Many genetic, internal and external risk factors impact the immature brain, resulting in cognitive and behavioral deficits at much later periods, with the delayed onset of symptoms often not before adulthood. Therefore, longitudinal modeling is critical in the context of neuropsychiatric disease. However, even after hundreds of studies published to date, functional genomics in the nervous system still faces a formidable barrier: Virtually all transcriptomic and epigenomic approaches currently available are cross-sectional, providing snapshots of genome function only for the time point of tissue harvest. The field is in urgent need of a toolbox that makes it feasible to pursue `retrospective functional genomics'. This would allow, for example, direct correlation of an animal's behavior in adulthood with the status of its neuronal (or glial) genomes in early life. This exploratory proposal will develop technology to map neuronal genome organization in a longitudinal context, starting with the exposure of juvenile and young adult mice to risk factors associated with long-lasting impairments in cognitive function, including subchronic treatment with NMDA receptor antagonist drugs and social isolation stress. We will map 3-dimensional genome organization and function in specific subtypes of cortical neurons, including excitatory projection neurons and inhibitory fast-spiking interneurons, and develop technology to map neuronal genome organization in a longitudinal context. Our retrospective 3D genome mapping approach is based on transient, Herpes-based vectors to express, in prefrontal cortex, chimeric constructs of bacterial Dam methyl-adenine methyltransferase, fused to synthetic DNA binding proteins anchored to cis-regulatory sequences of neuronal genes. These include Gad1 encoding GABA synthesis enzyme, Arc encoding an activity-regulated cytoskeletal protein and Bdnf encoding brain-derived neurotrophic factor. Our approach, as retrospective 3D-genome mapping, will allow us to directly correlate the animal's behavior and cognition with the spatial architectures of its neuronal genomes during the period of risk exposure dating back 3 months prior. The approaches presented here, if successful, could offer critical opportunities to explore the molecular and neuro-epigenetic underpinnings of mechanisms associated with long-lasting inter-individual variations in resilience to early life exposures and childhood adversity.
This exploratory proposal will develop technology to map neuronal genome organization in a longitudinal context, starting with the exposure of young mice to risk factors associated with long-lasting impairments in cognitive functions, including subchronic treatment with NMDA receptor antagonist drugs and social isolation stress.
| Mitchell, Amanda C; Javidfar, Behnam; Bicks, Lucy K et al. (2016) Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex. Nat Commun 7:12743 |
