|
| Status |
Public on Aug 01, 2011 |
| Title |
Topoisomerase II binds nucleosome-free DNA and acts redundantly with Topoisomerase I to enhance recruitment of RNA Pol II in budding yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
DNA topoisomerases are known to promote transcription in prokaryotes by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome free. However, while nucleosome loss enables Top2 occupancy the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enable Top2 binding which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.
|
| |
|
| Overall design |
For Agilent Data: Top2, Pol2 and H3 were ChIP'd from yeast strains and normalized to input or to each other.
For Affymetrix Data: Top2 and H3 were ChIP'd from yeast strains and normalized to input.
|
| |
|
| Contributor(s) |
Sperling AS, Jeong KS, Kitada T, Grunstein M |
| Citation(s) |
21771901 |
| |
| Submission date |
Jun 29, 2010 |
| Last update date |
Jan 09, 2016 |
| Contact name |
Adam S Sperling |
| E-mail(s) |
asperlin@ucla.edu
|
| Organization name |
University of California Los Angeles
|
| Department |
Biological Chemistry
|
| Lab |
Grunstein Lab
|
| Street address |
611 Charles E. Young Dr. East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL4130 |
Agilent-014741 Yeast Whole Genome ChIP-on-Chip Microarray 244K (G4491A) |
| GPL7250 |
[Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array |
|
| Samples (15)
|
| GSM570487 |
Top2 ChIP during H4 depletion |
| GSM570491 |
Top2 ChIP during Pol II inhibition |
| GSM570492 |
Pol II ChIP during Pol II inhibition |
| GSM745634 |
H3 ChIP in top1,top2-ts mutant |
| GSM745635 |
Top2 ChIP in top1,top2-ts mutant |
| GSM745636 |
Pol2 ChIP vs input in wild type at 37C |
| GSM745637 |
Pol2 ChIP vs input in top1,top2-ts at 37C |
| GSM745638 |
Pol2 ChIP vs input in top2-ts at 37C |
| GSM745639 |
Pol2 ChIP vs input in top1 at 37C |
| GSM745640 |
Top2 ChIP vs input in wild type at 37C |
| GSM745641 |
Top2 ChIP vs input in top1,top2-ts at 37C |
| GSM745642 |
Top2 ChIP vs input in top1 at 37C |
|
| Relations |
| BioProject |
PRJNA128205 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22626_79502_input_6.CEL.gz |
35.6 Mb |
(ftp)(http) |
CEL |
| GSE22626_79504_input_6.CEL.gz |
35.4 Mb |
(ftp)(http) |
CEL |
| GSE22626_81563_input_6.CEL.gz |
27.0 Mb |
(ftp)(http) |
CEL |
| GSE22626_81565_input_6.CEL.gz |
28.3 Mb |
(ftp)(http) |
CEL |
| GSE22626_81567_input_6.CEL.gz |
30.2 Mb |
(ftp)(http) |
CEL |
| GSE22626_83607_input_6.CEL.gz |
32.7 Mb |
(ftp)(http) |
CEL |
| GSE22626_83609_input_6.CEL.gz |
32.1 Mb |
(ftp)(http) |
CEL |
| GSE22626_83622_input_6.CEL.gz |
30.8 Mb |
(ftp)(http) |
CEL |
| GSE22626_83624_input_6.CEL.gz |
29.0 Mb |
(ftp)(http) |
CEL |
| GSE22626_83626_input_6.CEL.gz |
29.9 Mb |
(ftp)(http) |
CEL |
| GSE22626_85580_input_6.CEL.gz |
31.9 Mb |
(ftp)(http) |
CEL |
| GSE22626_85844_input_6.CEL.gz |
31.8 Mb |
(ftp)(http) |
CEL |
| GSE22626_85847_input_6.CEL.gz |
28.5 Mb |
(ftp)(http) |
CEL |
| GSE22626_RAW.tar |
1.9 Gb |
(http)(custom) |
TAR (of BAR, CEL, TSV, TXT) |
| Processed data provided as supplementary file |
| Processed data included within Sample table |
Less...
More...