|
| Status |
Public on Oct 18, 2010 |
| Title |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: ChIP-chip data |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the “default” chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy.
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| Overall design |
All experiments were done using two channels per chip, comparing DNA immunoprecipitated by the indicated antibody to matching input chromatin used for affinity purification. Where appropriate, replicate data sets were averaged.
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| Contributor(s) |
Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K |
| Citation(s) |
21074046 |
| |
| Submission date |
Feb 22, 2010 |
| Last update date |
Jun 23, 2014 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL6888 |
Henikoff_Dmel_r52_ChIP tiling design |
|
| Samples (21)
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| This SubSeries is part of SuperSeries: |
| GSE20472 |
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation |
|
| Relations |
| BioProject |
PRJNA129557 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20471_DSIF_Average_Adelman.txt.gz |
21.1 Mb |
(ftp)(http) |
TXT |
| GSE20471_NELF_Average_Adelman.txt.gz |
21.1 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_+Ecdysone_Average_Adelman.txt.gz |
21.1 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_-Ecdysone_Average_Adelman.txt.gz |
21.1 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_Average_Adelman.txt.gz |
21.3 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_Embryo_Average_Adelman.txt.gz |
21.4 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_Mock_RNAi_Adelman.txt.gz |
21.1 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_NELF_RNAi_Average_Adelman.txt.gz |
21.0 Mb |
(ftp)(http) |
TXT |
| GSE20471_Pol_II_Untreated_RNAi_Average_Adelman.txt.gz |
21.2 Mb |
(ftp)(http) |
TXT |
| GSE20471_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of PAIR) |
| GSE20471_Ser2-P_Pol_II_Average_Adelman.txt.gz |
21.2 Mb |
(ftp)(http) |
TXT |
| GSE20471_TFIIA_Average_Adelman.txt.gz |
18.4 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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