Emerging research has provided evidence for the critical importance of the inheritance of epigenetic states, whether that be DNA methylation, histone modifications, or even non-coding RNAs. Now, three recent studies focusing on the mechanism involved in passing down this information from parental to daughter cells while they replicate their DNA and divide in vitro provide evidence that the epigenetic inheritance of DNA methylation and histone modification profiles lies in a state somewhere between symmetry and instability.
The Unfaithful Inheritance of DNA Methylation Turns an Epigenetic Rock into a Source of Instability
Many see DNA methylation as an epigenetic rock, steadfast and sure when faced with the dynamic nature of the nuclear ocean; however, a new study reports that behind that stony façade, the unfaithful long-term inheritance of DNA methylation at intermediately methylated CpG sites suggests a degree of epigenetic instability.
Studies have reported that intermediately methylated CpGs spontaneously arise within subclonal cultures, while errors in maintenance/spontaneous de novo methylation may explain the inconsistent inheritance of intermediately methylated CpGs after cell division. A well-balanced team led by Felipe Karam Teixeira and Anne Ferguson-Smith (University of Cambridge) knew of models that explained intermediate DNA methylation inheritance through cell division; however, genome-wide intermediate DNA methylation and the principles underlying inherited DNA methylation stability remained relatively unstudied. A scientifically sound study by these rock-solid researchers provides evidence for the unfaithful clonal inheritance of intermediately methylated CpGs.
Hay and colleagues conducted a genome-wide analysis of DNA methylation via target DNA capture followed by high-throughput bisulfite sequencing (tcBS-seq) on mouse embryonic fibroblasts and subclones and found that:
- Intermediately methylated CpGs undergo unfaithful and probabilistic propagation
- Low-fidelity, intermediately methylated CpGs display enrichment in regions of low CpG density, do not undergo coordinated maintenance between neighboring sites and occur interspersed throughout the genome and within genes with no/low transcriptional activity (making any functional interpretations unreliable)
- The probabilistic increase in DNA methylation occurring at intermediately methylated sites may derive from the de novo function of DNMT1 activity but not DNMT3A/3B activity
- The probabilistic nature of DNA methylation changes at intermediate sites implies a weighted directionality of methylation inheritance during clonal expansion
- For example, a 70% methylated CpG in parental cells is more likely to gain and retain methylation during clonal expansion, while a 30% methylated CpG has a higher likelihood of losing methylation
These results illustrate that unfaithful maintenance of intermediate DNA methylation induces epigenetic instability, a finding that challenges the long-standing assumption that the entire DNA methylation landscape undergoes faithful mitotic inheritance and has implications for our current models of epigenetic inheritance.
Symmetrical Studies Reveal How the Symmetric Inheritance of Histones Keeps Stem Cell Fate in Balance!
While DNA methylation stability and faithful inheritance may have taken a hit, an epigenetic dyad of studies paints a different picture regarding histone modifications. Indeed, some almost perfectly symmetrical findings report that the faithful epigenetic inheritance of balanced histone modification profiles during the cell cycle underpins mammalian stem cell fate.
In the first of this perfect pair of related research findings, a team led by Robin Andersson, Joshua M. Brickman, and Anja Groth (University of Copenhagen) sought to explore how histone modification inheritance via the symmetrical segregation of parental histones to daughter DNA strands during replication sustains the epigenome and impacts stem cell fate. The authors employed mouse embryonic stem cells (mESCs) carrying mutations in the MCM2 protein that induce the asymmetric inheritance of parental histones into daughter strands without affecting DNA replication and applied variations on sister chromatids after replication (SCAR)-seq, quantitative ChIP–seq, mass spectrometry, and RNA-seq.
Let’s hear more from Wenger, Biran, Alcaraz, Redó-Riveiro, and Colleagues on how perfect symmetry during faithful epigenetic inheritance keeps stem cells in balance:
- Asymmetric recycling of modified histones H3-H4 in mutant mESCs results in sister-chromatid imbalances that become transmitted to daughter cells, which causes global and local redistribution of H3K27me3 and H3K9me3
- The unspecific deposition of histone modifications during asymmetric recycling suggests that correct histone recycling limits spurious enzyme activity
- Symmetric histone recycling may reduce noise, focus histone-modifying enzyme activity, and ensure balanced chromatin restoration
- The loss of H3K9me3 derepresses the expression of repeat elements, while the alteration of H3K27me3 at bivalent promoters correlates with the deregulated expression of developmental genes
- Gene expression changes reduced cell plasticity, with pluripotent states becoming favored over lineage priming, which leads to an overall reduction in developmental competence
- Overall, a diminishment of developmental competence correlates with impaired exit from pluripotency
- The restoration of symmetric histone recycling rescues both molecular and developmental phenotypes, which suggests that balanced inheritance in each cell cycle maintains a fine-tuned epigenome that supports ESC plasticity
In the second of this delightful duo of almost symmetrical studies, a team led by Haiyun Gan (Chinese Academy of Sciences/St. Jude Children’s Research Hospital) sought to explore a similar research aim; in their study, the team employed either MCM2 mutant or MCM2-mutant/POLE3-deleted mESCs to perturb symmetric parental histone inheritance during DNA replication and discovered complementary findings. In this study, the authors applied single-cell CUT&Tag and RNA-seq with lineage barcoding.
Let’s hear more on how symmetrical histone modification inheritance keeps stem cell fate in balance from Wen, Zhou, Tian, Li, Song, and Colleagues:
- mESCs displaying asymmetrical parental histone inheritance and aberrant histone landscapes do not correctly differentiate towards the neural lineage in response to the appropriate differentiation signals
- Therefore, daughter mESCs that inherit aberrant histone modification profiles suffer from altered fate
This pair of almost symmetrical studies reveals how the faithful inheritance of histone modification profiles helps to keep stem cells in balance. Our first study reports how the symmetrical inheritance of balanced histone H3-H4 modifications helps to maintain the chromatin environment underpinning the identity of mESCs, while our complimentary second study highlights the ability of symmetrical parental histone allocation during DNA replication to contribute to mammalian cell fate choice during differentiation by regulating H3K27me3 restoration.
Entering a State Somewhere Between Symmetry and Instability
For more on how the unfaithful maintenance of intermediate DNA methylation leads to epigenetic instability, see Nature Communications, September 2023; while for more details regarding how the epigenetic inheritance of histone modifications keeps stem cells in balance, check out these perfectly symmetrical studies from Wenger, Biran, Alcaraz, Redó-Riveiro, and Colleagues and Wen, Zhou, Tian, Li, Song, and Colleagues, both from Nature Genetics, September 2023.