RIKEN discovers that maternal and paternal genomes "live separately" inside fertilized eggs

When a sperm fertilizes an egg, separate female and male pronuclei inside the fertilized egg are formed, temporarily creating a multinucleated cell. It was discovered that by having the maternal and paternal genomes intentionally exist in separate compartments, they engage in communication mediated by the cytoplasm, which allows them to maintain high developmental potential.

The discovery was made by the international joint research group including: Visiting Scientist Hirohisa Kyogoku (also Associate Professor at the Graduate School of Agricultural Science, Kobe University) and Team Director Tomoya Kitajima from the Laboratory for Chromosome Segregation, Team Director Tatsuo Shibata from the Laboratory for Physical Biology, and Team Director Yoshihiro Shimizu from the Laboratory for Cell-Free Protein Synthesis at the RIKEN Center for Biosystems Dynamics Research; Team Director Azusa Inoue from the Laboratory for Epigenome Inheritance at the RIKEN Center for Integrative Medical Sciences; and Professor Akihito Harada from the Graduate School of Medical Sciences, Kyushu University. The findings were published in the online edition of Nature.

Kyogoku noted: "Until now, it was not well understood why the mother's and father's genomes remain separated as two distinct pronuclei within a fertilized egg. By manipulating the state of fertilized eggs one by one using micromanipulation techniques, we have revealed that this 'separate living arrangement' generates intracellular competition, which maintains the conditions necessary for development. I have a sense of accomplishment as we have demonstrated a simple principle embedded in the mechanisms of life in an easy-to-understand manner."

Previous studies have shown that maternal and paternal genomes possess different histone modification states within a fertilized egg, and significant changes in these states during the early stages of development are known to be essential for proper development. However, how the spatial separation of the maternal and paternal genomes, as well as the size of the pronuclei themselves, contribute to histone modifications and embryonic development had not been experimentally verified.

To clarify the biological significance of the maternal and paternal genomes "living separately" in two pronuclei within a fertilized egg, the research group analyzed its mechanism and its impact on embryonic development.

First, using mouse eggs and sperm, the researchers artificially created "one-pronucleus" fertilized eggs in which the maternal and paternal genomes cohabited within a single pronucleus, and compared them with normal "two-pronuclei" fertilized eggs.

They found that the one-pronucleus fertilized eggs formed a single massive pronucleus that was roughly equal in volume to the sum of the female and male pronuclei in normal fertilized eggs.

Analysis of histone modification states revealed that overall histone modification levels were reduced in the one-pronucleus fertilized eggs.

To investigate how pronuclear size is controlled, the team created and analyzed fertilized eggs possessing only a single pronucleus containing either only the maternal genome or only the paternal genome. In both cases, the pronucleus grew larger than normal.

This suggested that the factor determining size is not something unique to either the maternal or paternal genome, but rather that some factor contained within the cytoplasm acts upon the pronucleus.

When they manipulated the volume of the cytoplasm to be either halved or doubled, the pronuclear size changed in accordance with the amount of cytoplasm, decreasing when the cytoplasmic volume was reduced and increasing when it was expanded.

Next, the researchers analyzed the accumulation of components that make up nuclear pores and the rate of nuclear transport. They found that more nuclear pores were formed on the male pronucleus, and its rate of material uptake into the nucleus was faster than that of the female pronucleus. In other words, the number of nuclear pores determines the size and growth rate of the pronucleus.

Further analysis revealed an inverse correlation between changes in pronuclear size and histone modification levels. Specifically, as the pronucleus grew larger, histone modification levels decreased, whereas limiting the pronuclear size to an appropriate volume maintained these histone modification levels.

The researchers then tested whether one-pronucleus fertilized eggs could develop normally into pup mice. They found that the rate of successful birth (birthrate) for one-pronucleus fertilized eggs was lower compared to normal two-pronuclei fertilized eggs.

To determine if this decline could be reversed, they temporarily introduced a second pronucleus to create a competitive state between two nuclei. This intervention suppressed the pronuclear size, restored the diminished histone modifications, and improved the birthrate. Furthermore, the developmental rate was partially recovered through drug treatments that increase histone modification levels or through the manipulation of gene expression.

"In the future, manipulating histone modification levels might contribute to assisted reproductive technologies," noted Kyogoku.

These results demonstrate that because the maternal and paternal genomes exist in separate rooms, i.e., the two pronuclei, within a fertilized egg, competition arises between the pronuclei over limited factors within the cytoplasm, thereby properly regulating pronuclear size. This size control maintains histone modification levels, supporting subsequent embryonic developmental potential.

Kitajima said: "Where does the beginning of life lie? Some say it is the moment of fertilization, others say it is when the two genomes meet, and some say it is the moment of implantation. There are many answers. Even though the maternal and paternal genomes are separated into different spaces, they engage in remote communication through cytoplasmic competition, which helps the child develop. We have discovered a fascinating spatial mechanism when it comes to thinking about the beginning of life."

Journal Information
Publication: Nature
Title: Cytoplasmic competition between separate parental pronuclei in zygotes
DOI: 10.1038/s41586-026-10417-7