Welcome to the Research Group Neural Epigenomics
Most of our brain cells (neurons) are generated before we are born and can only be replaced to a very limited extent during our lifetime. Therefore, the brain must maintain its function throughout our lives without cell replacement. Professor Tomohisa Toda and his team are trying to understand how our brain cells are maintained and how they are affected by aging and age-related diseases. To do this, the scientists use state-of-the-art imaging and sequencing techniques.
To maintain cellular function, cells must express the correct combination of genes. This process is regulated by so-called epigenetic mechanisms, which regulate the gene activity of neurons without changing their DNA sequence. Toda’s team is investigating this epigenetic regulation at different levels – from small scales such as DNA modification to large scales such as nuclear rigidity and cell nucleus geometry.
Their research addresses two main questions. First, the scientists want to investigate the fundamental mechanisms underlying the long-term maintenance of cell type-specific epigenetic regulation. They also want to ascertain how the different levels of epigenetic regulation are linked. In particular they are interested in whether and how physical information from the cell nucleus can be used as epigenetic information. The second central topic of interest to the researchers is how aging impacts the identified mechanisms. It is known that epigenetic regulation is impaired during aging, but it is not clear how. Understanding the fundamental mechanisms underlying the longevity and survival of neurons is key to preventing and forming the basis for future treatment approaches for age-related neurological diseases such as Alzheimer's.
Why is this relevant?
Aging is the primary risk factor for the development of neurodegenerative diseases (ND) such as Alzheimer’s disease. Importantly, most patients develop their diseases sporadically at an advanced age without known genetic causes, but several key pathologies are common despite heterogeneous genetic backgrounds. This indicates that there are common mechanisms caused by aging, which are yet to be identified. In-depth understanding of the biology of brain aging is indispensable to preventing and treating age-related ND.
Research Overview
Nuclear architecture in brain plasticity and aging
The brain is made up of thousands of different cell types, each of which must maintain its cellular identity and plasticity for decades. Toda’s group aims to understand how neural identity is robustly maintained over the long term by focusing on nuclear architecture, a fundamental structure in cell nuclei. Although the same amount of DNA, the blueprint of life, is stored in the nuclei, the nuclear architecture is distinct in different cell types (Fig. 1). What regulates this cell type-specific nuclear architecture? Is it important for cell type-specific epigenetic regulation? How does ageing or stress affect this nuclear architecture?
Long-lived proteins in epigenetic regulation, cellular identity and brain plasticity
Most proteins are replaced within a few days to maintain cellular homeostasis. However, some nuclear structural proteins, such as lamins or nuclear pore proteins, are not replaced for years. Thus, these stable nuclear proteins could act as a stable platform for epigenetic regulation, including nuclear architecture. Indeed, Tomohisa Toda has shown that lamins and nuclear pore proteins are critical to epigenetic regulation in adult neural stem cells in the hippocampus (Fig. 2) [Bedrosian et al., 2021; Toda et al., 2017].
Long-lived RNAs in brain maintenance and brain aging
The researchers of the Toda lab have recently identified long-lived RNAs (LL-RNAs) in the brain (Fig. 3) [Zocher et al., 2024]. Although RNA is generally considered to be an unstable molecule, their findings show that some RNA can be maintained for years (Fig. 3), challenging this dogma. Most LL-RNAs are localized in the nucleus and associated with chromatin. The team is currently investigating their biological roles, structures, and the molecular and physical causes of maintaining RNA for years.
In parallel, the scientists are investigating the link between epigenetic regulation and nuclear biophysical features. Interestingly, nuclear architecture changes with age and pathology, but its relationship to epigenetic regulation is unclear. The role of long-lived components in this context is also part of their research.
Aim of the research
Toda and his team aim to understand the mechanisms underlying the long-term maintenance of neural plasticity and age-related epigenetic dysregulation. Their focus is on the molecular and physical basis of cellular longevity and the maintenance of cognitive functions, as well as on the integrative understanding of epigenetic regulation across different levels.
Contact
Research Group Tomohisa Toda
Max-Planck-Zentrum für Physik und Medizin
Kussmaulallee 2
91054 Erlangen, Germany
Research team leader Prof. Tomohisa Toda