Pituitary Tumor Transforming Gene 1 orchestrates gene regulatory variation in mouse ventral midbrain during aging

Background Dopaminergic neurons in the midbrain are of particular interest due to their role in diseases such as Parkinson’s disease and schizophrenia. Genetic variation between individuals can affect the integrity and function of dopaminergic neurons but the DNA variants and molecular cascades modulating dopaminergic neurons and other cells types of ventral midbrain remain poorly defined. Three genetically diverse inbred mouse strains — C57BL/6J, A/J, and DBA/2J — differ significantly in their genomes (~7 million variants), motor and cognitive behavior, and susceptibility to neurotoxins. Results To further dissect the underlying molecular networks responsible for these variable phenotypes, we generated RNA-seq and ChIP-seq data from ventral midbrains of the 3 mouse strains. We defined 1000–1200 transcripts that are differentially expressed among them. These widespread differences may be due to altered activity or expression of upstream transcription factors. Interestingly, transcription factors were significantly underrepresented among the differentially expressed genes, and only one TF, Pttg1 , showed significant differences among all strains. The changes in Pttg1 expression were accompanied by consistent alterations in histone H3 lysine 4 trimethylation at Pttg1 transcription start site. The ventral midbrain transcriptome of three-month-old C57BL/6J congenic Pttg1-/- mutants was only modestly altered, but shifted towards that of A/J and DBA/2J in nine-month-old mice. Principle component analysis identified the genes underlying the transcriptome shift and deconvolution of these bulk RNA-seq changes using midbrain single cell RNA-seq data suggested that the changes were occurring in several different cell types, including neurons, oligodendrocytes, and astrocytes. Conclusion Taken together, our results show that Pttg1 contributes to gene regulatory variation between mouse strains and influences mouse midbrain transcriptome during aging. ### Competing Interest Statement The authors have declared no competing interest. * DAns : dopaminergic neurons DEGs : differentially expressed genes EDTA : ethylenediamine tetraacetic acid H3K4me3 : histone H3 lysine 4 trimethylation LCSB : Luxembourg Centre for Systems Biomedicine log2FC : log2-fold change NP-40 : 4-Nonylphenyl-polyethylene glycol PC : principle component PCA : principle component analysis PD : Parkinson’s disease PI : Proteinase Inhibitor Pttg1 : Pituitary Tumor Transforming Gene 1 RPKM : Reads Per Kilobase Million SDS : sodium odecylsulfate SN : substantia nigra TFs : transcription factors TSS : transcription start sites VTA : ventral tegmental area.