Epigenetic changes influence neuronal functions and cortical plasticity in rodents

The nervous system acts at the interface between an organism and its surrounding environment: the integration of incoming stimuli from the sensory systems results in long-lasting changes in neuronal circuitry that influence brain functions and behaviour. The modification of synaptic connections initiated by experience is referred to as plasticity and it requires a regulated programme of activity-dependent gene expression. A prominent role in transcriptional regulation is performed by epigenetic mechanisms, a vast set of enzymatic reactions altering chromatin structure. To study the contribution of epigenetic factors in the regulation of plasticity, two complementary experimental systems are the early postnatal development of the visual cortex and the exposure of adult animals to environmental enrichment (EE). In both these paradigms, experience alters cortical circuits at the anatomical and physiological level and elicits defined behavioural responses. Light re-exposure after three days of dark rearing induces global histone H3 phosphorylation and histone H3-H4 acetylation in visual cortices of mice during the critical period, but not in adult animals. We recently found that methylation of lysine 4 in histone H3 is also increased by this protocol of visual stimulation. To characterize further these histone modifications we performed chromatin immunoprecipitation on the cAMP-responsive-element (CRE) at the promoter of the immediate-early gene c-fos and two activity-regulated microRNAs: miR132 and miR212. We found that histone H3 acetylation and methylation of lysine 4 is increased at the CRE of c-fos after visual stimulation while miR312 but not the miR212 CRE showed increased H3 phosphoacetylation and lysine 4 methylation. This combination of histone marks correlates with the activation of transcription of these genes. Histone acetylation has been demonstrated to mediate at least in part the effects of short-term exposure to EE. To gain further insight we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIPSeq) to screen for genome-wide changes in acetylation of histone H3 elicited by EE in the mouse cortex. A computational analysis identified SINE repeats as a potentially relevant genomic element that induces gene expression, possibly mediating the rearrangements of chromosomes inside the nucleus. The binding of transcription factors and histone modifications at SINEs has been validated for selected genes in primary cortical neurons. Finally, we performed reporter gene assay to provide a structure-to-function analysis of SINEs in activity-dependent gene expression in primary cortical neurons. Alteration of the chromatin structure by epigenetic mechanisms is a fundamental process by which the nervous system is able to orchestrate the transcriptional programme necessary for plasticity of its synaptic connections throughout the whole life of an organism, thus allowing it flexibility in learning and behavioural responses