Generation of a transgenic mouse embryonic stem cell line overexpressing DNMT1.

DNMT1 overexpression is reported in disorders like schizophrenia, bipolar, epilepsy and multiple cancer types. Here, we used non-homologous recombination to generate R1Dnmt1WT-1, a mouse embryonic stem cell (ESC) line carrying a Dnmt1 cDNA transgene to achieve about two-fold overexpression. This ESC line showed increased transcript levels of Sox2 pluripotency marker. R1Dnmt1WT-1 embryoid bodies showed increased levels of Lefty1 (endoderm), Tbxt and Acta2 (mesoderm), and Pax6 (ectoderm) transcripts. This new line showed normal karyotype and microsatellite profiles making it useful in studying carcinogenesis and abnormal neurogenesis due to DNMT1 overexpression.

Generation of a transgenic mouse embryonic stem cell line expressing Dnmt1Y495C mutation associated with HSAN1E disorder.

DNMT1 Y495C is the most common mutation associated with hereditary sensory and autonomic neuropathy type 1E, and dementia. Here we employed non-homologous recombination and generated a mouse embryonic stem cell line carrying a transgene expressing DNMT1 Y495C mutation in the wild-type background. The resultant cell line, Dnmt1Y495C-1 showed increased transcript levels of the Oct4 and Sox2 pluripotency markers and Gata6 and Pax6 germ layer markers. This cell line showed normal karyotype, expression of the mutant Dnmt1 and wild-type transcripts in approximately equal ratios and is a useful model for studying the abnormal neurogenesis due to the DNMT1 Y495C mutation.

Functional Analysis of DNMT1 SNPs (rs2228611 and rs2114724) Associated with Schizophrenia.

A recent study showed the association of minor alleles of rs2228611 (T allele) and rs2114724 (T allele) of DNMT1 with schizophrenia (SZ) and suggested their effects on splicing of the transcripts. We performed a replication study using 310 controls and 304 SZ patients and confirmed the association of the homozygous minor allele genotypes with SZ (P = 0.04 for rs2114724 and P = 0.007 for rs2228611). This significant association persisted after Bonferroni correction when the previously published data of 301 controls and 325 patients were also considered (P ≤ 0.0002). In addition, we found that the proportion of male patients with homozygous minor alleles at rs2114724 was significantly higher than that of females (P = 0.002). When haplotype analysis of both loci was performed, we observed a significant association of T/T-T/T and T/T-C/T (P = 0.04) haplotypes with SZ. To gain insights into the functional effects of the two SNPs on the levels of DNMT1 transcripts, quantitative real-time PCR experiments were performed using peripheral blood monocytes from 10 individuals each with T/T-T/T (homozygous minor allele), C/T-C/T (heterozygous), and C/C-C/C (homozygous major allele) haplotypes. Independently, the levels of DNMT1 protein were also compared in three individuals each by immunofluorescence. These results suggest that neither DNMT1 transcript nor the protein levels were significantly different in the peripheral blood monocytes among the individuals studied for the three groups. Taken together, our results confirm that the two minor alleles in homozygosity are associated with SZ but with no discernible effects on transcript or protein levels of DNMT1 in the peripheral blood monocytes of the small number of samples tested.

Reproducible differentiation and characterization of neurons from mouse embryonic stem cells.

Investigation on the effects of disease-associated mutations on neurodevelopment is an essential approach to understand the molecular basis of neurological disorders and can be achieved by generating suitable animal models. However, some of the mutations preclude development of animal models, leaving cell-based models as the only options. Mouse embryonic stem cells (mESCs) are attractive because of the well-established technologies for introducing disease-associated mutations and the feasibility of investigating the abnormalities during different stages of neurogenesis. Importantly, such transgenic mESCs enable large-scale screening and identification of the most promising small molecules and/or drug candidates before undertaking expensive animal studies. Although neuronal differentiation from mESCs is one of the earliest methods to be developed, we observed that the published as well as publicly available methods did not yield neurons consistently. Here, we describe a 16-day differentiation protocol that consistently induced differentiation of mESCs into neurons. This step-wise protocol enables monitoring of the neuronal differentiation process at different stages as well as characterization using the markers for immature and mature neurons by using immunocytochemistry and quantitative real-time PCRs.•Development of a method for differentiating mouse ES cells into neurons.•Differentiating the mouse ES cells into embryoid bodies prior to induction of neuronal differentiation results in better neuron formation.

Genome-wide methylation data from R1 (wild-type) and the transgenic Dnmt1Tet/Tet mouse embryonic stem cells overexpressing DNA methyltransferase 1 (DNMT1).

Defects in epigenetic mechanisms are well-recognized in multiple neurodevelopmental disorders including Schizophrenia (SZ). In addition to aberrant epigenetic marks, dysregulated epigenetic machinery was also identified among the contributory factors in SZ patients. Among these, overexpression of DNA methyltransferase 1 (DNMT1) was the first to be identified. In this context, Dnmt1tet/tet (Tet/Tet), a mouse embryonic stem cell (ESC) line that overexpresses DNMT1 in ESCs and neurons, was developed to study abnormal neurogenesis. In an attempt to understand whether DNMT1 overexpression is associated with aberrant DNA methylation, we compared the genome-wide methylation levels of R1 (wild-type) and Tet/Tet ESCs and their neuronal derivatives by RRBS. The RRBS data (GSE152817) showed an average mappability of ∼59% and an average coverage of 40X per locus. The data was processed to determine the methylation percentages of target genes and was visualized using the UCSC genome browser. The observed methylation differences were validated by Combined Bisulfite Restriction Analysis (COBRA). The methylome data described here can be used to study the relationship between DNMT1 overexpression, alterations in methylation levels and dysregulation of SZ-associated genes.

Analysis of transcript levels of a few schizophrenia candidate genes in neurons from a transgenic mouse embryonic stem cell model overexpressing DNMT1.

Overexpression of DNA Methyltransferase I (DNMT1) is considered as one of the etiological factors for schizophrenia (SZ). However, information on genes subjected to dysregulation because of DNMT1 overexpression is limited. To test whether a larger group of SZ-associated genes are affected, we selected 15 genes reported to be dysregulated in patients (Gad1, Reln, Ank3, Cacna1c, Dkk3, As3mt, Ppp1r11, Smad5, Syn1, Wnt1, Pdgfra, Gsk3b, Cxcl12, Tcf4 and Fez1). Transcript levels of these genes were compared between neurons derived from Dnmt1tet/tet (Tet/Tet) mouse embryonic stem cells (ESCs) that overexpress DNMT1 with R1 (wild-type) neurons. Transcript levels of thirteen genes were significantly altered in Tet/Tet neurons of which, the dysregulation patterns of 11 were similar to patients. Transcript levels of eight out of these eleven were also significantly altered in Tet/Tet ESCs, but the dysregulation patterns of only five were similar to neurons. Comparative analyses among ESCs, embryoid bodies and neurons divided the 15 genes into four distinct groups with a majority showing developmental stage-specific patterns of dysregulation. Reduced Representational Bisulfite Sequencing data from neurons did not show any altered promoter DNA methylation for the dysregulated genes. Doxycycline treatment of Tet/Tet ESCs that eliminated DNMT1, reversed the direction of dysregulation of only four genes (Gad1, Dkk3, As3mt and Syn1). These results suggest that 1. Increased DNMT1 affected the levels of a majority of the transcripts studied, 2. Dysregulation appears to be independent of promoter methylation, 3. Effects of increased DNMT1 levels were reversible for only a subset of the genes studied, and 4. Increased DNMT1 levels may affect transcript levels of multiple schizophrenia-associated genes.

CalPen (Calculator of Penetrance), a web-based tool to estimate penetrance in complex genetic disorders.

Mutations conferring susceptibility to complex disorders also occur in healthy individuals but at significantly lower frequencies than in patients, indicating that these mutations are not completely penetrant. Therefore, it is important to estimate the penetrance or the likelihood of developing a disease in presence of a mutation. Recently, a method to calculate penetrance and its credible intervals was developed on the basis of the Bayesian method and since been used in literature. However, in the present form, this approach demands programming skills for its utility. Here, we developed 'CalPen', a web-based tool for straightforward calculation of penetrance and its credible intervals by entering the number of mutations identified in controls and patients, and the number of patients and controls studied. For validation purposes, we show that CalPen-derived penetrance values are in good agreement with the published values. As further demonstration of its utility, we used schizophrenia as an example of complex disorder and estimated penetrance values for 15 different copy number variants (CNVs) reported in 39,059 patients and 55,084 controls, and 145 SNPs reported in 45,405 patients and 122,761 controls. CNVs showed an average penetrance of 7% with 22q11.21 CNVs having highest value (~20%) and 15q11.2 deletions with lowest value (~1.4%). Most SNPs, on the other hand showed a penetrance of 0.7% with rs1801028 having the highest penetrance (1.6%). In summary, CalPen is an accurate and user-friendly web-based tool useful in human genetic research to ascertain the ability of the mutation/ variant to cause a complex genetic disorder.

Phenotypic association of 15q11.2 CNVs of the region of breakpoints 1-2 (BP1-BP2) in a large cohort of samples referred for genetic diagnosis.

In view of conflicting reports on the pathogenicity of 15q11.2 CNVs of the breakpoints 1-2 (BP1-BP2) region and lack of association with a specific phenotype, we collected phenotypic data on 51,462 patients referred for genetic testing at two centers (Magee-Womens Hospital of UPMC and Baylor Genetics Laboratories, Baylor College of Medicine). Using array CGH, 262 patients with deletions and 215 with duplications were identified and tested for their association with four phenotypes (developmental delay, dysmorphic features, autism group of disorders, and epilepsy/seizures). Only association of deletions with dysmorphic features was observed (P = 0.013) with low penetrance (3.8%). Our results, viewed in the context of other reports suggesting the lack of a clear phenotypic outcome, underscore the need for detailed phenotypic studies to better understand the pathogenicity of 15q11.2 (BP1-BP2) CNVs.

Stem Cell Models to Investigate the Role of DNA Methylation Machinery in Development of Neuropsychiatric Disorders.

Epigenetic mechanisms underlie differentiation of pluripotent stem cells into different lineages that contain identical genomes but express different sets of cell type-specific genes. Because of high discordance rates in monozygotic twins, epigenetic mechanisms are also implicated in development of neuropsychiatric disorders such as schizophrenia and autism. In support of this notion, increased levels of DNA methyltransferases (DNMTs), DNMT polymorphisms, and dysregulation of DNA methylation network were reported among schizophrenia patients. These results point to the importance of development of DNA methylation machinery-based models for studying the mechanism of abnormal neurogenesis due to certain DNMT alleles or dysregulated DNMTs. Achieving this goal is strongly confronted by embryonic lethality associated with altered levels of epigenetic machinery such as DNMT1 and expensive approaches in developing in vivo models. In light of literature evidence that embryonic stem cells (ESCs) are tolerant of DNMT mutations and advancement in the technology of gene targeting, it is now possible to introduce desired mutations in DNMT loci to generate suitable ESC lines that can help understand the underlying mechanisms by which abnormal levels of DNMTs or their specific mutations/alleles result in abnormal neurogenesis. In the future, these models can facilitate development of suitable drugs for treatment of neuropsychiatric disorders.

Transient DNMT1 suppression reveals hidden heritable marks in the genome.

Genome-wide demethylation and remethylation of DNA during early embryogenesis is essential for development. Imprinted germline differentially methylated domains (gDMDs) established by sex-specific methylation in either male or female germ cells, must escape these dynamic changes and sustain precise inheritance of both methylated and unmethylated parental alleles. To identify other, gDMD-like sequences with the same epigenetic inheritance properties, we used a modified embryonic stem (ES) cell line that emulates the early embryonic demethylation and remethylation waves. Transient DNMT1 suppression revealed gDMD-like sequences requiring continuous DNMT1 activity to sustain a highly methylated state. Remethylation of these sequences was also compromised in vivo in a mouse model of transient DNMT1 loss in the preimplantation embryo. These novel regions, possessing heritable epigenetic features similar to imprinted-gDMDs are required for normal physiological and developmental processes and when disrupted are associated with disorders such as cancer and autism spectrum disorders. This study presents new perspectives on DNA methylation heritability during early embryo development that extend beyond conventional imprinted-gDMDs.

Cell and molecular biology of DNA methyltransferase 1.

The DNA cytosine methyltransferase 1 (DNMT1) is a ubiquitous nuclear enzyme that catalyzes the well-established reaction of placing methyl groups on the unmethylated cytosines in methyl-CpG:CpG base pairs in the hemimethylated DNA formed by methylated parent and unmethylated daughter strands. This activity regenerates fully methylated methyl-CpG:methyl-CpG pairs. Despite the straightforward nature of its catalytic activity, detailed biochemical, genetic, and developmental studies revealed intricate details of the central regulatory role of DNMT1 in governing the epigenetic makeup of the nuclear genome. DNMT1 mediates demethylation and also participates in seemingly wide cellular functions unrelated to maintenance DNA methylation. This review brings together mechanistic details of maintenance methylation by DNMT1, its regulation at transcriptional and posttranscriptional levels, and the seemingly unexpected functions of DNMT1 in the context of DNA methylation which is central to epigenetic changes that occur during development and the process of cell differentiation.

Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder.

An unanticipated and tremendous amount of the noncoding sequence of the human genome is transcribed. Long noncoding RNAs (lncRNAs) constitute a significant fraction of non-protein-coding transcripts; however, their functions remain enigmatic. We demonstrate that deletions of a small noncoding differentially methylated region at 16q24.1, including lncRNA genes, cause a lethal lung developmental disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), with parent-of-origin effects. We identify overlapping deletions 250 kb upstream of FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete lung-specific lncRNA genes. These deletions define a distant cis-regulatory region that harbors, besides lncRNA genes, also a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter. We suggest that lung-transcribed 16q24.1 lncRNAs may contribute to long-range regulation of FOXF1 by GLI2 and other transcription factors. Perturbation of lncRNA-mediated chromatin interactions may, in general, be responsible for position effect phenomena and potentially cause many disorders of human development.

A therapeutic trial of pro-methylation dietary supplements in Angelman syndrome.

Angelman syndrome (AS) is due to deficient ubiquitin protein ligase 3a, the gene for which (UBE3A) maps to chromosome 15q11-q13 and is imprinted such that only the maternally inherited gene is expressed. The paternally inherited UBE3A gene is silenced, a process mediated by an antisense transcript. We conducted a trial using methylation-promoting dietary supplements (betaine, metafolin, creatine, and vitamin B(12) ) in an attempt to reduce antisense transcript production, increase UBE3A expression, and ameliorate the symptoms of AS. Neuropsychological evaluations, biochemical testing, and assessment of DNA methylation were performed at the beginning and at the end of 1 year of supplementation. The primary outcome measures were changes in the level of developmental function (cognitive, motor, and language) as measured using standardized instruments. The secondary outcomes measures were changes in biochemical parameters and global DNA methylation. These data were compared to those of a control group from a previous randomized double-blind trial using folic acid and betaine. There were no statistically significant changes in the developmental performance of children treated with supplements. There were no unexpected changes in biochemical parameters and no change in site-specific DNA methylation when comparing samples from before and after treatment. There were 10 adverse events that resulted in study withdrawal of 7 participants (worsening of seizures, onset, or worsening of sleep problems, constipation, and anorexia). Supplementation with betaine, metafolin, creatine, and vitamin B(12) appears safe but ineffective in decreasing the severity of AS.

Mouse ES cells overexpressing DNMT1 produce abnormal neurons with upregulated NMDA/NR1 subunit.

High levels of DNA methyltransferase 1 (DNMT1), hypermethylation, and downregulation of GAD(67) and reelin have been described in GABAergic interneurons of patients with schizophrenia (SZ) and bipolar (BP) disorders. However, overexpression of DNMT1 is lethal, making it difficult to assess the direct effect of high levels of DNMT1 on neuronal development in vivo. We therefore used Dnmt1(tet/tet) mouse ES cells that overexpress DNMT1 as an in vitro model to investigate the impact of high levels of DNMT1 on neuronal differentiation. Although there is down-regulation of DNMT1 during early stages of differentiation in wild type and Dnmt1(tet/tet) ES cell lines, neurons derived from Dnmt1(tet/tet) cells showed abnormal dendritic arborization and branching. The Dnmt1(tet/tet) neuronal cells also showed elevated levels of functional N-methyl d-aspartate receptor (NMDAR), a feature also reported in some neurological and neurodegenerative disorders. Considering the roles of reelin and GAD(67) in neuronal networking and excitatory/inhibitory balance, respectively, we studied methylation of these genes' promoters in Dnmt1(tet/tet) ES cells and neurons. Both reelin and GAD(67) promoters were not hypermethylated in the Dnmt1(tet/tet) ES cells and neurons, suggesting that overexpression of DNMT1 may not directly result in methylation-mediated repression of these two genes. Taken together, our results suggest that overexpression of DNMT1 in ES cells results in an epigenetic change prior to the onset of differentiation. This epigenetic change in turn results in abnormal neuronal differentiation and upregulation of functional NMDA receptor.

Distinct roles of DMAP1 in mouse development.

DMAP1 (DNMT1-associated protein 1) is a member of the TIP60-p400 complex that maintains embryonic stem (ES) cell pluripotency and a complex containing the somatic form of DNA methyltransferase 1 (DNMT1s). DMAP1 interacts with DNMT1s through a domain that is absent in Dnmt1(V)(/)(V) mice expressing just the oocyte form (DNMT1o). A Dmap1-null allele was generated to study the role of DMAP1 in development. Consistent with the phenotypes of loss of other members of the TIP60-p400 complex, Dmap1(-/-) mice died during preimplantation in both Dnmt1(+/+) and Dnmt1(V)(/)(V) backgrounds. Unexpectedly, in the Dnmt1(V)(/)(V) background, Dmap1(+/-) parents produced mainly Dmap1(+/-) mice. Most Dmap1(+/+) progeny died during midgestation, with loss of DNA methylation on imprinted genes, suggesting that DMAP1 influences maintenance methylation mediated by DNMT1o. In this regard, a DMAP1-DNMT1o complex was detected in ES cells when DNMT1o was stably expressed but not when transiently expressed, indicating a novel interaction between DMAP1 and DNMT1o. These results suggest that DMAP1-DNMT1s and DMAP1-DNMT1o interactions are essential for normal development and that DMAP1-DNMT1o complexes are not readily formed in the embryo. Therefore, DMAP1 mediates distinct preimplantation epigenetic reprogramming processes: TIP60-p400 nucleosome remodeling and DNMT1 maintenance methylation.

Dissection of structure and function of the N-terminal domain of mouse DNMT1 using regional frame-shift mutagenesis.

Deletion analysis of mouse DNMT1, the primary maintenance methyltransferase in mammals, showed that most of the N-terminal regulatory domain (amino acid residues 412-1112) is required for its enzymatic activity. Although analysis of deletion mutants helps to identify regions of a protein sequence required for a particular activity, amino acid deletions can have drastic effects on protein structure and/or stability. Alternative approaches represented by rational design and directed evolution are resource demanding, and require high-throughput selection or screening systems. We developed Regional Frame-shift Mutagenesis (RFM) as a new approach to identify portions required for the methyltransferase activity of DNMT1 within the N-terminal 89-905 amino acids. In this method, a short stretch of amino acids in the wild-type protein is converted to a different amino acid sequence. The resultant mutant protein retains the same amino acid length as the wild type, thereby reducing physical constrains on normal folding of the mutant protein. Using RFM, we identified three small regions in the amino-terminal one-third of the protein that are essential for DNMT1 function. Two of these regions (amino acids 124-160 and 341-368) border a large disordered region that regulates maintenance methylation activity. This organization of DNMT1's amino terminus suggests that the borders define the position of the disordered region within the DNMT1 protein, which in turn allows for its proper function.

Identification of a region of the DNMT1 methyltransferase that regulates the maintenance of genomic imprints.

Reprogramming of DNA methylation patterns during mammalian preimplantation development involves the concurrent maintenance of methylation on differentially methylated domains (DMDs) of imprinted genes and a marked reduction of global (non-DMD) genomic methylation. In the developing mammalian embryo, one allele of a DMD is unmethylated, and the opposite parental allele is methylated, having inherited this methylation from the parental gamete. The maintenance of DMDs is important for monoallelic imprinted gene expression and normal development of the embryo. Because the DNMT1 cytosine methyltransferase governs maintenance methylation in mammals, rearrangements of non-DMD, but not DMD methylation in preimplantation embryos suggest that the preimplantation DNMT1-dependent maintenance mechanism specifically targets DMD sequences. We explored this possibility using an engineered mouse ES cell line to screen for mutant DNMT1 proteins that protect against the loss of DMD and/or global (non-DMD) methylation in the absence of the wild-type endogenous DNMT1 methyltransferase. We identified DNMT1 mutants that were defective in maintenance of either DMD and/or non-DMD methylation. Among these, one mutant maintained non-DMD methylation but not imprinted DMD methylation and another mutant maintained just DMD methylation. The mutated amino acids of these mutants reside in a mammal-specific, disordered region near the amino terminus of DNMT1. These findings suggest that DNMT1 participates in epigenetic reprogramming through its ability to distinguish different categories of methylated sequences.

Isolation and analysis of sequences showing sex-specific cytosine methylation in the mealybug Planococcus lilacinus.

Genomic libraries of Planococcus lilacinus, a mealybug in which paternal chromosomes are facultatively heterochromatic and inactive in sons but not in daughters, were probed with subtraction probes in order to estimate the number of sequences displaying sex-specific cytosine methylation in CpG dinucleotides. Sequences showing male-specific methylation were found to occur approximately 2.5 times more often than those showing female-specific methylation. In order to directly isolate sequences showing sex-specific CpG methylation, we employed methylation-specific arbitrarily primed (MS-AP) polymerase chain reaction (PCR) and identified 72 sex-specific products, of which 51 were from males and 21 from females. Amplification of bisulfite-modified DNA and subsequent Southern hybridization showed that in 33 out of these 72 sex-specific products, there was differential methylation of homologous sequences; i.e., both methylated and unmethylated copies of the same sequence occurred in one sex whereas only unmethylated copies were present in the opposite sex. Sequencing of bisulfite-modified DNA showed an interspersion of CpG and non-CpG methylation among the sex-specifically methylated sequences. Sequences showing male-specific CpG methylation are organized as transcriptionally silent chromatin in males but not in females, whereas those showing female-specific CpG methylation are organized as transcriptionally silent chromatin in females but not in males. The sequences identified in this study that show differential methylation in males, but are unmethylated in females, may prove useful in the study of imprinting in the mealybug system.

Characterization of the genome of the mealybug Planococcus lilacinus, a model organism for studying whole-chromosome imprinting and inactivation.

The co-occurrence of three chromosome-wide phenomena--imprinting, facultative heterochromatization and diffuse centromere--in the mealybug Planococcus lilacinus makes investigation of the genomics of this species an attractive prospect. In order to estimate the complexity of the genome of this species, 300 random stretches of its DNA, constituting approximately 0.1% of the genome, were sequenced. Coding sequences appear to constitute approximately 53.5%, repeat sequences approximately 44.5% and non-coding single-copy sequences approximately 2% of the genome. The proportion of repetitive sequences in the mealybug is higher than that in the fruit fly Drosophila melanogaster (approximately 30%). The mealybug genome (approximately 220 Mb) is about 1.3 times the size of the fly genome (approximately 165 Mb) and its GC content (approximately 35%) less than that of the fly genome (approximately 40%). The relative abundance of various dinucleotides, as analysed by the method of Gentles and Karlin, shows that the dinucleotide signatures of the two species are moderately similar and that in the mealybug there is neither over-representation nor under-representation of any dinucleotide.