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| Status |
Public on Jul 31, 2012 |
| Title |
Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution.
Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA.
Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states.
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| |
|
| Overall design |
Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.
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| |
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| Contributor(s) |
LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA |
| Citation(s) |
22897906 |
| |
| Submission date |
Jul 23, 2012 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Iouri Chepelev |
| E-mail(s) |
ichepelev@gmail.com
|
| Organization name |
US Department of Veterans Affairs Medical Center
|
| Street address |
3200 Vine St
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45220 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL6480 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
|
| Samples (5)
|
| GSM971955 |
HEK293_Control_shRNA_KD_Replicate_1 |
| GSM971956 |
HEK293_Control_shRNA_KD_Replicate_2 |
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| This SubSeries is part of SuperSeries: |
| GSE39581 |
Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins |
|
| Relations |
| BioProject |
PRJNA171164 |
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