PXD007582 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers |
Description | The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type–specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K36me2/K4me1 marks transcribed enhancers, while H3K36me3/K4me1 and H3K79me2/K4me1 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics. |
HostingRepository | PRIDE |
AnnounceDate | 2017-10-09 |
AnnouncementXML | Submission_2017-10-09_07:20:42.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Monica Soldi |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | monomethylated residue; N6: N6; acetylated residue; dimethylated residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-08-29 02:02:56 | ID requested | |
⏵ 1 | 2017-10-09 07:20:44 | announced | |
Publication List
Soldi M, Mari T, Nicosia L, Musiani D, Sigismondo G, Cuomo A, Pavesi G, Bonaldi T, Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers. Nucleic Acids Res, 45(21):12195-12213(2017) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: histone PTMs, enhancers, LC-MSMS |
Contact List
Monica Soldi |
contact affiliation | European Institute of Oncology |
contact email | monica.soldi@ieo.it |
lab head | |
Monica Soldi |
contact affiliation | European Institute of Oncology |
contact email | monica.soldi@ieo.it |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD007582
- Label: PRIDE project
- Name: Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers