Genomic imprinting typically lets our parents leave their mark on our genomes; however, new technological advances are now allowing us to leave our mark on imprinting! The first of our epigenetic exposés that went into print reports on how multiple modalities uncovered complex epigenetic crosstalk that regulates allele-specific gene expression at potential imprinting control regions (ICRs) in early mammalian embryos. Then, giving new meaning to editorials (!), a compelling read demonstrates how epigenetic editing can be used to modulate DNA methylation at a classic ICR to reveal the site-specific effects of this epigenetic modification.
Epigenetic Exposé Reveals How DNA and Histone Methylation Crosstalk Supports Development
Previous front-page stories from researchers led by Wenqiang Liu, Shaorong Gao, and Yong Zhang (Tongji University, Shanghai, China) revealed how H3K4me3, H3K27me3, and H3K9me3 all take distinct reprogramming paths on maternal and paternal alleles during preimplantation embryogenesis, suggesting complex interplay. Related studies revealed that crosstalk between certain histone modifications and DNA methylation affects epigenetic reprogramming during developmental processes; however, the genomic loci involved and the outcomes induced remained unknown.
This headline-grabbing mystery prompted roving reporters to explore the interdependence of H3K9me3 and DNA methylation in developing preimplantation embryos. Their article now describes allele-specific CpG-rich genomic loci with high H3K9me3 signal and DNA methylation (or CHMs) as potential ICRs, which display parent-of-origin DNA methylation patterns between two alleles and control the expression of their targeted imprinted genes.
Let’s hear all the details on this late-breaking news taking place in mouse preimplantation embryos from Yang and Colleagues:
- H3K9me3 at the two-cell stage predicts the DNA methylation status of the inner cell mass stage at CpG-rich regions
- DNA methylation guides high H3K9me3 levels at paternal-specific CHMs of the two-cell stage instead of being inherited from gametes
- These findings suggest complex crosstalk between epigenetic modifications during early embryogenesis
- Most CHMs escape DNA demethylation (thereby representing sites of DNA methylation maintenance) during preimplantation embryogenesis
- High-resolution allele-specific epigenetic mapping of CHMs in gynogenetic (two maternal genomes) and androgenetic (two paternal genomes) embryos captures over 1,200 allele-specific regions, including 19 known ICRs
- Further evaluation of the CHM-modified region identifies 22 ICR-like regions that may regulate allele-specific transcription similarly to ICRs
- The authors confirm the crucial nature of five of the 22 regions for proper mouse embryo development
What a scoop! Before, we knew of only a few genomic loci that possess epigenetic asymmetry; now, these findings demonstrate the widespread nature of these loci (based on the analysis of CHMs) and their functional importance for embryonic development.
Epigenetic Edit-orial Defines How DNA Methylation Regulates ICRs
In our second sizzling story, researchers led by Yoichi Sekita (Kitasato University, Japan) focused on new goings-on with an old favorite – the Dlk1-Dio3 imprinted domain. This “editorial” piece sought to define how DNA methylation regulates the Dlk1-Dio3-associated ICR known as the intergenic differentially methylated region (IG-DMR, which lies between Dlk1 and Meg3) using dCas9-based epigenetic editing. Typically, this ICR possesses a hypermethylated paternal allele and a hypomethylated maternal allele in embryonic stem cells (ESCs).
So, let’s read on and discover how Kojima and colleagues disclosed DNA methylation as a driver of allele-specific behavior in ESCs:
- Transient expression of dCas9-TET1 to induce hypomethylation or dCas9-DNMT3A to induce hypermethylation in ESCs shows that altered methylation at a specific region of the IG-DMR influences the imprinting status of the whole domain
- These changes result in altered imprinted gene expression and histone modification profiles
- Methylation status impacts ZFP57 transcription factor binding to motifs present in the targeted area (with DNA hypermethylation supporting ZFP57 binding)
- Modulation of methylation at other DMRs of the Dlk1-Dio3 imprinted locus fails to induce a similar effect
- These dCas9-mediated epigenomic editing findings suggest a model in which:
- Hypomethylation of the maternal IG-DMR activates Meg3 transcription, while hypermethylation of the paternal IG-DMR represses Meg3 transcription
- Expressed Meg3 incorporates into PRC2 to repress Dlk1 expression
- Demethylation of the hypermethylated paternal allele IG-DMR prompts hypomethylation of the entire region to activate Meg3 expression on the paternal allele
- Methylation of the hypomethylated maternal allele IG-DMR prompts hypermethylation of the entire region to repress maternal Meg3 expression and induce the biallelic expression of Dlk1
- Hypomethylation of the maternal IG-DMR activates Meg3 transcription, while hypermethylation of the paternal IG-DMR represses Meg3 transcription
This effectively-edited article provides evidence that DNA methylation at the IG-DMR represents the primary factor influencing allele-specific expression. Furthermore, the described epigenome-editing tools will support further studies into how DNA methylation dynamics impact essential cis-regulatory elements.
What’s Tomorrow’s News? The Next Chapters for the Epigenetic Analysis of Imprinting
These two articles provide a glimpse at the true face of imprinting by divulging the importance of various epigenetic modifications at crucial control loci, but what news will tomorrow bring?
For all the fine print regarding how epigenetic crosstalk at ICRs supports development, see Nature Cell Biology, April 2022. For more page-turning info on how DNA methylation at ICRs drives allele-specific behavior, see Nucleic Acids Research, May 2022.