PXD006358-2

PXD006358 is an original dataset announced via ProteomeXchange.

Title	Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis
Description	The RNA binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis, but its expression is reduced in Diamond Blackfan Anemia (DBA). To understand the role of Csde1 in DBA, and the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. Protein expression of ribogenesis factors Rpf2, Nop56 and Ebna1bp2 was reduced in the deletion mutant, while mRNA was unchanged. Protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced. Strikingly, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. The correlation efficient between protein (iBAQ) and mRNA (RPKM) expression was not different between Csde1-bound and other transcripts. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens oscillations in gene expression.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:36:47.541.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kat Moore
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-24 02:05:58	ID requested
1	2018-10-24 14:08:39	announced
⏵ 2	2024-10-22 04:36:51	announced	2024-10-22: Updated project metadata.

10.1371/journal.pone.0201690;

Moore KS, Yagci N, van Alphen F, Meijer AB, 't Hoen PAC, von Lindern M, Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One, 13(8):e0201690(2018) [pubmed]

curator keyword: Biological

submitter keyword: proteomics,Csde1, Label-free qauntification, IBAQ, RNA-binding protein, erythropoiesis, translation

Alexander B Meijer
contact affiliation	Dept. Plasma Proteins, Sanquin Research, Amsterdam, The Netherlands. Dept. Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands.
contact email	s.meijer@sanquin.nl
lab head
Kat Moore
contact affiliation	Sanquin Research
contact email	k.s.moore113@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006358
     1. Label: PRIDE project
     2. Name: Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis