PXD038103

PXD038103 is an original dataset announced via ProteomeXchange.

Title	Identification of SAFB and HnrnpU interactors
Description	Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type mouse embryonic stem cells (ESCs) and in ESCs in which SAFB and SAFB2 were knocked out. The transcript most enriched in SAFB association was the lncRNA Malat1, which contains a series of purine-rich motifs in its 5 end. Beyond Malat1, SAFB predominantly associated with introns of protein-coding genes also through purine-rich motifs. Knockout of SAFB/2 led to down- and upregulation of genes in multiple biological pathways. The nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes the expression of these genes. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of nascent transcripts. Proteomic analyses indicate an enrichment of nuclear speckle-associated, SR proteins in FLAG-tagged SAFB immunoprecipitated samples. Comparison to immunoprecipitates made from FLAG-tagging of another nuclear-enriched RNA-binding protein called HNRNPU (also known as SAF-A) identified both similarities and differences. Perhaps most notably, we observed a stronger enrichment for speckle-associated proteins in SAFB immunoprecipitations and a strong enrichment for paraspeckle-associated proteins in HNRNPU immunoprecipitations. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB directly promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:02:38.173.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christine Mills
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-11 09:02:22	ID requested
1	2023-07-20 10:42:47	announced
⏵ 2	2023-11-14 09:02:39	announced	2023-11-14: Updated project metadata.

Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM, A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biol Open, 12(6):(2023) [pubmed]

submitter keyword: stem cell, development,RNA Binding Proteins

Mauro Calabrese
contact affiliation	Department of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill
contact email	jmcalabr@med.unc.edu
lab head
Christine Mills
contact affiliation	University of North Carolina - Chapel Hill
contact email	allie.mills@unc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD038103
     1. Label: PRIDE project
     2. Name: Identification of SAFB and HnrnpU interactors