Post-mitotic neurons in the mammalian brain form synapses that dynamically remodel throughout an individual?s lifetime to encode short- and long-term memories. Synaptic plasticity involves spatiotemporal fine- tuning of gene expression levels in response to environmental stimuli, including rapid transcription of immediate early genes on the time scale of minutes and longer-term global chromatin remodeling. The cis- acting genetic and epigenetic elements that govern activity-dependent expression are of outstanding interest towardunderstandinghowexperiencessculptthebrain.Here,wesubmitaproposalentitled?Elucidatingthe3- Depigeneticdeterminantsofactivity-dependentgeneexpressioninmammalianneurons?.Wehaveassembled an interdisciplinary team with critical expertise in genome folding, epigenetics, chromatin engineering, neurobiology, synaptogenesis, electrophysiology, and computational biology.
We aim to elucidate the causal linkamonglong-rangeloopinginteractions,epigeneticmodificationsonthelineargenome,expressionoftheir spatial target genes, and the activity of mammalian neurons. We hypothesize that immediate early genes will functionallyengageinsingularshort-rangeloopstorapidlyactivateexpressiononthetimescaleofsecondsto minutesinresponsetotheenvironmentalstimulusofneuronalactivation.Bycontrast,wepositthatsecondary response genes will spatially connect via architectural proteins into complex, long-range, pre-existing topological configurations topoise thegenome for a second wave of expression on theorder of hours to days in response to neuronal firing. To test our hypotheses, we will create high-resolution genome folding maps using the Hi-C during a time course of activation in mouse hippocampal neurons. We will identify activity- dependent enhancers and gene expression genome-wide and determine their temporal profile with respect pre-formedand activity-dependent loops. We willformulate mathematical models topredict activity-dependent expression of immediate early genes and secondary response genes from the timing of enhancer activation andloopingcontacts.Byintegratingsinglenucleotidevariantslinkedtoautism,schizophrenia,bipolardisorder, addiction, and attention-deficit/hyperactivity disorder with our models, we will predict the specific target genes and potential pathways involved in neurological disease. Finally, we will dissect the functional role for loops and enhancer activity in regulating the activity-dependent transcription of Bdnf and c-fos using CRISPR genome editing of architectural protein binding motifs and CRISPRi inhibition of specific enhancers. Our work will uncoverthegenome?s long-range interaction landscape in mammalianneuronsand reveal thecausal link between the 3-D Epigenome and the kinetics of transcriptional response to environmentally stimulated neuronalactivation.
Brains have evolved to process and store information from the outside world and do so through synaptic connections among interconnected networks of neurons. Our work will illuminate higher-order genome folding as an unexplored dimension of the long-range epigenetic control governing neuronal activation in the mammalian brain. Synaptic defects underlie many neurological disorders, therefore understanding the molecular mechanisms governing activity-dependent expression is of tremendous importance toward our knowledge of how neural circuits are disrupted in brain disease.