Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Extensive DNA methylome rearrangement during early lamprey embryogenesis

DNA methylation (5mC) is a repressive gene regulatory mark widespread in vertebrate genomes, yet the developmental dynamics in which 5mC patterns are established vary across species. While mammals undergo two rounds of global 5mC erasure, teleosts, for example, exhibit localized maternal-to-paternal 5mC remodeling. Here, we studied 5mC dynamics during the embryonic development of sea lamprey, a jawless vertebrate which occupies a critical phylogenetic position as the sister group of the jawed vertebrates. We employed 5mC quantification in lamprey embryos and tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects ~30% of the embryonic genome and is predominantly associated with partially methylated domains. We further demonstrate that sequences eliminated during programmed genome rearrangement (PGR), are hypermethylated in sperm prior to the onset of PGR. Our study thus unveils important insights into the evolutionary origins of vertebrate 5mC reprogramming, and how this process might participate in diverse developmental strategies.

Childhood environment influences epigenetic age and methylation concordance of a CpG clock locus in British-Bangladeshi migrants

Migration from one location to another often comes with a change in environmental conditions. Here, we analysed features of DNA methylation in young, adult British-Bangladeshi women who experienced different environments during their childhoods: a) migrants, who grew up in Bangladesh with exposure to comparatively higher pathogen loads and poorer health care, and b) second-generation British-Bangladeshis, born to Bangladeshi parents, who grew up in the UK. We used buccal DNA to estimate DNA methylation-based age (DNAm age) from 14 migrants and 11 second-generation migrants, aged 18-35 years. 'AgeAccel,' a measure of DNAm age, independent of chronological age, showed that the group of women who spent their childhood in Bangladesh had higher AgeAccel (P = 0.028), compared to their UK peers. Since epigenetic clocks have been proposed to be associated with maintenance processes of epigenetic systems, we evaluated the preference for concordant DNA methylation at the luteinizing hormone/choriogonadotropin receptor (LHCGR/LHR) locus, which harbours one of the CpGs contributing to Horvath's epigenetic clock. Measurements on both strands of individual, double-stranded DNA molecules indicate higher stability of DNA methylation states at this LHCGR/LHR locus in samples of women who grew up in Bangladesh. Together, our two independent analytical approaches imply that childhood environments may induce subtle changes that are detectable long after exposure occurred, which might reflect altered activity of the epigenetic maintenance system or a difference in the proportion of cell types in buccal tissue. This exploratory work supports our earlier findings that adverse childhood environments lead to phenotypic life history trade-offs.

DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation

In mammalian embryos, DNA methylation is initialized to maximum levels in the epiblast by the de novo DNA methyltransferases DNMT3A and DNMT3B before gastrulation diversifies it across regulatory regions. Here we show that DNMT3A and DNMT3B are differentially regulated during endoderm and mesoderm bifurcation and study the implications in vivo and in meso-endoderm embryoid bodies. Loss of both Dnmt3a and Dnmt3b impairs exit from the epiblast state. More subtly, independent loss of Dnmt3a or Dnmt3b leads to small biases in mesoderm-endoderm bifurcation and transcriptional deregulation. Epigenetically, DNMT3A and DNMT3B drive distinct methylation kinetics in the epiblast, as can be predicted from their strand-specific sequence preferences. The enzymes compensate for each other in the epiblast, but can later facilitate lineage-specific methylation kinetics as their expression diverges. Single-cell analysis shows that differential activity of DNMT3A and DNMT3B combines with replication-linked methylation turnover to increase epigenetic plasticity in gastrulation. Together, these findings outline a dynamic model for the use of DNMT3A and DNMT3B sequence specificity during gastrulation.

Epigenetics and its therapeutic potential in colorectal cancer

It is estimated that colorectal cancer (CRC) is the leading cause of cancer-related death around the globe. 'Epigenetics' refers to changes in the chromosome rather than the DNA sequence, which may be transmitted down to daughter cells. Epigenetics is an essential part of controlling the development and variation of a single cell. ncRNAs have a role in epigenetic regulation in CRC, which will be discussed in this review in the context of DNA methylation and histone modifications. A greater survival rate for CRC patients might be achieved by addressing epigenetic mediators, as the authors show. In this review, they aim to thoroughly examine the role of epigenetics in the prognosis, diagnosis and treatment of CRC.

DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift.

Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.

Hairpin-Bisulfite PCR

Ligation of a hairpin oligonucleotide to genomic DNA prior to bisulfite conversion and PCR amplification physically links the two complementary DNA strands. This additional step in the conversion procedure overcomes the limitations of conventional bisulfite sequencing where information of the cytosine methylation status is only obtained from one of the two strands of an individual DNA molecule. Sequences derived from hairpin bisulfite PCR products reveal the dynamics of this epigenetic memory system on both strands of individual DNA molecules. The chapter describes a reliable step-by-step procedure to generate hairpin-linked DNA. It also provides a guide for efficient bisulfite conversion that is suitable for both conventional and hairpin bisulfite sequencing approaches.

Mitotic inheritance of DNA methylation: more than just copy and paste

Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

Propagation of clonal regulatory programs contributes to cancer development. It is poorly understood how epigenetic mechanisms interact with genetic drivers to shape this process. Here, we combine single-cell analysis of transcription and DNA methylation with a Luria-Delbrück experimental design to demonstrate the existence of clonally stable epigenetic memory in multiple types of cancer cells. Longitudinal transcriptional and genetic analysis of clonal colon cancer cell populations reveals a slowly drifting spectrum of epithelial-to-mesenchymal transcriptional identities that is seemingly independent of genetic variation. DNA methylation landscapes correlate with these identities but also reflect an independent clock-like methylation loss process. Methylation variation can be explained as an effect of global trans-acting factors in most cases. However, for a specific class of promoters-in particular, cancer-testis antigens-de-repression is correlated with and probably driven by loss of methylation in cis. This study indicates how genetic sub-clonal structure in cancer cells can be diversified by epigenetic memory.

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity

DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in mouse embryonic stem cells. We find that enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state DNA methylation. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils a genome-scale map of methylation kinetics, revealing highly variable and context-specific activity for the DNA methylation machinery.

UHRF1-repressed 5'-hydroxymethylcytosine is essential for the male meiotic prophase I

5’-hydroxymethylcytosine (5hmC), an important 5’-cytosine modification, is altered highly in order in male meiotic prophase. However, the regulatory mechanism of this dynamic change and the function of 5hmC in meiosis remain largely unknown. Using a knockout mouse model, we showed that UHRF1 regulated male meiosis. UHRF1 deficiency led to failure of meiosis and male infertility. Mechanistically, the deficiency of UHRF1 altered significantly the meiotic gene profile of spermatocytes. Uhrf1 knockout induced an increase of the global 5hmC level. The enrichment of hyper-5hmC at transcriptional start sites (TSSs) was highly associated with gene downregulation. In addition, the elevated level of the TET1 enzyme might have contributed to the higher 5hmC level in the Uhrf1 knockout spermatocytes. Finally, we reported Uhrf1, a key gene in male meiosis, repressed hyper-5hmC by downregulating TET1. Furthermore, UHRF1 facilitated RNA polymerase II (RNA-pol2) loading to promote gene transcription. Thus our study demonstrated a potential regulatory mechanism of 5hmC dynamic change and its involvement in epigenetic regulation in male meiosis.

Hemimethylation of CpG dyads is characteristic of secondary DMRs associated with imprinted loci and correlates with 5-hydroxymethylcytosine at paternally methylated sequences

BACKGROUND

In mammals, the regulation of imprinted genes is controlled by differential methylation at imprinting control regions which acquire parent of origin-specific methylation patterns during gametogenesis and retain differences in allelic methylation status throughout fertilization and subsequent somatic cell divisions. In addition, many imprinted genes acquire differential methylation during post-implantation development; these secondary differentially methylated regions appear necessary to maintain the imprinted expression state of individual genes. Despite the requirement for both types of differentially methylated sequence elements to achieve proper expression across imprinting clusters, methylation patterns are more labile at secondary differentially methylated regions. To understand the nature of this variability, we analyzed CpG dyad methylation patterns at both paternally and maternally methylated imprinted loci within multiple imprinting clusters.

RESULTS

We determined that both paternally and maternally methylated secondary differentially methylated regions associated with imprinted genes display high levels of hemimethylation, 29-49%, in comparison to imprinting control regions which exhibited 8-12% hemimethylation. To explore how hemimethylation could arise, we assessed the differentially methylated regions for the presence of 5-hydroxymethylcytosine which could cause methylation to be lost via either passive and/or active demethylation mechanisms. We found enrichment of 5-hydroxymethylcytosine at paternally methylated secondary differentially methylated regions, but not at the maternally methylated sites we analyzed in this study.

CONCLUSIONS

We found high levels of hemimethylation to be a generalizable characteristic of secondary differentially methylated regions associated with imprinted genes. We propose that 5-hydroxymethylcytosine enrichment may be responsible for the variability in methylation status at paternally methylated secondary differentially methylated regions associated with imprinted genes. We further suggest that the high incidence of hemimethylation at secondary differentially methylated regions must be counteracted by continuous methylation acquisition at these loci.

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice

Exposure to environmental stressors is known to increase disease susceptibility in unexposed descendants in the absence of detectable genetic mutations. The mechanisms mediating environmentally-induced transgenerational disease susceptibility are poorly understood. We showed that great-great-grandsons of female mice exposed to tributyltin (TBT) throughout pregnancy and lactation were predisposed to obesity due to altered chromatin organization that subsequently biased DNA methylation and gene expression. Here we analyzed DNA methylomes and transcriptomes from tissues of animals ancestrally exposed to TBT spanning generations, sexes, ontogeny, and cell differentiation state. We found that TBT elicited concerted alterations in the expression of “chromatin organization” genes and inferred that TBT-disrupted chromatin organization might be able to self-reconstruct transgenerationally. We also found that the location of “chromatin organization” and “metabolic” genes is biased similarly in mouse and human genomes, suggesting that exposure to environmental stressors in different species could elicit similar phenotypic effects via self-reconstruction of disrupted chromatin organization.

Methylation dynamics during the maternal-to-zygotic genome transition in dioecious species

The starting point of a new generation in sexually reproducing species is fertilization. In many species, fertilization is followed by cell divisions controlled primarily by maternal transcripts, with little to no zygotic transcription. The activation of the zygotic genome (ZGA) is part of a process called maternal-to-zygotic transition (MZT), during which transcripts from the zygotic genome take control of development, setting the conditions for cellular specialization. While we know that epigenetic processes (e.g. methylation) are involved in the MZT, their roles and interplay in the transition are largely unknown. I developed a model and used simulations to elucidate the interaction between possible epigenetic processes, namely methylation processes, involved in the MZT. The model focuses on the dynamics of global methylation levels and how these interact with factors such as a parental repressor and the nucleocytoplasmic ratio to trigger the ZGA, followed by development from fertilization to adulthood. In addition, I included transgenerational effects transmitted to the zygote from both parents through their gametes to show that these may set the stage for plastic developmental processes. I demonstrate that the rates of maintenance methylation and demethylation, which are important for the achievement of the final methylation levels of an individual, exhibit a certain level of flexibility in terms of parameter values. I find that high final methylation levels require more restricted combinations of parameter values. The model is discussed in the context of the current empirical knowledge and provide suggestions for directions of future empirical and theoretical studies.