Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-? associated gene regulation (ChIP-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 performed a global, model-based analysis of PARIS genomic occupancy using chromatin immune-precipitation followed by sequencing (ChIP-seq) on SHSY-5Y in human cell line. The dataset is composed of PARIS and control samples, each with one replicate only. For each sample, after quality control as mentioned above, reads were separately aligned to the latest human genome (NCBI; GRCh38) using Bowtie with the parameter “-m 1” to retain uniquely mapped reads only. The R packages ChIPQC v1.20.0 and PhantomPeakQualTools v1.2.2 were used to confirm the quality of the aligned bam files based on the ChIP-seq guidelines by ENCODE consortium (NSC >= 1.05; RSC >= 0.8, Qtag={-2,-1,0,1,2}). QC-confirmed bam files were subject to differential peak calling using MACS v1.4.220 with the following parameters: -t Sample.sam -c Control.sam --format SAM -g hs -B -S --call-subpeaks. Peak annotation and visualization were done using the R packages ChIPseeker v1.20.0 and clusterProfiler v3.12.0, respectively. RESULTS: We showed that PPAR? acts as a master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila dopaminergic neurons. Also, we revealed that PARIS directly modulates expression of PPAR? target genes by physically binding to the promoter regions. And finally, we observed a PARIS binding motif at the promoter proximal site of PPAR?, implying a direct regulatory effect of PARIS on PPAR? expression profile. CONCLUSION: PARIS displays adverse effects on modulation of PPAR? associated gene clusters. Our work revealed a pivotal role of PPAR? in PARIS-driven neurodegeneration. Overall design: Examination of PARIS binding sites in neuroblastoma (SHSY-5Y) cell line.