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PXD000361

PXD000361 is an original dataset announced via ProteomeXchange.

Dataset Summary
Title3xMBT protein pull-down
DescriptionLysine methylation of histone proteins regulates chromatin dynamics and plays important roles in diverse physiological and pathological processes. However, beyond histone proteins, the proteome-wide extent of lysine methylation is largely unknown. We have developed the naturally occurring MBT domain repeats of L3MBTL1 (3xMBT) to serve as a universal affinity reagent for detecting, enriching, and identifying proteins carrying a mono- or dimethylated lysine. The domain is broadly specific for methylated lysine ("pan-specific") and can be applied to any biological system. In experiments using two different instruments (experiment 1 - Orbitrap Elite, experiment 2 - Orbitrap Velos) we have used SILAC to compare proteins captured by 3xMBT to proteins captured by the D355N mutant, which does not bind methylated lysine. Data was analyzed using MaxQuant version 1.3.0.5 using default parameters except that mono and di-methylated lysine were included as variable modifications and modification-specific false discovery rate was set to 10%. Several hundred proteins are specifically enriched by 3xMBT and we have directly detected lysine methylation on about two dozen. We have also used our approach to identify candidate in-cell substrates of G9a and the related methyltransferase GLP. Three-way SILAC was used to compare methylated proteins between cells treated with UNC0638, a specific inhibitor of G9a and GLP, and cells treated with vehicle control. We find reduced capture of the known G9a substrates WIZ and ACIN1, as well as identifying DNA ligase 1 as a potential target for G9a/GLP. Together, our results demonstrate a powerful new approach for global and quantitative analysis of methylated lysine, and they represent the first systems biology understanding of lysine methylation.
HostingRepositoryPRIDE
AnnounceDate2014-08-08
AnnouncementXMLSubmission_2014-08-08_00:31:12.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterScott Carlson
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListN6: N6-dimethyl-L-lysine; monomethylated L-lysine
InstrumentLTQ Orbitrap Velos; Q Exactive; LTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-07-24 02:11:51ID requested
12013-11-11 03:38:29announced
12013-11-11 03:39:37announced
22014-07-25 01:25:38announcedUpdated project metadata.
32014-08-08 00:31:13announcedUpdated project metadata.
Publication List
Moore KE, Carlson SM, Camp ND, Cheung P, James RG, Chua KF, Wolf-Yadlin A, Gozani O, A general molecular affinity strategy for global detection and proteomic analysis of lysine methylation. Mol Cell, 50(3):444-56(2013) [pubmed]
Keyword List
curator keyword: Biomedical
submitter keyword: Methylation, Dimethylation, 3xMBT, L3MBTL1
Contact List
Scott Carlson
contact affiliationBiology
contact emailscottmc@stanford.edu
dataset submitter
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