Complementary proteomics strategies capture an ataxin-1 interactome in Neuro-2a cells

Sci Data. 2018 Nov 20;5:180262. doi: 10.1038/sdata.2018.262.

Abstract

Ataxin-1 mutation, arising from a polyglutamine (polyQ) tract expansion, is the underlying genetic cause of the late-onset neurodegenerative disease Spinocerebellar ataxia type 1 (SCA1). To identify protein partners of polyQ-ataxin-1 in neuronal cells under control or stress conditions, here we report our complementary proteomics strategies of proximity-dependent biotin identification (BioID) and affinity purification (via GFP-Trap pulldown) in Neuro-2a cells expressing epitope-tagged forms of ataxin-1[85Q]. These approaches allowed our enrichment of proximal proteins and interacting partners, respectively, with the subsequent protein identification performed by liquid chromatography-MS/MS. Background proteins, not dependent on the presence of the polyQ-ataxin-1 protein, were additionally defined by their endogenous biotinylation (for the BioID protocol) or by their non-specific interaction with GFP only (in the GFP-Trap protocol). All datasets were generated from biological replicates. Following the removal of the identified background proteins from the acquired protein lists, our experimental design has captured a comprehensive polyQ-ataxin-1 proximal and direct protein partners under normal and stress conditions. Data are available via ProteomeXchange, with identifier PXD010352.

Publication types

  • Dataset
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Ataxin-1* / metabolism
  • Ataxin-1* / physiology
  • Cell Line
  • Mice
  • Neurodegenerative Diseases / metabolism
  • Neurodegenerative Diseases / physiopathology
  • Neurons / metabolism
  • Peptides*
  • Protein Interaction Maps*
  • Proteomics / methods*
  • Tandem Mass Spectrometry
  • Trinucleotide Repeats

Substances

  • Ataxin-1
  • Atxn1 protein, mouse
  • Peptides
  • polyglutamine

Associated data

  • figshare/10.6084/m9.figshare.c.4235057