Neural function requires accurate control of gene transcription in response to environmental stimuli. Aberrant gene expression is believed to drive drug addiction. Therefore, studying the regulation of gene expression in drug addiction may provide mechanistic insights to this disease, which still offers limited options for treatment and represents a vast social and economic burden. It is estimated that there are up to one million regulatory elements in the mammalian genome, which are often located great distances from their target genes. Although recent developments in next generation sequencing have provided large-scale identification of regulatory DNA elements, which genes they regulate remains largely unknown. Recently, the ordered compaction and organization of linear DNA into the nucleus has been recognized as having a major influence on gene transcription by facilitating interactions between gene promoters and distal regulatory elements. However, how this three-dimensional chromatin architecture is organized in the brain and how it is changed, particularly in drug addiction, is still obscure. Here we propose to study the long- range looping interactions between distal DNA elements and all annotated mouse gene promoters within the specific neuronal subtypes differentially engaged in addiction. To achieve this, we will apply the cutting edge promoter capture Hi-C technology to profile the entire promoter interactome in D1- and D2- medium spiny neurons (MSNs) in nucleus accumbens, the key brain reward structure. We will also examine the neuron subtype-specific higher order genome organization in both cocaine and heroin addicted mice. We anticipate to elucidate neuron subtype specific and drug specific three-dimensional chromosome architecture changes. Many of these changes may involve previously identified genetic variation sites conserved between rodents and human. Manipulation of these regulatory regions may not only alter regulation of their target gene's expression, but may also change the associated addiction behaviors. Upon completion, our study will not only indisputably advance our understanding of drug addiction to the unachieved dimension of genome architecture organization, it will also open a new avenue to a plausible manipulation of the disease, which has potential utility for future therapeutic applications.
The compaction and organization of the linear DNA into the nucleus has been demonstrated to have a major influence on gene transcription by facilitating interactions between gene promoters and distal regulatory elements. To elucidate the uncharacterized three-dimensional chromatin architecture in drug addiction, we propose to study the long-range looping interactions between distal DNA elements and gene promoters within the specific neuronal subtypes differentially engaged in addiction. Our study will therefore provide novel insights into the transcriptional regulation underlying drug addiction.