Title: From 3D genomes to neural connectomes: Higher-order chromatin mechanisms encoding long- term memory Summary The Cremins Lab focuses on higher-order genome folding and how classic epigenetic modifications work through long-range, spatial mechanisms to govern genome function in the developing brain. Much is already known regarding how transcription factors work in the context of the linear genome to regulate gene expression. Yet, severe limitations exist in our ability to engineer chromatin in neural circuits to correct synaptic defects in vivo. At the lab’s inception, it remained unclear whether and how genome folding would functionally influence cell type-specific gene expression. Thus far, we have developed and applied new molecular and computational technologies to discover that nested chromatin domains and long-range loops undergo marked reconfiguration during neural lineage commitment, somatic cell reprogramming, neuronal activity stimulation, and in repeat expansion disorders. We have demonstrated that loops induced by cortical neuron stimulation, engineered through synthetic architectural proteins, and miswired in fragile X syndrome were tightly connected to transcription, thus providing early insight into the genome’s structure-function relationship. We will now focus on a fundamental mystery in neuroscience: how memory is encoded over decades despite rapid turnover of synaptic proteins/RNAs. We hypothesize that the 3D genome integrates molecular traces of synaptic plasticity written on chromatin to store long-term memory in neural circuits. We will employ single-cell genomics and imaging technologies to dissect the extent to which individual synaptic inputs create 3D epigenetic traces. We will perform genome-wide CRISPR screens to identify specific loops and epigenetic modifications functionally important for synaptic plasticity. We will also re-direct technologies used for genome architecture mapping to create molecular activity-dependent connectome maps, and computationally integrate neuronal connectome maps across length scales with 3D epigenetic data sets. Successful completion of this work will shed new light on the genetic and epigenetic mechanisms governing structural and functional synaptic plasticity in physiologically relevant in vitro and in vivo models of memory encoding and consolidation. Many neurological disorders exhibit synaptic defects, and alterations in neuronal activity-dependent gene expression underlie pathological neural phenotypes. Addressing this knowledge gap will provide an essential foundation for our long-term goals to understand how, when, and why pathologic genome misfolding leads to synaptic dysfunction, and to engineer the 3D genome to reverse pathologic synaptic defects in debilitating neurological diseases.

Public Health Relevance/Narrative Emerging evidence indicates that epigenetic mechanisms are centrally linked to the development of the mammalian central nervous system and go awry in neurological disorders. Here, we unravel the functional link between long-range 3D genome folding patterns and synaptic plasticity during the encoding of long-term memory in the mammalian brain. Because many key neurological disorders are thought to be diseases of the synapse, successful completion of this work will provide a foundation for future studies unraveling the role for misfolded genome topology on the onset and progression of neurodevelopmental and neurodegenerative disorders.