The DNA molecule is not naked in the nucleus. Instead, it is folded in a highly organized fashion using different proteins to establish a unique spatial organization of genetic information. This 3D spatial organization of the genome is fundamental for the regulation of our genes and must be established de novo by each individual during early embryogenesis. Researchers from the MPI of immunobiology and epigenetics in Friborg in collaboration with colleagues from the Friedrich Mischer Institute in Basel are now revealing a still unknown and critical role of the HP1a protein in the reorganization of the 3D genome after fertilization. The study published in the scientific journal Nature identifies HP1a as an epigenetic regulator involved in establishing the overall structure of the genome in the first Drosophila embryo.
The information of the human genome is encoded by approximately 3 billion base pairs of DNA and packaged into 23 pairs of chromosomes. If all the chromosomes could be disentangled and aligned linearly, they would be a thin wire of about 2 meters. The DNA molecule must be largely conditioned to fit inside the nucleus, which is on the order of micrometers in size. “The DNA strand is not simply inserted into the nucleus of the cell. Instead, it’s folded in a very organized fashion to ensure that different parts of the genome, sometimes several thousand base pairs apart from each other, can communicate with each other for appropriate genetic functions. says Nicola Iovino, group leader at the MPI Immunobiology and Epigenetics in Friborg.
Part of this packaging is made up of histone proteins acting as coils around which DNA is wrapped and thus compacted. This complex of DNA and proteins is called chromatin. As such, chromatin is the foundation for further conditioning of genetic material into chromosomes, the structure of which is primarily known for its characteristic cross shape. The chromosomes themselves occupy distinct positions in the nucleus, called chromosomal territories, which also allow efficient conditioning and organization of the genome.
All the machines contributing to this organization of 3D chromatin remain unexplored. Nicola Iovino’s laboratory at the MPI in Friborg, in collaboration with Luca Giorgetti from the Friedrich Miescher Institute in Basel (Switzerland), was able to show the fundamental role of the protein of heterochromatin 1a (HP1a) in the reorganization of the 3D chromatin structure after fertilization. By combining the powerful genetics of Drosophila with 3D modeling of the genome, they discovered that HP1a is required to establish an appropriate 3D chromatin structure at several hierarchical levels during early embryonic development.
The first embryos as a model for studying chromatin reprogramming
The degree of packaging as well as the corresponding gene activity is influenced by epigenetic modifications. These are small chemical groups that are installed on histones. “The proteins that make these epigenetic modifications can be considered to be writers, erasers or readers of the given epigenetic modification. We have discovered that the HP1a read protein is necessary to establish chromatin structure during early embryonic development in Drosophila, ”explains Fides Zenk, first author of the study.
Early embryonic development is a particularly interesting time window for studying the processes governing the organization of chromatin. During fertilization, two highly specialized cells – the sperm and the egg – merge. The resulting totipotent zygote will eventually give rise to all of the different cells in the body. Interestingly, most of the epigenetic changes that shape chromatin are erased and need to be established de novo. In Drosophila, the laboratory of Nicola Iovino had previously shown that after fertilization, the chromatin undergoes major restructuring events. It is therefore the ideal model system to study the processes underlying the establishment of chromatin structure.
De novo implementation of the architecture of the 3D genome
When the zygote genome is first activated after fertilization, it triggers a global de novo 3D chromatin reorganization comprising a clustering of strongly compacted regions around the centromere (pericentromer), folding of chromosomal arms and chromosome segregation. in assets and inactive compartments. “We have identified HP1a as an important epigenetic regulator necessary to maintain the integrity of individual chromosomes, but also central to establishing the overall structure of the genome in the early embryo,” explains Nicola Iovino.
3D genome simulation
These findings and data collected in Drosophila embryos were then used by collaborators at the Friedrich Miescher Institute (FMI) led by Luca Giorgetti to build realistic three-dimensional models of chromosomes. This is possible because the chromosomes inside the cell nucleus are polymers, very large molecules made up of chains of smaller components (monomers) – in this case consecutive DNA base pairs and binding proteins. to DNA that together make up the chromatin fiber. Like all other polymers, be it silk, polyethylene or polyester, chromatin obeys a general set of physical laws described by a branch of physics called “polymer physics.” These laws can be encoded in computer programs and used to simulate the three-dimensional shape of chromosomes in the nucleus.
“The advantage of this approach is that it allows the effects of a very large number of mutations to be simulated. This allows researchers to explore scenarios that are beyond experimental scope, such as the simultaneous depletion of many proteins. by comparing the simulations to the results of experiments, this approach also makes it possible to test alternative hypotheses concerning the mechanisms which are the basis of the experimental observations ”, explains Luca Giorgetti, group leader at the Friedrich Miescher Institute in Basel.
In this case, the IMF researchers used polymer models of the entire Drosophila genome to ask the question: Based on the basic laws of polymer physics, is it possible that the depletion of d ‘a single protein – HP1 – causes a massive change in associations and forms chromosomes in the nucleus? Or are additional mechanisms needed to explain the experimental observations? “We found that the removal of the protein at its binding sites in the simulations represented the full set of experimental results, thus providing further confirmation that HP1 plays a key role in establishing the three-dimensional structure of the genome.” , explains Yinxiu Zhan, co-first author of the study.