Developmentally regulated histone modification and DNA methylation changes, shaping gene expression patterns and genome organization, are likely to be of fundamental importance for orderly ontogenesis and cellular differentiation. Therefore, comprehensive and high resolution mapping of cell type-specific epigenomes from brain bear enormous merit both from the viewpoint of developmental biology and translational medicine alike. To date, however, comprehensive and genome-wide maps of epigenomes for defined cell populations from brain, and their developmental trajectories, do not exist. This important gap in epigenetic information can finally be addressed with a recently introduced protocol that efficiently separates-in brain tissue-chromatin from different cell types. In this proposal, we will explore, for the first time, the histone methylation landscapes of ventral midbrain dopaminergic neurons of the human brain. These cells play a key role in the neurobiology of a wide range of neuropsychiatric disorders ranging from drug addiction to neurodegenerative (e.g., Parkinson's) conditions. Focus will be on tri-methyl-histone H3-lysine 4 (H3K4me3), a mark enriched at transcription start sites (H3K4me3) and a subset of CpG-rich sequences, and tri-methyl-H3K36me3, a mark associated with RNA polymerase II activity and transcriptional elongation across coding and non-coding regions. Beyond the goals of this R21 proposal, the long-term vision for the collaboration between our two groups at Wayne State and UMASS is to explore changes in the dopaminergic epigenome of subjects diagnosed with stimulant and other substance abuse.
For the majority of patients diagnosed with neuropsychiatric diseases (including but not limited to drug addiction) no straightforward genetic cause has been identified. Many of the molecular pathways involved in substance abuse disorders involve genes expressed in a type of cell called the 'dopaminergic neuron'. These comprise only a small fraction of cells in a brain region called 'ventral midbrain'. These nerve cells exert a powerful effect on the brain's motivational and affective states. To further understand the role of the dopaminergic neurons in neuropsychiatric illness, and to clarify gene expression activities in normal and disease states, it will be critically important to explore their genomes and chromatin architectures at high resolution. This grant proposal is based on extremely innovative techniques that were recently developed in our laboratories. We will be able, for the first time, t selectively isolate chromosomal materials and chromatin from the dopamine neurons of the human brain for the study of epigenetic markings (basically, chemical modifications that regulate gene expression and function without altering the genetic code) on a genome-wide level. We expect that the work resulting from this project will provide a valuable resource /chromatin atlas for the neuroscience research community and will shed light on some of the mechanisms that govern gene expression activity in dopamine neurons of subjects exposed to drugs of abuse.
|Peter, Cyril J; Fischer, Laura K; Kundakovic, Marija et al. (2016) DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition. Biol Psychiatry 80:765-774|
|Bai, Guang; Cheung, Iris; Shulha, Hennady P et al. (2015) Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Hum Mol Genet 24:1441-56|
|de Boni, Laura; Riedel, Linda; Schmitt, Ina et al. (2015) DNA methylation levels of Î±-synuclein intron 1 in the aging brain. Neurobiol Aging 36:3334.e7-11|
|Hoss, Andrew G; Kartha, Vinay K; Dong, Xianjun et al. (2014) MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. PLoS Genet 10:e1004188|
|Roussos, Panos; Mitchell, Amanda C; Voloudakis, Georgios et al. (2014) A role for noncoding variation in schizophrenia. Cell Rep 9:1417-29|
|Mitchell, Amanda C; Bharadwaj, Rahul; Whittle, Catheryne et al. (2014) The genome in three dimensions: a new frontier in human brain research. Biol Psychiatry 75:961-9|
|Bharadwaj, Rahul; Jiang, Yan; Mao, Wenjie et al. (2013) Conserved chromosome 2q31 conformations are associated with transcriptional regulation of GAD1 GABA synthesis enzyme and altered in prefrontal cortex of subjects with schizophrenia. J Neurosci 33:11839-51|
|Shulha, Hennady P; Crisci, Jessica L; Reshetov, Denis et al. (2012) Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol 10:e1001427|
|Jakovcevski, Mira; Akbarian, Schahram (2012) Epigenetic mechanisms in neurological disease. Nat Med 18:1194-204|