|
| Status |
Public on Dec 12, 2011 |
| Title |
Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two ways: NURD, (P)BAP and INO80 increase histone density at their target sequences, which disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Thus, both selective targeting and distinct mechanisms of remodeling underlie the functional differentiation of remodelers. We conclude that chromatin organization involves a class-specific antagonism between remodeler activity and DNA sequence-driven nucleosome placement.
The supplementary bed files (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed contain high quality binding sites for each remodeler obtained by intersecting the sets of significant ChIP-chip peaks for each antibody.
|
| |
|
| Overall design |
Genome-wide remodelers and chromatin profiling in Drosophila by ChIP-chip and FAIRE-chip
|
| |
|
| Contributor(s) |
Moshkin YM, Verrijzer CP |
| Citation(s) |
22124157 |
| |
| Submission date |
Sep 27, 2011 |
| Last update date |
Jul 08, 2015 |
| Contact name |
Yuri Moshkin |
| E-mail(s) |
[email protected]
|
| Phone |
0031-10-7043335
|
| Organization name |
Erasmus University Medical Center
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL6629 |
[DM_tiling2_MR] Affymetrix Drosophila Tiling 2.0R Array |
|
| Samples (51)
|
|
| Relations |
| BioProject |
PRJNA146395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32404_(P)BAP_sites.bed.gz |
26.1 Kb |
(ftp)(http) |
BED |
| GSE32404_INO80_sites.bed.gz |
61.3 Kb |
(ftp)(http) |
BED |
| GSE32404_ISWI_sites.bed.gz |
29.7 Kb |
(ftp)(http) |
BED |
| GSE32404_NURD_sites.bed.gz |
59.4 Kb |
(ftp)(http) |
BED |
| GSE32404_RAW.tar |
6.2 Gb |
(http)(custom) |
TAR (of BAR, BED, CEL, SGR) |
| GSE32404_S2_input_1.CEL.gz |
31.0 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_input_2.CEL.gz |
31.7 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_input_3.CEL.gz |
31.2 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_input_4.CEL.gz |
30.1 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_input_5.CEL.gz |
31.6 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_preimmune_1.CEL.gz |
22.1 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_preimmune_2.CEL.gz |
21.1 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_preimmune_3.CEL.gz |
27.4 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_preimmune_4.CEL.gz |
27.8 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_1.CEL.gz |
23.4 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_2.CEL.gz |
24.6 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_3.CEL.gz |
25.4 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_4.CEL.gz |
25.9 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_5.CEL.gz |
21.0 Mb |
(ftp)(http) |
CEL |
| GSE32404_S2_mock_protA_6.CEL.gz |
24.6 Mb |
(ftp)(http) |
CEL |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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