Pathway analysis for genes identified in controls showed enrich ment for normal neuronal processes such as axon guid ance, but also for genes associated with long term depression, a form of synaptic plasticity typically associ ated with synaptic weakening. The repressive functional categories and pathways enriched in controls suggest thing that training counteracts these pathways for memory formation. Alternatively, pathways Inhibitors,Modulators,Libraries upregulated in controls may be those that are needed to maintain homeostatic processes and basal neuronal functions in the absence of learning. To validate whether genes differentially acetylated for H4K5 are also differentially expressed, Inhibitors,Modulators,Libraries we quantified mRNA expression of twelve randomly chosen genes called by MACS.
mRNA levels were measured in hippocampal samples collected from animals from an independent CFC experiment to avoid sample or experimental bias associ ated with the ChIP Seq. Seven out of twelve genes had sig nificantly higher Inhibitors,Modulators,Libraries expression after CFC than in controls. In contrast, in the cerebellum, a brain region not recruited for the formation of contextual fear memory, gene expression did not change after CFC, except for one. Taken together, our data suggests that genes dif ferentially acetylated for H4K5 are specific to memory for mation in the hippocampus with CFC. Discussion The present study provides a comprehensive genome wide analysis of H4K5ac in the hippocampus following fear memory formation, and identifies a novel set of genes associated with H4K5ac induced by learning.
It demonstrates that H4K5ac is a ubiquitous histone PTM in the genome, present on one third of genes with above average H4K5ac in the adult mouse hippocampus. Genes associated with high H4K5ac, in both promoter and CDS, are highly expressed, but H4K5ac is most promin ent within 1000 kb upstream of the TSS. Our results Inhibitors,Modulators,Libraries suggest that H4K5ac may be required in both the pro moter and CDS, over the entire length of the Inhibitors,Modulators,Libraries gene, for transcription of full and intermediate transcripts and that the presence of H4K5ac is a reliable marker of actively transcribed genes. However, we found that en richment of H4K5ac in the promoter is determined, to an extent, by TF binding in which the absence of distal TFBS, 150 bp upstream of the TSS, dramatically in creases H4K5ac enrichment in the promoter. We also provide evidence that H4K5ac may be a hallmark of activity dependent genes that are expressed with learn ing. By identifying genes differentially acetylated for H4K5, we have uncovered key Ganetespib Phase 3 genes, both known and novel, involved in memory formation. These genes are specific to functions and pathways involved in synaptic plasticity and memory formation, but also to basic cellu lar processes, with learning.