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| Status |
Public on Jul 08, 2013 |
| Title |
The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes [array] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by array
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| Summary |
The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5′ and 3′ ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5′ end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5′ end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5′ end of genes by sliding promoter proximal nucleosomes.
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| Overall design |
Data sets for each strain were generated from three biological replicates and experimental dye swap duplicates of each replicate.
The six wildtype raw data files linked below were used to generate normalized, log2 (mutant/WT) ratios for all 3 Samples.
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| Contributor(s) |
Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu W |
| Citation(s) |
23779104 |
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| Submission date |
Jul 07, 2013 |
| Last update date |
Sep 06, 2013 |
| Contact name |
Wei-Hua Wu |
| E-mail(s) |
wwu@gru.edu
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| Organization name |
IMMAG/MCG/GRU
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| Department |
Neurology
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| Street address |
1462 Laney Walker Blvd
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| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
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| Platforms (1) |
| GPL9294 |
Agilent-015072 Yeast Oligo Microarray 4x44K G2519F (Probe Name version) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE48571 |
The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes |
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| Relations |
| BioProject |
PRJNA210720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48570_RAW.tar |
229.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE48570_US45102975_251507210187_S01_GE2-v5_95_Feb07_1_1.txt.gz |
13.0 Mb |
(ftp)(http) |
TXT |
| GSE48570_US45102975_251507210188_S01_GE2-v5_95_Feb07_1_1.txt.gz |
12.9 Mb |
(ftp)(http) |
TXT |
| GSE48570_US45102975_251507210189_S01_GE2-v5_95_Feb07_1_1.txt.gz |
12.8 Mb |
(ftp)(http) |
TXT |
| GSE48570_US45102975_251507210200_S01_GE2-v5_95_Feb07_1_1.txt.gz |
12.6 Mb |
(ftp)(http) |
TXT |
| GSE48570_US45102975_251507210201_S01_GE2-v5_95_Feb07_1_1.txt.gz |
12.6 Mb |
(ftp)(http) |
TXT |
| GSE48570_US45102975_251507210202_S01_GE2-v5_95_Feb07_1_1.txt.gz |
12.5 Mb |
(ftp)(http) |
TXT |
| GSE48570_readme_6wildtype_rawfiles.txt |
1.3 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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