Identification of the ataxin-1 interaction network and its impact on spinocerebellar ataxia type 1

• Published in: Human genomics 2022-07, Vol.16 (1), p.1-29, Article 29
• Main Authors: Chen, Jiu-Ming, Chen, Shi-Kai, Jin, Pei-Pei, Sun, Shun-Chang
• Format: Article
• Language: English
• Subjects: Antibodies; Ataxia; Ataxin; Ataxin-1; Chromatin; Chromatography; Cloning; Deoxyribonucleic acid; DNA; Fluorides; Gene expression; Immunoprecipitation; Mutants; Mutation; Neurodegenerative diseases; Neurotoxicity; Next-generation sequencing; Pathway analysis; Peptides; Plasmids; Polyglutamine diseases; Polyglutamine expansion; Polymerase chain reaction; Protein interaction; Protein purification; Proteins; Protein–protein interaction; Ribonucleic acid; RNA; RNA-binding protein; Spinocerebellar ataxia; Spinocerebellar ataxia type 1 (SCA1); Trinucleotide repeat diseases; Western blotting
• ISSN: 1479-7364; 1473-9542; 1479-7364
• DOI: 10.1186/s40246-022-00404-0

Background Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by a polyglutamine expansion in the ataxin-1 protein. The pathogenic mechanism resulting in SCA1 is still unclear. Protein–protein interactions affect the function and stability of ataxin-1. Methods Wild-type and mutant ataxin-1 were expressed in HEK-293T cells. The levels of expression were assessed using real-time polymerase chain reaction (PCR) and Western blots. Co-immunoprecipitation was done in HEK-293T cells expressing exogenous wild-type and mutant ataxin-1 using anti-Flag antibody following by tandem affinity purification in order to study protein–protein interactions. The candidate interacting proteins were validated by immunoprecipitation. Chromatin immunoprecipitation and high-throughput sequencing and RNA immunoprecipitation and high-throughput sequencing were performed using HEK-293T cells expressing wild-type or mutant ataxin-1. Results In this study using HEK-293T cells, we found that wild-type ataxin-1 interacted with MCM2, GNAS, and TMEM206, while mutant ataxin-1 lost its interaction with MCM2, GNAS, and TMEM206. Two ataxin-1 binding targets containing the core GGAG or AAAT were identified in HEK-293T cells using ChIP-seq. Gene Ontology analysis of the top ataxin-1 binding genes identified SLC6A15, NTF3, KCNC3, and DNAJC6 as functional genes in neurons in vitro. Ataxin-1 also was identified as an RNA-binding protein in HEK-293T cells using RIP-seq, but the polyglutamine expansion in the ataxin-1 had no direct effects on the RNA-binding activity of ataxin-1. Conclusions An expanded polyglutamine tract in ataxin-1 might interfere with protein–protein or protein–DNA interactions but had little effect on protein–RNA interactions. This study suggested that the dysfunction of protein–protein or protein–DNA interactions is involved in the pathogenesis of SCA1.