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PXD023903

PXD023903 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCharacterization of chromatin associated RNA-binding proteins by SPACE
DescriptionChromatin 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.
HostingRepositoryPRIDE
AnnounceDate2021-11-25
AnnouncementXMLSubmission_2021-11-25_08:59:13.323.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMahmoudreza Rafiee
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-31 22:55:04ID requested
12021-11-25 08:59:13announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: chromatin, proteomics, RBP, pluripotency, IDR, Dazl
Contact List
Nicholas Luscombe
contact affiliationThe Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
contact emailnicholas.luscombe@crick.ac.uk
lab head
Mahmoudreza Rafiee
contact affiliationThe Francis Crick Institute
contact emailrafieem@crick.ac.uk
dataset submitter
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