RPXD000667 is an
old-style reanalysis announcement missing a container. This dataset should be updated with a proper container and revision following 2019 ProteomeXchange protocols.
Outdated Reanalysis Missing a Container Summary
Title | Reprocessed: Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives |
Description | Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC) and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC) and adult mouse brain tissue. Readers for these modifications are only partially overlapping and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation. Peptides were separated on an EASY-nLC (Proxeon) connected online to an LTQ-Orbitrap-Velos mass spectrometer. Spectra were recorded in CID mode. A gradient of organic solvent (5-30% acetonitrile) was applied (120 minutes) and the top 15 most abundant peptides were fragmented for MS/MS, using an exclusion list of 500 proteins for 45 seconds. Reprocessed by PeptideAtlas; |
HostingRepository | PeptideAtlas |
AnnounceDate | 2013-12-23 |
AnnouncementXML | Submission_2013-12-23_12:17:39.xml |
DigitalObjectIdentifier | |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Reanalysis of PXD000143 |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Zhi Sun |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | isotope labeled residue; 6x(13)C labeled L-arginine; 6x(13)C,4x(15)N labeled L-arginine; 6x(13)C,2x(15)N labeled L-lysine; L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine |
Instrument | LTQ Orbitrap Velos |
Dataset History
Reanalysis | Revision | Datetime | Status | Title / ChangeLog Entry |
| 0 | 2013-12-23 11:33:14 | ID requested | |
| 1 | 2013-12-23 12:17:59 | announced | Reprocessed: Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives |
Publication List
Keyword List
curator keyword: 5-hydroxymethylcytosine, stem cells, differentiation, quantitative mass spectrometry, chromatin readers |
Contact List
Zhi Sun |
contact affiliation | Institute for Systems Biology |
contact email | zhi.sun@systemsbiology.org |
dataset submitter | |
Eric Deutsch |
contact affiliation | Institute for Systems Biology |
contact email | edeutsch@systemsbiology.org |
lab head | |
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