PXD002560 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Systems level analysis of histone H3 post-translational modifications reveals features of PTM crosstalk in chromatin regulation |
| Description | Chromatin structure and function is maintained by dynamic protein-protein and protein-nucleic acid interactions. Histones are a family of proteins that are abundant chromatin constituents and that carry numerous post-translational modifications (PTMs). Histone PTMs mediate a variety of biological activities, including recruitment of enzymatic readers, writers and erasers that modulate protein activities, DNA replication, transcription and repair. Individual histone molecules contain multiple co-existing PTMs some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. We here present an integrated experimental and computational approach for systems level molecular characterization of PTMs and PTM crosstalk. Using wildtype and engineered mouse embryonic stem cells with perturbations in the Polycomb Repressive Complex 1 (PRC1, suz12-/-), PRC2 (Ring1A/b-/-) and DNA methyltransferases (Dnmt1/3a/3b-/-) we performed comprehensive PTM analysis of histone H3 tails. We identified unique histone H3 PTM features of each of the four cell lines and we detected common combinatorial PTM features across cell lines. Using quantitative middle-down proteomics combined with probabilistic and statistical data analysis we extracted histone H3 PTM profiles for all four mESC systems. PTM crosstalk emerged as mutually exclusive histone PTMs or coordinately regulated PTMs independent of histone peptide abundance in the four model systems. We detected positive crosstalk between adjacent mono-methylated marks but strong negative crosstalk among most of the seven characterized di- and tri-methylations on lysines. We report novel features of PTM interplay involving hitherto poorly characterized arginine methylation and lysine methylation sites in histone H3, including H3R2me, H3R8me and H3K37me, which exhibited specific PTM codes suggesting a particular role in chromatin. All histone H3 PTM data is available in our publicly available CrossTalkDB repository at http://crosstalkdb.bmb.sdu.dk |
| HostingRepository | PRIDE |
| AnnounceDate | 2016-07-06 |
| AnnouncementXML | Submission_2016-07-06_04:13:21.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD002560 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Simone Sidoli |
| SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
| ModificationList | N6: N6-dimethyl-L-lysine; N6: N6; acetylated residue; monomethylated residue; symmetric dimethyl-L-arginine |
| Instrument | LTQ Orbitrap Velos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2015-07-20 01:51:25 | ID requested | |
| 1 | 2016-06-16 06:18:09 | announced | |
| ⏵ 2 | 2016-07-06 04:13:22 | announced | Updated project metadata. |
Publication List
| Schw, รค, mmle V, Sidoli S, Ruminowicz C, Wu X, Lee CF, Helin K, Jensen ON, Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation. Mol Cell Proteomics, 15(8):2715-29(2016) [pubmed] |
Keyword List
| curator keyword: Biological |
| submitter keyword: post-translational modification |
| crosstalk |
| histone |
| mass spectrometry |
| proteomics |
Contact List
| Ole N. Jensen |
|---|
| contact affiliation | Centre for Epigenetics and Department of Biochemistry and Molecular Biology, University of Southern Denmark Campusvej 55 DK-5230 Odense M, Denmark |
| contact email | jenseno@bmb.sdu.dk |
| lab head | |
| Simone Sidoli |
|---|
| contact affiliation | University of Pennsylvania |
| contact email | simone.sidoli@gmail.com |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD002560 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002560
- Label: PRIDE project
- Name: Systems level analysis of histone H3 post-translational modifications reveals features of PTM crosstalk in chromatin regulation
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