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| Status |
Public on May 12, 2010 |
| Title |
Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging, ChIP-chip, and MeDIP-chip data |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by genome tiling array
Expression profiling by array
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| Summary |
Epigenetic environment of histone H3.3 on promoters revealed by integration of imaging and genome-scale chromatin and methyl-DNA immunoprecipitation information.
Chromatin regions with different transcriptional outputs are distinguished by the deposition of histone variants. Histone H3.3 is incorporated into chromatin in a replication-independent manner; yet the relationship between H3.3 deposition, chromatin environment is incompletely understood. We have integrated imaging and genome-scale chromatin and methyl-DNA immunoprecipitation approaches to investigate the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation and transcription.
Results: Imaging shows that H3.3, in contrast to replicative H3.1 or H2B, is enriched in chromatin marked by histone modifications of active genes. A genome-wide survey identifies 1,649 H3.3-enriched promoters, only a subset of which is co-enriched in H3K4me3, H3K9me3 and/or H3K27me3, with a preference for H3K4me3, corroborating imaging data. H3.3-enriched promoters are depleted of H3.3 at the TSS in a transcription-independent manner. H3.3 is found predominantly on CpG-rich unmethylated promoters, creating a condition favourable for transcription. In undifferentiated mesenchymal stem cells, H3.3 target genes are linked to signaling and mesodermal differentiation, suggesting that H3.3 may be a mark of lineage priming.
Conclusions: A minor fraction of H3.3 is targeted to promoters, which are predominantly CpG-rich, DNA unmethylated and devoid of detectable trimethylated H3K4, K9 and K27. Among H3.3 target promoters co-marked by methylated H3, H4K4me3 is preferred, with or without H3K27me3, arguing that in mesenchymal stem cells H3.3 marks transcriptionally active or potentially active promoters.
Key words: Imaging, ChIP-chip, MeDIP-chip, histone H3.3, mesenchymal stem cells
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| Overall design |
ChIP-chip and MeDIP-chip experiments: Performed with two independent biological replicates.
Gene expression profiling experiments: Total RNA obtained from H3.3-EGFP transfected or empty-EGFP transfected mesenchymal stem cells compared to untransfected mesenchymal stem cells. Raw expression data linked below as supplementary file (GSE17053_Illumina_non-normalized_data.txt).
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| Contributor(s) |
Reiner AH, Jacobsen BM |
| Citation(s) |
20375147, 20410135 |
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| Submission date |
Jul 10, 2009 |
| Last update date |
Jan 08, 2019 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Street address |
PO Box 1112 Blindern
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| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platforms (2) |
| GPL7363 |
Illumina HumanWG-6_V2_0_R2 |
| GPL7408 |
Nimblegen HG18 RefSeq promoter array |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA117783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE17053_Illumina_non-normalized_data.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
| GSE17053_RAW.tar |
167.6 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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