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| Status |
Public on Aug 11, 2006 |
| Title |
Yeast FAIRE_Cell Cycle Study |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence.
Keywords: FAIRE
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| Overall design |
We arrested cells in late G1 using the mating pheromone α-factor, released the cells into fresh YPD, and collected synchronized cells at seven time points spanning a single cell cycle. The collected time-point samples were then subjected to FAIRE, followed by microarray detection.
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| Contributor(s) |
Hogan GJ, Lee CK, Lieb JD |
| Citation(s) |
17002501 |
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| Submission date |
Apr 25, 2006 |
| Last update date |
Sep 21, 2012 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
[email protected]
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| Phone |
919-842-3228
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Department of Biology
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| Lab |
Jason Lieb
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| Street address |
203 Fordham Hall
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-3280 |
| Country |
USA |
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| Platforms (1) |
| GPL3700 |
Lieb Lab at UNC-CH_Yeast Whole-genome Array (PCR-based) |
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| Samples (35)
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| GSM106509 |
Yeast FAIRE_time 72, cell cycle #4 (dye swap) |
| GSM106510 |
Yeast FAIRE_time 72, cell cycle #5 |
| GSM106511 |
Yeast FAIRE_time 90, cell cycle #1 |
| GSM106512 |
Yeast FAIRE_time 90, cell cycle #2 |
| GSM106513 |
Yeast FAIRE_time 90, cell cycle #3 |
| GSM106514 |
Yeast FAIRE_time 90, cell cycle #4 |
| GSM106515 |
Yeast FAIRE_time 90, cell cycle #4 (dye swap) |
| GSM106517 |
Yeast FAIRE_time 90, cell cycle #5 |
| GSM106518 |
Yeast FAIRE_time 0, cell cycle #2 |
| GSM106519 |
Yeast FAIRE_time 0, cell cycle #3 |
| GSM106520 |
Yeast FAIRE_time 0, cell cycle #4 |
| GSM106521 |
Yeast FAIRE_time 18, cell cycle #2 |
| GSM106522 |
Yeast FAIRE_time 18, cell cycle #3 |
| GSM106523 |
Yeast FAIRE_time 18, cell cycle #4 |
| GSM106524 |
Yeast FAIRE_time 18, cell cycle #4 (dye swap) |
| GSM106525 |
Yeast FAIRE_time 36, cell cycle #1 |
| GSM106526 |
Yeast FAIRE_time 36, cell cycle #2 |
| GSM106527 |
Yeast FAIRE_time 36, cell cycle #3 |
| GSM106528 |
Yeast FAIRE_time 36, cell cycle #4 |
| GSM106529 |
Yeast FAIRE_time 36, cell cycle #4 (dye swap) |
| GSM106530 |
Yeast FAIRE_time 36, cell cycle #5 |
| GSM106531 |
Yeast FAIRE_time 54, cell cycle #3 |
| GSM106532 |
Yeast FAIRE_time 54, cell cycle #4 |
| GSM106533 |
Yeast FAIRE_time 54, cell cycle #4 (dye swap) |
| GSM106534 |
Yeast FAIRE_time 63, cell cycle #3 |
| GSM106535 |
Yeast FAIRE_time 63, cell cycle #4 |
| GSM106536 |
Yeast FAIRE_time 63, cell cycle #4 (dye swap) |
| GSM106537 |
Yeast FAIRE_time 63, cell cycle #5 |
| GSM106538 |
Yeast FAIRE_time 72, cell cycle #1 |
| GSM106541 |
Yeast FAIRE_time 54, cell cycle #1 |
| GSM106542 |
Yeast FAIRE_time 54, cell cycle #5 |
| GSM106543 |
Yeast FAIRE_time 0, cell cycle #5 |
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| This SubSeries is part of SuperSeries: |
| GSE4736 |
Yeast FAIRE Study_Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. |
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| Relations |
| BioProject |
PRJNA104545 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE4719_RAW.tar |
55.2 Mb |
(http)(custom) |
TAR (of GPR) |
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