Deregulation of 3D genome structure in models of memory and learning disability

• Applicant: Professorin Ana Pombo, Ph.D.
• Subject Area: General Genetics and Functional Genome Biology ; Bioinformatics and Theoretical Biology ; Developmental Neurobiology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 508057632

Chromatin regulators are often mutated in developmental disorders accompanied by neurological impairments. For example, intellectual disability is associated with mutations in chromatin proteins with diverse functions, such as CTCF, ATRX and SATB2. Depletion of either factor in post-mitotic pyramidal neurons, using conditional knockout (cKO) mouse models, results in eletrophysiological dysfunction and impairs hippocampal-related learning and long-term memory in fear-based experiments. However, the direct effects of CTCF, SATB2 and ATRX loss on chromatin regulation and the affected genes remain to be investigated.Here, we propose to dissect the consequences CTCF, ATRX or SATB2 loss in vivo, directly in pyramidal glutamatergic neurons of the mature murine hippocampus. We will use state-of-the-art methodologies, Genome Architecture Mapping (GAM), to map 3D chromatin structure, and 10x Genomics multiome, to profile both gene expression and chromatin accessibility in single cells. We will deliver an atlas of cKO-affected regulatory regions for all hippocampal cells, and the landscape of altered chromatin contacts. We will map the changes in chromatin structure genome-wide at different levels of 3D genome organization, and the transcription factors and chromatin regulatory pathways underlying the altered gene expression and 3D genome folding. We will focus on changes in chromatin structure and gene expression common to the three mutants, to identify candidate pathways involved in the learning and memory dysfunctions. We will validate genes affected in all cKOs, as these provide candidate targets with potential for intervention to ameliorate learning disabilities. Ultimately, we also aim to advance our knowledge of chromatin regulation in specialized post-mitotic neurons. Our hypothesis is that the inception of hippocampal dysfunction in learning disabilities is rooted in chromatin dysfunction mechanisms, and expect to develop a framework that can be adopted to accelerate the evaluation human patient samples.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2202: Spatial Genome Architecture in Development and Disease
• Co-Investigator: Dr. Alexander Kukalev