PXD031221

PXD031221 is an original dataset announced via ProteomeXchange.

Title	Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6
Description	The Jumonji domaining-containing protein JMJD6 is a 2-oxoglutarate dependent dioxygenase that has been implicated in a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing and co-transcriptional processing. Although not all studies agree, JMJD6 has been reported to catalyse both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and the indirect implication of JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a site of reported prolyl hydroxylation within a lysine-rich region of the bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalysed by Jmjd6. This prompted a wider search for JMJD6-catalysed protein modifications deploying mass spectrometric methods designed to identify novel substrate associations and facilitate analysis of lysine-rich regions by LC-MSMS. Using derivatization of lysine with propionic anhydride to improve the analysis of tryptic peptides and a pharmacological inhibitor of JMJD6 to stabilise enzyme/substrate associations, we report over 100 sites of JMJD6-catalysed lysyl hydroxylation on 48 protein substrates including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in this study have been associated with membraneless organelle formation. Taken together with findings implicating lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia. This deposition contains all hydroxylysine assignment data.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:54:13.423.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD031221
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Cockman
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; dihydroxylated residue; dimethylated L-arginine; N6-propanoyl-L-lysine; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-25 00:45:55	ID requested
1	2022-08-02 10:49:55	announced
⏵ 2	2023-11-14 08:54:13	announced	2023-11-14: Updated project metadata.

10.6019/PXD031221;

submitter keyword: Human, LC-MSMS, Hydroxylation, JMJD6, Lysine derivatisation

Peter Ratcliffe
contact affiliation	Francis Crick Institute 1 Midland Road London NW1 1AT
contact email	peter.ratcliffe@crick.ac.uk
lab head
Matthew Cockman
contact affiliation	Francis Crick Institute
contact email	matthew.cockman@crick.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD031221
     1. Label: PRIDE project
     2. Name: Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6