Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-\u03b3 associated gene regulation

Volkan Yazar,Ted M Dawson,Shinwon Ha,Sung-Ung Kang,Valina L Dawson

doi:10.1038/s41598-021-00858-7

Abstract

The transcriptional repressor called parkin interacting substrate (PARIS; ZNF746) was initially identified as a novel co-substrate of parkin and PINK1 that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through peroxisome proliferator-activated receptor gamma (PPARγ) coactivator -1α (PGC-1α) suppression. Since its initial discovery, growing evidence has linked PARIS to defective mitochondrial biogenesis observed in PD pathogenesis. Yet, dopaminergic (DA) neuron-specific mechanistic underpinnings and genome-wide PARIS binding landscape has not been explored. We employed conditional translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines expressing human PARIS wild type (WT) or mutant (C571A). We also generated genome-wide maps of PARIS occupancy using ChIP-seq in human SH-SY5Y cells. The results demonstrated that PPARγ functions as a master regulator of PARIS-induced molecular changes at the transcriptome level, confirming that PARIS acts primarily on PGC-1α to lead to neurodegeneration in PD. Moreover, we identified that PARIS actively modulates expression of PPARγ target genes by physically binding to the promoter regions. Together, our work revealed how PARIS drives adverse effects on modulation of PPAR-γ associated gene clusters in DA neurons.

Highlights

As the second most common neurodegenerative disorder worldwide with a prevalence as high as 572 people per 100,000 in the US1, Parkinson’s disease is referred to as a “silent epidemic” of our times
To investigate the breadth and the extent of transcriptomic changes caused by human parkin interacting substrate (PARIS) gene in fly dopaminergic (DA) neurons, the double transgenic UAS-GFP::RpL10A; UAS-PARIS-wild type (WT) and UAS-GFP::RpL10A; UAS-PARIS C571A lines were crossed with dTH-GAL4 line to perform translating ribosome affinity purification (TRAP)-seq (Fig. 1a, Supplementary Fig. 1)
In an attempt to combine two independent datasets to find common genes that are both physically regulated and significantly suppressed by PARIS, we identified 52 peak-annotated genes shared with the “TRAP control versus PARIS WT” comparison, and 23 genes with the “PARIS WT versus C571A mutant” comparison (Fig. 5a,b)

Summary

Introduction

As the second most common neurodegenerative disorder worldwide with a prevalence as high as 572 people per 100,000 in the US1, Parkinson’s disease is referred to as a “silent epidemic” of our times. We performed a global, model-based analysis of PARIS genomic occupancy using chromatin immune-precipitation followed by sequencing (ChIP-seq) on SH-SY5Y (in-house dataset) and 293 T (public dataset) human cell lines By combining these two approaches in a single study to measure the regulatory capacity of PARIS, we identified a set of direct target genes that are differentially expressed by PARIS. Based on these findings, we showed using both approaches separately and combined that PPARγ acts as a potential master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila DA neurons.

Objectives

Methods

Results

Discussion

Conclusion