Exploring the expression patterns of palmitoylating and de-palmitoylating enzymes in the mouse brain using the curated RNA-seq database BrainPalmSeq

Abstract
Data availability
Article and author information
Metrics

Abstract

Protein S-palmitoylation is a reversible post-translational lipid modification that plays a critical role in neuronal development and plasticity, while dysregulated S-palmitoylation underlies a number of severe neurological disorders. Dynamic S-palmitoylation is regulated by a large family of ZDHHC palmitoylating enzymes, their accessory proteins, and a small number of known de-palmitoylating enzymes. Here, we curated and analyzed expression data for the proteins that regulate S-palmitoylation from publicly available RNAseq datasets, providing a comprehensive overview of their distribution in the mouse nervous system. We developed a web-tool that enables interactive visualization of the expression patterns for these proteins in the nervous system (http://brainpalmseq.med.ubc.ca/), and explored this resource to find region and cell-type specific expression patterns that give insight into the function of palmitoylating and de-palmitoylating enzymes in the brain and neurological disorders. We found coordinated expression of ZDHHC enzymes with their accessory proteins, de-palmitoylating enzymes and other brain-expressed genes that included an enrichment of S-palmitoylation substrates. Finally, we utilized ZDHHC expression patterns to predict and validate palmitoylating enzyme-substrate interactions.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for all Figures.

The following previously published data sets were used

Article and author information

Author details

Angela R Wild

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Peter W Hogg

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2176-4977
Stephane Flibotte

Life Sciences Institute Bioinformatics Facility, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Glory Nasseri

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Rocio Hollman

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Danya Abazari

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.
Kurt Haas

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4754-1560
Shernaz X Bamji

Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

For correspondence
shernaz.bamji@ubc.ca

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0102-9297

Funding

Canadian Institutes of Health Research (F18-00650)

Peter W Hogg

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.