Whole genome expression studies have shown that some of these programs are needed for basal homeo static cellular functions, while others are specific for cog nitive functions. The composition and regulation of most transcriptional programs however may depend on the strength and duration of training. Its well known, for ex ample, that practice or repeated training of a skill or con cept can improve memory for the subject. Multiple training sessions required to form strong memory traces may, therefore, be associated with increased gene expres sion or the reinforcement of existing transcriptional pro grams, such as those necessary for structural changes to strengthen synaptic circuits. How this is induced at the level of chromatin and which genes are targeted by epigenetic processes remains poorly understood.

With the emergence of the post genomic era, recent studies in the field of learning and memory have investi gated the implication of chromatin remodeling in cognitive processes. Several studies have revealed that chromatin re modeling plays a critical role in memory formation. Chromatin remodeling is a complex molecular and structural process that involves the dynamic regulation of nucleosomes through different epigenetic mechanisms including histone posttranslational modifications, DNA methylation and RNA interference. In the ro dent brain, several histone PTMs are rapidly induced and are associated with altered gene transcription following training.

Acetylation of lysine 9 and 14 on H3, of lysine 5, 8 and 12 on H4, and of lysine 5, 12, 15, and 20 on H2B, in creases in the hippocampus following contextual fear con ditioning, a well established behavioral paradigm for the establishment of contextual fear memory. Moreover, inhibition of histone deacetylases by HDAC inhibitors such as suberoylanilide hydroxamic acid, sodium butyrate, valproic acid or trichostatin A can enhance memory and rescue deficits in contextual memory in rodents. Although these studies provide strong evidence that his tone acetylation is modulated by memory formation, a global assessment of histone acetylation at the level of the genome and the mechanism with which it regulates gene expression in memory processes is lacking.

Using a genome wide approach, we examined the distribution of H4K5ac, a mark of active chromatin implicated in tran scriptional re activation of post mitotic cells through gene bookmarking, and its role in regulating Cilengitide transcrip tional activity following the establishment of contextual fear memory in the adult mouse. We propose that gene bookmarking may also be relevant in the hippocam pus following learning, whereby genes may be primed for rapid induction through activity induced histone acetyl ation. Using chromatin immunoprecipitation followed by deep sequencing and bioinformatics analysis, we show that H4K5ac in the hippocampus is prevalent throughout the genome and is a mark characteristic of ac tively transcribed genes.