Awakening the genome

Researchers from the Tachibana lab show that the pioneer factor Nr5a2 can awaken the inactive genome in the early embryo. Part of this work was carried out at IMBA before the Tachibana lab moved to the Max Planck Institute of Biochemistry (MPIB). The findings are published in Science.

The beginning of life is a fascinating process in biology. The female egg cell is fertilized through fusion with the male sperm cell. From this first cell of an embryo, the entire organism can develop. What molecular processes take place in the DNA of a fertilized egg to enable this cell to have the potential to generate a new organism? Kikuë Tachibana, director at MPIB and head of the research department ‘Totipotency’ and former junior group leader at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), is investigating this question together with her research team using the mouse model.

It is known that so-called pioneer factors bind to specific areas of inactive DNA to activate them. Finding out which factors these are in the case of fertilized oocytes was the subject of the current study. For this research, it took a multi-disciplinary effort of the four first authors and their complementary expertise. “The core team of this work consists of experts in embryology, biochemistry, bioinformatics, microscopy, and genomics. Together we were able to see hints in the genome, discover the transcription factor Nr5a2 and study the mechanism inside and outside of cells,” says Tachibana.

From DNA to Proteins

The fundamental building blocks of DNA - adenosine, thymine, guanine, and cytosine - encode the blueprints of all proteins occurring in the organism like in a library. Through a process called transcription, certain DNA regions, also called genes, are read and transcribed into messenger RNA (mRNA). Subsequently, proteins are produced based on mRNA instruction. Cellular structures, channels, signaling molecules, or molecular machines among others are built according to these molecular messages.

Siwat Ruangroengkulrith, molecular biologist and bioinformatician, explains, “The genetic information is not simply freely accessible in the cell nucleus. It is present in the form of a long DNA thread wrapped around small packaging proteins, known as histones, like a string of pearls. DNA and histones are twisted into each other to such an extent that the DNA thread is shortened up to 40,000 times. That is why we can see DNA as chromosomes under the microscope, all because of this compaction by histones.”

Pioneer factor Nr5a2

Pioneer factors can bind to tightly packed DNA. They belong to the large family of transcription factors. They bind to specific sequence patterns on the DNA to transcribe the gene sequence. Imre Gáspár, an expert in microscopy and bioinformatics, explains: “We searched for a common sequence pattern for the early-stage mRNA molecules produced in embryos and were able to find several sequence motifs. The discovered motifs are close to each other and form a so-called super motif. The newly discovered super motif resembles the known sequence motif SINE B1 element and is very closely related to the highly conserved ALU element in the human genome. These elements are also known as ‘jumping genes’ because they can move from one position to another position in the genome at certain cellular stages, such as in the early embryo.”

Nr5a2 binds to this super motif. Johanna Gassler, an embryologist, explains, “Originally, Nr5a2 was discovered in the liver. In the field of developmental biology, Nr5a2 was known to be important at the late stage of embryo implantation. How important Nr5a2 is directly after fertilization was not yet known. In our experiments, we were able to show that the majority of early embryonic mRNA molecules are no longer produced once Nr5a2 has been blocked. Furthermore, the embryos are inhibited in their further development. This shows that Nr5a2 plays a central role in the earliest stage of embryo development.”

Using the latest biochemical and genomic methods, the researchers have tested how Nr5a2 functions during early development. Wataru Kobayashi, a biochemist, explains, ‘We have experimentally shown that Nr5a2 can open inactive DNA regions, making more areas of DNA accessible for subsequent transcription processes.’ Thus, the genome is activated at the two-cell stage, and an embryo, and eventually a fully viable organism, can develop.

Tachibana, looking to the future, “The discovery that Nr5a2 is a key factor driving genome awakening is an important stepping stone towards achieving a mechanistic understanding of the start of life. It is equally clear that there must be other contributing factors that remain to be identified. So far, our work provides a conceptual framework ‘ex uno plura’, (lat. many from one), that can explain how the transcriptional activation occurs robustly in early embryos to ensure development into a whole organism.”