A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of aging yeast

Replicative aging of 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 purif...

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Bibliographic Details
Published in:eLife 2018-10, Vol.7
Main Authors: Hendrickson, David G, Soifer, Ilya, Wranik, Bernd J, Kim, Griffin, Robles, Michael, Gibney, Patrick A, McIsaac, R Scott
Format: Article
Language:English
Subjects:
Age
Aging
ATAC-Seq
Chromatin
Chromatin - metabolism
Computational and Systems Biology
Deoxyribonucleic acid
DNA
DNA Replication
Gene expression
Gene Expression Profiling
Genetic engineering
Genetics and Genomics
Genomes
Growth rate
Life span
longevity
Microbiological Techniques - methods
Mothers
proteasome
Proteasomes
Purification
rDNA
Ribosomal DNA
Saccharomyces cerevisiae - growth & development
Saccharomyces cerevisiae - isolation & purification
Sequence Analysis, RNA
Signal recognition particle
Tools and Resources
Transcription
transposons
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Summary:Replicative aging of 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.
ISSN:2050-084X
2050-084X
DOI:10.7554/elife.39911