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| Status |
Public on Oct 16, 2009 |
| Title |
Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila |
| Project |
modENCODE
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| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Full title: Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila development
Trimethylation of histone H3 on lysine 9 (H3K9me3) and lysine 27 (H3K27me3) is strongly associated with gene silencing and transcriptional repression in both Drosophila and mammals. H3K9me3 is linked to the formation of heterochromatin, while H3K27me3 is a hallmark of repression of euchromatic genes by Polycomb group proteins. We examined the genomic distribution of the two modifications at high resolution over nine different stages of Drosophila development, and found that they are present in large overlapping domains in euchromatin. These dual-mark domains are stable throughout the life of the fly, and cover genomic regions greatly enriched in developmental regulatory genes with spatially restricted expression.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
In this study we have performed ChIP-chip in triplicate for 2 repressive histone marks in Drosophila: H3K27me3 and H3K9me3. Hybridizations on Agilent microarrays have been perfomed to compare with Input chromatin sample as a negative control to calculate enrichments.
ChIP-chip experiments have been performed for 9 developmental time points: E0-4h; E4-8h; E12-16h; E16-20h; E20-24h; L1; L2; Pupae and Adult Males.
In addition, 3 ChIP-seq experiments have been performed for validation for E-0-4h, L1 and Pupae time-points where one replicate has been analyzed on the Solexa platform.
To complement this study, total RNA (Poly-A +) has been sequenced on the Solexa platform (2 lanes each) for matching time-points, in order to survey the gene expression levels associated with the ChIP experiments.
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| Contributor(s) |
Wagner U, Nègre N, Li Z, Ishii H, Miller SW, Shah PK, Hon GC, Morrison CA, Heinz EH, Bild NA, Hanley D, Grossman RH, Ren B, Posakony JW, White KP |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63467 |
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| Submission date |
Oct 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
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| Organization name |
University of Chicago
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| Department |
Institute for Genomics and Systems Biology
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| Street address |
900 E. 57th STR. 10th FL.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
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| Platforms (3) |
| GPL6949 |
Agilent-019182 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 3 |
| GPL6951 |
Agilent-019184 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 3 of 3 |
| GPL9058 |
Illumina Genome Analyzer (Drosophila melanogaster) |
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| Samples (49)
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE18572_RAW.tar |
2.3 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT) |
SRA Run Selector |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
| Processed data included within Sample table |
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