High-resolution mapping of embryonic genome activation unveils a decoupling of transcription activation from precocious H3K4me3 removal.
Science Advances 7 August 2026
10.1126/sciadv.aec9545
How embryos switch on their genome
Researchers at EMBL Rome developed a precision in vitro fertilisation protocol to obtain unprecedented insight into embryonic genome activation in mammals. Their work reveals previously unknown patterns in genes activated during the earliest moments of mammalian development
A new study from EMBL Rome shows how embryos precisely coordinate gene activity during early development.
Shortly after fertilisation, the newly formed embryo faces a remarkable challenge: it must switch from relying on molecules supplied by the mother to using its own genome. This process, known as embryonic genome activation (EGA), is one of the earliest and most important steps in development.
EGA has been studied in detail in model systems such as the fruit fly and zebrafish. However, data from mammals are relatively scarce. This is because mammalian embryos are difficult to access and hard to analyse regularly over time.
Researchers in Ana Boskovic’s group at EMBL Rome developed a precision in vitro fertilisation (IVF) protocol in mice to precisely control when fertilisation occurs. They combined this technique with the analysis of gene activity in individual embryos at several time points during early development. This allowed them to obtain an unprecedented high-resolution view of embryonic genome activation.
The work was published in Science Advances and shows that even embryos that look identical can contain vastly different RNA landscapes, depending on slight differences in their developmental timing (time after fertilisation). Moreover, the study provides a comprehensive resource detailing the gradual gene expression changes that occur during embryonic genome activation.
The embryo’s genome gradually takes control
The team followed the embryos over a nine-hour period and found extensive changes in their gene activity. As the embryo’s own genome became increasingly active, RNA inherited from the mother was gradually depleted. This switch from maternal provisions to embryonically derived molecules was marked by an increase in activation of genes involved in processes such as RNA production, protein synthesis, and ribosome construction.
At the same time, the early embryo undergoes widespread changes to its epigenome – the system that helps control which genes are switched on or off and modulate their expression levels. These include resetting chemical tags on proteins called histones, as well as removing and rebuilding DNA methylation patterns, contributing to gene regulation during EGA. However, because many changes take place at the same time, determining which ones are directly contributing to genome activation is difficult.
“We were particularly interested in a chemical modification of histone proteins called H3K4me3,” said Jasmina Al-Mousawi, former PhD student in the Boskovic group and lead author of the publication. “Previous research had suggested that the inheritance of specific patterns of this modification from the mother might contribute to keeping genes off. Using our precision-IVF approach, we could see that this modification is removed at the same time as the genome is activated. We were therefore interested in whether these processes are causally linked.”
Looking for the molecular switch
To test this idea, the researchers increased the activity of an enzyme, which removes H3K4me3 from histones. This caused the modification to be removed earlier than it normally would be.
Surprisingly, early H3K4me3 removal had only a modest effect on gene activity and did not cause the embryonic genome to switch on earlier. The embryos with H3K4me3 removed continued through embryonic genome activation and developed into blastocysts at rates comparable to control embryos.
These observations imply that the presence of this specific histone modification on the genome is not the molecular feature keeping the genome silent.
“One of the most important findings is how resilient to perturbations the early embryo appears to be,” said Ana Boskovic. “Even when an abundant chromatin modification was removed prematurely, the embryos were still able to progress through this critical developmental transition without major adverse outcomes.”
The detailed dataset emerging from this study provides a useful framework for understanding the earliest stages of mammalian development and for investigating how changes in the embryonic epigenome influence development, and ultimately, phenotype.
The study also shows how flexible gene regulation is in early embryos, and could inspire and enable researchers to precisely assess the quantitative impact of different perturbations on the process of genome activation. Together, the findings point towards a more complex picture of the earliest moments of embryonic development, in which the genome is switched on through a coordinated and flexible process rather than by a single molecular trigger.
