PXD044218

PXD044218 is an original dataset announced via ProteomeXchange.

Title	3'-tRF-CysGCA overexpression alters the expression profile of HEK-293 cells and modulates cellular processes and pathways
Description	tRNA fragments (tRFs) are small non-coding RNA molecules that are generated through the cleavage of tRNAs and have been implicated in various biological processes. Among the different types of tRFs, the 3′-tRFs have attracted considerable scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3′-tRF-CysGCA, a tRF derived from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3′-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3′-tRF-CysGCA levels in human cells have not been investigated so far. To address this gap, we stably overexpressed 3′-tRF-CysGCA in HEK-293 cells and performed transcriptomics and proteomics experiments. Moreover, we validated the interaction of this tRF with putative targets whose levels were affected after 3′-tRF-CysGCA overexpression. Last, we investigated the implication of 3′-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3′-tRF-CysGCA overexpression led to changes in the cell expression profile, and we identified multiple pathways that were affected by the deregulation of this tRF. Additionally, our reporter assays demonstrated that 3′-tRF-CysGCA directly interacted with TMPO and ERGIC1, leading to changes in their expression levels. Taken together, these findings suggest that 3′-tRF-CysGCA plays a significant role in the regulation of gene expression and highlight the potential importance of this tRF in cellular processes.
HostingRepository	PRIDE
AnnounceDate	2023-11-30
AnnouncementXML	Submission_2023-11-30_07:08:25.529.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Samiotaki
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-31 06:38:55	ID requested
⏵ 1	2023-11-30 07:08:27	announced

Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK, overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways. Funct Integr Genomics, 23(4):341(2023) [pubmed]

10.1007/s10142-023-01272-0;

submitter keyword: tRNA-derived RNA fragment (tRF)

non-coding RNA

post-transcriptional regulation

transcriptomics

proteomics

Christos Kontos
contact affiliation	Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, Greece;
contact email	chkontos@biol.uoa.gr
lab head
Martina Samiotaki
contact affiliation	Protein Analysis Laboratory B.S.R.C. "Alexander Fleming", Alexander Fleming Street 34 16672, Vari, Greece
contact email	samiotaki@fleming.gr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044218
     1. Label: PRIDE project
     2. Name: 3'-tRF-CysGCA overexpression alters the expression profile of HEK-293 cells and modulates cellular processes and pathways