Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-? associated gene regulation (TRAP-Seq).

PURPOSE: The transcriptional repressor PARIS (ZNF746) was initially identified as a pathogenic co-substrate of PINK1 and parkin that leads to Parkinson's disease (PD) by disrupting mitochondrial biogenesis through PPAR? coactivator -1a (PGC-1a) suppression. Later, accumulation of PARIS in dopamine (DA) neurons that cause neurotoxicity has been studied widely and growing evidence has linked defective mitochondrial biogenesis to PD pathogenesis. Yet, the mechanistic underpinnings of this link remain elusive. METHODS: We employed translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines we generated expressing human PARIS or human PARIS mutant (C571A). Together with TRAP control and whole brain samples, this data set is composed of a total of 10 (3, 3, 3, and 1 respectively) replicate samples representing 4 different treatment groups for a set of gene-level (a parametric F-test) and transcript-level (a Wald test or a likelihood ratio test) differential expression analysis. RESULTS: Firstly, we identified differentially expressed genes by human PARIS in fly DA neurons successfully. Then, we showed that PPAR? acts as a master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila dopaminergic neurons. Also, we validated this finding in human neuroblastoma cell line. CONCLUSION: PPAR? plays a crucial regulatory role in PARIS phenotype. Drosophila models of PARIS-induced neurodegeneration used in this work to represent PD phenotype and our TRAP-seq protocol serve as a paradigm for future studies to unravel mechanistic underpinnings of PARIS biology. Overall design: TRAP control (3X), PARIS wild type (3X), PARIS mutant (C571A) (3X), and whole brain (1X) samples, adding up to a total of 10 replicate samples representing 4 different groups. Whole brain serves as a control for TRAP enrichment. TRAP control serves as a control for PARIS transgenic constructs.