Phenotypic differences in dopaminergic circuitries of mouse strains are associated with extensive regulatory variation in the midbrain

The nigrostriatal circuitry in the substantia nigra (SN) exerts control over the motor system and the loss of dopaminergic neurons (DAns) in the SN is the primary cause of Parkinson's disease (PD). We have performed RNA-seq, ChIP-seq, and ATAC-seq analysis of the ventral midbrains of three widely used mouse strains, C57BL/6J, A/J and DBA/2J strains and found 1000-1200 genes to be differentially expressed between each of the strains. Such extensive transcriptome changes could be due to altered activity of upstream transcription factors (TFs) or due to cumulative regulatory variation across genes.