A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast
- Calico Life Sciences, LLC, United States
Abstract
Replicative aging of Saccharomyces cerevisiae is an established model system for eukaryotic cellular aging. A limitation in yeast lifespan studies has been the difficulty of separating old cells from young cells in large quantities. We engineered a new platform, the Miniature-chemostat Aging Device (MAD), that enables purification of aged cells at sufficient quantities for genomic and biochemical characterization of aging yeast populations. Using MAD, we measured DNA accessibility and gene expression changes in aging cells. Our data highlight an intimate connection between aging, growth rate, and stress. Stress-independent genes that change with age are highly enriched for targets of the signal recognition particle (SRP). Combining MAD with an improved ATAC-Seq method, we find that increasing proteasome activity reduces rDNA instability usually observed in aging cells, and contrary to published findings, provide evidence that global nucleosome occupancy does not change significantly with age.
Data availability
We've included all processed data in easily accessible tables.Sequencing data have been deposited in GEO under accession codes GSE118581
-
Genomic analysis of aging yeastPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE118581).
Article and author information
Author details
Funding
This was work was funded by Calico Life Sciences, LLC
Copyright
© 2018, Hendrickson 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.
Metrics
-
- 13,453
- views
-
- 1,390
- downloads
-
- 56
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Citations by DOI
-
- 56
- citations for umbrella DOI https://doi.org/10.7554/eLife.39911
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast
eLife 7:e39911.
https://doi.org/10.7554/eLife.39911
