Skip to main content

Control of gene expression in developing diencephalon by the transcription factor Pax6

Final Report Summary - PAXBRAIN (Control of gene expression in developing diencephalon by the transcription factor Pax6)

Among all of the genes in our genome (over 20000) only a small proportion are considered high level “controller genes” or transcription factors. These special class of genes have the ability to bind the DNA and control the expression of many other genes and molecular networks. Comprehensive studies of these genes, their downstream pathways and how they are interconnected are necessary to understand the mechanisms of brain development and the causes of neurodevelopmental diseases. Our project was focused on the study of one transcription factor called Pax6 and how it controls the embryonic development some brain structures. Although Pax6 has been extensively studied for its implication in cell cycle control and cancer, there are several regions of the brain in which its actions are totally unexplored.
Our main aim was to explore the molecular actions of Pax6 in the developing thalamus and cortex. For this we made use of high-throughput sequencing techniques and performed a screening for gene expression changes after Pax6 removal from embryonic mice.

Work performed during this project can be divided in three main phases
1. Material collection and sequencing
We dissected the brain areas of interest of controls and experimental Pax6 deficient embryonic mice, extracted the RNA and performed high throughput sequencing. This way we identified all the genes that are being made by the genome in Pax6 deficient brains versus controls.

2. Bioinformatic analysis and elaboration of the first hypothesis
By analyzing the differences in gene expression between controls and Pax6 deficient embryos, we tried to identify what biological processes might be controlled by Pax6 in the different areas. Since we identified over 3000 differentially expressed genes across conditions we explored the data with bioinformatic tools. Thanks to the quantity and quality of the data collected, we were able to elaborate some hypothesis on what are the specific molecular actions of Pax6 in the areas studied.
3. Experimental testing of most interesting hypothesis in vivo and in vitro
We performed the experimental validation and refinement of our bioinformatic predictions. For this, we looked into the brain tissue to see where those genes of interest are located and in which way the biological processes identified are disrupted in the Pax6 deficient brain.

Understanding the molecular control of embryonic brain development will help to comprehend the process of generation and maturation of new neurons and how it can be controlled. This will greatly impact in our understanding of neurodegenerative diseases (like Parkinson, Alzheimer, Huntington disease) and the generation of potential therapies as well as processes of neuroregeneration.
Overall, we have started to shed light on the roles that Pax6 is playing in some underexplored regions of the brain. Most important results and their potential impact are summarized here:
- We have observed that Pax6 not always controls gene expression in the same way. In fact, Pax6 seems to have the opposite effect on the cell cycle between different parts of the brain. Moreover, we have identified some potential molecular interactions with important signaling pathways by which Pax6 might be controlling the proliferation and specification of particular parts of the brain. The elucidation of these molecular mechanisms may impact in the study of cell proliferation and will inform related fields like stem cells and cancer.
- We have started to understand how Pax6 controls the formation of some brain connections, particularly the one that connects the thalamus with the cortex. Understanding how the brain develops its connections and why some aberrations happen will contribute towards the comprehension of some diseases that have their origin during embryonic development (neurodevelopmental diseases). Some of these diseases include complex neurological syndromes and disorder spectrums like autism, intellectual disabilities or even schizophrenia. The association between embryonic errors and the development of these disorders has been recognized but the mechanisms underlying this association remain poorly understood.
- Finally, we have generated a huge amount of gene expression data that we will release to the scientific community. This will allow hundreds of scientists around the world working on a variety of fields to use it, explore it and exploit it, greatly increasing the potential socio-economic impact of the original project.