Humboldt-Universität zu Berlin

Summary

Our identity and actions are shaped by our memories and learning experiences. Long-term memory formation depends on the activity of the hippocampal pyramidal neurons. These neurons are affected in Alzheimer’s and other neuropsychiatric disorders, emphasizing the importance of understanding their function. One of the current views is that the function of pyramidal neurons depends on their capacity to form lasting changes in the connections with other neurons. However, recent evidence shows that this is also accompanied by changes in the geometry of their nuclei.

On average, a mammalian cell packs 2 meters of DNA into a 10 μm diameter nucleus, by hierarchically folding it into fibers of different sizes. Recent studies show that DNA folding is essential for cell identity and function because it determines the on/off status of genes by controlling their proximity to their regulatory elements. DNA folding is dynamic and is coordinated by a multitude of proteins, known as remodelling factors. Disruption of DNA contacts or remodelling factors leads to disease such as cancer or neuropsychiatric disorders.

In my Master’s project, I investigated a protein called SATB2 (which stands for Special AT-rich Sequence Binding Protein 2). SATB2 is a remodelling factor which is crucial for the function of pyramidal neurons. Patients with mutations in this gene present severe learning disabilities. Additionally, loss of SATB2 in the mouse brain makes the mice unable to form long-term memories, and changes the nuclear shape of their pyramidal neurons. This suggests a link between nuclear shape, DNA folding and cell function.

In my project, I have investigated the contribution of DNA folding to the function of pyramidal neurons in healthy mice and mice that are depleted for SATB2, and which cannot form memories. I was the first to produce DNA contact maps from mouse pyramidal neurons in the CA1 region of the hippocampus, without tissue dissociation. I used and further developed a novel technique for mapping 3D chromosome topologies, called Genome Architecture Mapping (GAM). I first develop the strategy to apply GAM specifically in pyramidal neurons and I identified complex DNA folding patterns which are specific to these cells and involve genomic regions containing genes that are important for their function. Comparisons between DNA folding in the healthy and the affected neurons show both conserved and changing contacts. These differences are now being investigated to identify altered genomic regions and identify target genes affected by the SATB2 depletion, to help understand the mechanisms of SATB2 syndrome. My unpublished results were also used to support a grant application for technology development to apply GAM on human brain samples, which was successful.

Altogether, this study is the first to reveal how DNA is folded in 3D in the intact nucleus of mouse hippocampal pyramidal neurons and makes the first steps in showing the connection between nuclear geometry, DNA folding and the function of pyramidal neurons in learning and memory.