Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD
- Fred Hutchinson Cancer Research Center, United States
Abstract
DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). While DUX4's transcriptional activity has been extensively characterized, the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes to DUX4-induced pathology.
Data availability
Mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaino et al., 2013) with the dataset identifier PXD010221. To enable easy access to processed peptide-spectrum match data, we have also deposited peptide-level data to Dryad (doi:10.5061/dryad.ck06k75). The previously published RNA-seq data are available through the NCBI SRA database under accession number GSE85461
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Proteomics analysis of DUX4-expressing myoblastsPRIDE PRoteomics IDEntifications database, PXD010221.
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Data from: Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD.Dryad Digital Repository, doi:10.5061/dryad.ck06k75.
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Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cellsNCBI Gene Expression Omnibus, GSE85461.
Article and author information
Author details
Sujatha Jagannathan
Stephen J Tapscott
Funding
National Institute of Neurological Disorders and Stroke (P01NS069539)
- Stephen J Tapscott
- Robert K Bradley
FSH Society (FSHS-22014-01)
- Sujatha Jagannathan
Leukemia and Lymphoma Society
- Robert K Bradley
National Institutes of Health (P30 CA015704)
- Yuko Ogata
- Philip R Gafken
M.J. Murdock Charitable Trust
- Yuko Ogata
- Philip R Gafken
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Version history
- Received: September 5, 2018
- Accepted: January 14, 2019
- Accepted Manuscript published: January 15, 2019 (version 1)
- Version of Record published: January 28, 2019 (version 2)
- Version of Record updated: July 2, 2020 (version 3)
Copyright
© 2019, Jagannathan et al.
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.
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Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD
eLife 8:e41740.
https://doi.org/10.7554/eLife.41740
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