A significant breakthrough challenges longstanding beliefs about DNA replication. This study reveals that DNA replication during early embryonic development differs from previous understanding and entails a phase of instability that increases the risk of chromosomal copying errors. Since chromosomal abnormalities are often linked to miscarriages and developmental issues, these findings could greatly influence reproductive medicine, potentially leading to enhanced in vitro fertilization (IVF) practices.
A groundbreaking study by scientists at the RIKEN Center for Biosystems Dynamics (BDR) in Japan challenges established ideas about DNA replication. Spearheaded by Ichiro Hiratani and his team, the research published on August 28 in Nature indicates that DNA replication in early embryos is distinct from traditional views and includes a period marked by instability and susceptibility to chromosomal copying errors. Given that chromosomal abnormalities frequently contribute to miscarriages and developmental disorders, these insights may reformulate approaches in the field of reproductive medicine, potentially enhancing techniques for in vitro fertilization (IVF).
In the embryo development process, the fertilized egg divides repeatedly, and every new batch of daughter cells also divides. By the third day post-fertilization, the embryo has completed three divisions, resulting in 16 cells. Each division corresponds with DNA replication, guaranteeing that every daughter cell inherits a copy of the entire genome. In their research, the RIKEN BDR team aimed to identify the characteristics of DNA replication in early embryos. They utilized an innovative single-cell genomics method known as scRepli-seq and applied it to developing mouse embryos. This technique allowed them to capture single-cell DNA snapshots at various points during the replication process. Their findings contradicted prior scientific beliefs about DNA replication in embryos.
“We discovered several specialized forms of DNA replication during early mouse embryogenesis, which had not been observed before,” explains Hiratani. “We also noted that at certain stages, genomic DNA experiences temporary instability, leading to elevated chromosomal aberrations.”
Traditionally, it is understood that DNA does not replicate all at once. Instead, specific regions of a chromosome are duplicated in a defined order. The team’s initial discovery was that the replication-timing domains found in mature cells do not develop until an embryo has reached the 4-cell stage. Thus, in 1- and 2-cell embryos, DNA is replicated uniformly rather than sequentially, distinguishing them from other body cells.
As a segment of a chromosome unravels for replication, it creates a structure resembling a fork in the road. For replication to advance, the fork must progress along the DNA strand, re-zipping replicated regions and unzipping the next section. The investigation’s second key finding was that the speed of the fork is considerably slower during the 1-, 2-, and 4-cell stages compared to after the 8-cell stage of embryonic development. The 4-cell embryo is thus seen as a transitional point where uniform DNA replication shifts to a sequential process, while still exhibiting the slow fork movement typical of 1- and 2-cell embryos. Conversely, 8-cell embryos replicate more similarly to mature cells, showcasing sequential replication and faster fork movement.
During the initial days following fertilization, errors in DNA replication can lead to chromosomal irregularities such as extra or missing copies, breaks, or incomplete copies. Some of these replication errors result in miscarriages, while others are linked to developmental disorders like Down Syndrome, also referred to as trisomy 21. The team’s third crucial finding was that the occurrence of chromosomal copying errors was temporarily heightened in early embryos, particularly at the 4-cell stage.
Using scRepli-seq once more, the researchers aimed to identify chromosome copy number abnormalities. They observed very few errors during the transitions between the 1- and 2-cell stages or between the 8- and 16-cell stages. However, about 13% of cells exhibited chromosomal abnormalities during the shift between the 4- and 8-cell stages, likely stemming from copying errors at the 4-cell stage. Additional tests suggested that these errors were associated with the slow-moving replication forks at that stage.
“Our findings raise numerous new questions,” Hiratani states. “For instance, are these phenomena evolutionarily preserved in other species, including humans? And what happens to cells with chromosomal abnormalities afterwards?” This discovery, aside from directing future foundational research, has the potential to assist fertility clinics in developing more effective strategies to reduce chromosomal abnormalities that are prevalent in the initial days after fertilization.
