained statistically significant after Bonferroni's correction for multiple comparisons. Similar results were obtained when the analysis was restricted to women who conceived a DS child before 35 years of age. To the best of our knowledge, this is the first genetic association study aimed at evaluating DNMT3B polymorphisms as maternal risk factors for DS. Replication of the findings in other populations is required. If confirmed in subsequent studies, DNMT3B promoter polymorphisms might be additional markers to be taken into account when evaluating the contribution of one-carbon (folate) metabolism to the maternal risk of birth of a child with DS.

Abstract 996: MBD-capture coupled with next generation sequencing elucidates genome-wide crosstalk between epigenetic marks and its role in cancer

Abstract Aberrations in DNA methylation are a hallmark of cancer, and these epigenetic changes lead to tumor suppressor gene silencing by hypermethylation, global genomic hypomethylation, and genomic instabilities. Post-translational histone modifications are important epigenetic marks that have been implicated in regulating DNA methylation patterning. Several known histone marks, including methylation of histone H3 at lysines 4 and 27 and monoubiquitylation of histone H2A (H3K4me, H3K27me, and H2Aub, respectively), are believed to differentially regulate DNA methyltransferase activity on DNA. The histone mark H3K4me is associated with gene activation, and H3K27me and H2Aub are associated with loci of transcriptional repression and DNA methylation, especially at hypermethylated genes in cancer. Recent studies have examined the genome-wide distribution of these histone modifications or have studied how their distribution relates to DNA methylation within specific loci, but these studies have not ascribed specific roles to these histone modifications in DNA methylation patterning, nor do we understand why only subsets of genes throughout the genome become hypermethylated in cancer. This poster demonstrates how the histone marks H3K4me, H3K27me, and H2Aub affect genome-wide DNA methylation patterning and transcriptional regulation, and we highlight several epigenetic targets of H3K27me and H2Aub epigenetic repression that participate in the pathogenesis of cancer. We have used siRNA transfection in NCCIT human embryonic carcinoma cells to target critical subunits of the complexes that establish each of these histone modifications. Through these siRNA treatments, we assessed the roles of each mark in establishing DNA methylation patterns throughout the genome and how these patterns relate to genome-wide gene expression. The effects of histone mark deficiency were analyzed by an assay that isolates methylated-CpG-containing DNA (MBD-capture) coupled to massively parallel DNA sequencing to identify sequences with altered methylation patterns. These sequencing results were correlated with patterns of gene expression determined by expression microarray analysis to identify gene targets whose epigenetic misregulation results in alterations in gene expression. In total, this poster demonstrates how histone modifications contribute to the control of the human DNA methylome and postulates how these marks exert downstream effects toward the pathogenesis of cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 996. doi:1538-7445.AM2012-996

Role of DNMT3B in the regulation of early neural and neural crest specifiers

The de novo DNA methyltransferase DNMT3B functions in establishing DNA methylation patterns during development. DNMT3B missense mutations cause immunodeficiency, centromere instability and facial anomalies (ICF) syndrome. The restriction of Dnmt3b expression to neural progenitor cells, as well as the mild cognitive defects observed in ICF patients, suggests that DNMT3B may play an important role in early neurogenesis. We performed RNAi knockdown of DNMT3B in human embryonic stem cells (hESCs) in order to investigate the mechanistic contribution of DNMT3B to DNA methylation and early neuronal differentiation. While DNMT3B was not required for early neuroepithelium specification, DNMT3B deficient neuroepithelium exhibited accelerated maturation with earlier expression, relative to normal hESCs, of mature neuronal markers (such as NEUROD1) and of early neuronal regional specifiers (such as those for the neural crest). Genome-wide analyses of DNA methylation by MethylC-seq identified novel regions of hypomethylation in the DNMT3B knockdowns along the X chromosome as well as pericentromeric regions, rather than changes to promoters of specific dysregulated genes. We observed a loss of H3K27me3 and the polycomb complex protein EZH2 at the promoters of early neural and neural crest specifier genes during differentiation of DNMT3B knockdown but not normal hESCs. Our results indicate that DNMT3B mediates large-scale methylation patterns in hESCs and that DNMT3B deficiency in the cells alters the timing of their neuronal differentiation and maturation.

Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue

The Dnmt3a DNA methyltransferase is responsible for establishing DNA methylation patterns during mammalian development. We show here that the mouse Dnmt3a DNA methyltransferase is able to transfer the methyl group from S-adenosyl-l-methionine (AdoMet) to a cysteine residue in its catalytic center. This reaction is irreversible and relatively slow. The yield of auto-methylation is increased by addition of Dnmt3L, which functions as a stimulator of Dnmt3a and enhances its AdoMet binding. Auto-methylation was observed in binary Dnmt3a AdoMet complexes. In the presence of CpG containing dsDNA, which is the natural substrate for Dnmt3a, the transfer of the methyl group from AdoMet to the flipped target base was preferred and auto-methylation was not detected. Therefore, this reaction might constitute a regulatory mechanism which could inactivate unused DNA methyltransferases in the cell, or it could simply be an aberrant side reaction caused by the high methyl group transfer potential of AdoMet. Dnmt3a is a DNA-(cytosine C5)-methyltransferase, EC 2.1.1.37. • Dnmt3a methylates Dnmt3a by methyltransferase assay (View interaction) • Dnmt3a and DNMT3L methylate Dnmt3a by methyltransferase assay (View interaction).