Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of S. cerevisiae IFO 0233 diploid strain sampled at multiple time point to investigate genome wide oscillations


ABSTRACT: In order to test the idea that the cell is an attractor and to examine in detail the connectivity relationships among genes, it was essential to have a very reproducible and precise biological system. Oscillations in respiratory activity in budding yeast and other organisms have been known for many years. This benchmark oscillation is now shown to be a global manifestation of a genome wide oscillation in transcription. Using Affymetrix S98 chips, the patterns of gene expression were followed by sampling at 4-minute intervals through three cycles of the DO oscillation. Phase assignments were made based on the dissolved oxygen cycle. Two different cultures were sampled and a total of 68 RNA samples were prepared. Choices of samples for microarray analysis were based on RNA quality, consistent with having a complete set of 32 samples chosen to represent three cycles of the DO oscillation. Ten were chosen from the first experiment and 22 from the second experiment. Analysis using singular value decomposition recognizes a small difference in cycle time between the two experiments. Strictly speaking, there are no replicates. The time of maximum gene expression in the cycle was determined by phase grouping and averaging gene expression in the three replicates, assigning the phase of maximum expression to each transcript then examining how well this assignment is reproduced through the three cycles. We found that 5329 expressed genes were present in at least one sample and used them in our analysis. The correct order is GSM48136, GSM48137, GSM48138, GSM48139, GSM48140, GSM48131, GSM48132, GSM48133, GSM48134, GSM48135, GSM48149, GSM48150, GSM48141, GSM48151, GSM48142, GSM48143, GSM48144, GSM48145, GSM48146, GSM48147, GSM48148, GSM48160, GSM48161, GSM48162, GSM48157, GSM48158, GSM48152, GSM48159, GSM48153, GSM48154, GSM48155, GSM48156

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Robert Klevecz 

PROVIDER: E-GEOD-2583 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A genomewide oscillation in transcription gates DNA replication and cell cycle.

Klevecz Robert R RR   Bolen James J   Forrest Gerald G   Murray Douglas B DB  

Proceedings of the National Academy of Sciences of the United States of America 20040120 5


Microarray analysis from a yeast continuous synchrony culture system shows a genomewide oscillation in transcription. Maximums in transcript levels occur at three nearly equally spaced intervals in this approximately 40-min cycle of respiration and reduction. Two temporal clusters (4,679 of 5,329) are maximally expressed during the reductive phase of the cycle, whereas a third cluster (650) is maximally expressed during the respiratory phase. Transcription is organized functionally into redox-st  ...[more]

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