PXD023903 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Characterization of chromatin associated RNA-binding proteins by SPACE |
Description | Chromatin processes such as DNA replication, transcription and RNA processing are mediated by intermolecular transactions among proteins, RNAs and the genome. Although DNA-protein and RNA-protein interactions have been studied extensively, reliable and efficient identification of chromatin-associated RNA-binding proteins (caRBPs) has remained technically challenging; especially using limited sample material. Here, we present SPACE (Silica Particle Assisted Chromatin Enrichment), a stringent and straightforward chromatin-purification method, which works efficiently with as few as 100,000 cells. Using SPACE we have enriched 1825 chromatin-associated proteins in mES cells. Among many known and novel chromatin-associated proteins, we identified 743 RBPs. Considering protein counts RBPs consist 40% of the chromatin composition, while, weighted by their abundances they comprise ~70% of the chromatome. Furthermore, using a double tryptic digestion strategy (SPACE2) we have determined how the caRBPs bind to chromatin. By applying SPACE to mES cells in 2i and serum conditions, we have detected significant changes in the chromatome of the cells that are neglected in traditional full proteome analyses. Overall, SPACE and SPACE2 are sensitive and powerful methods for providing a global view of chromatin composition and RBP-chromatin interactions. |
HostingRepository | PRIDE |
AnnounceDate | 2021-11-25 |
AnnouncementXML | Submission_2021-11-25_08:59:13.323.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Mahmoudreza Rafiee |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-01-31 22:55:04 | ID requested | |
⏵ 1 | 2021-11-25 08:59:13 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: chromatin, proteomics, RBP, pluripotency, IDR, Dazl |
Contact List
Nicholas Luscombe |
contact affiliation | The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. |
contact email | nicholas.luscombe@crick.ac.uk |
lab head | |
Mahmoudreza Rafiee |
contact affiliation | The Francis Crick Institute |
contact email | rafieem@crick.ac.uk |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD023903
- Label: PRIDE project
- Name: Characterization of chromatin associated RNA-binding proteins by SPACE