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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 22, 2008 |
| Title |
Chip-seq from MEF cells H3K27me3 |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons.
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| Overall design |
mapping of H3K27me3 histone modification in one MEF cell line (MEFF)
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| Contributor(s) |
Pauler FM, Sloane MA, Barlow DP |
| Citation(s) |
19047520 |
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| Submission date |
Sep 10, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Florian M Pauler |
| E-mail(s) |
florian.pauler@univie.ac.at
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| Phone |
+43 1 4277 54323
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| Fax |
+43 1 42770 9546
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| Organization name |
CeMM
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| Lab |
Denise P Barlow
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| Street address |
Dr Bohrgasse 9/4
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| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
A1030 |
| Country |
Austria |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE11389 |
Mouse Chromosome 17 Mapping in Two MEF Cell Lines |
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| Relations |
| SRA |
SRP000705 |
| BioProject |
PRJNA112659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12721_RAW.tar |
135.6 Mb |
(http)(custom) |
TAR (of GFF, TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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