PXD029684

PXD029684 is an original dataset announced via ProteomeXchange.

Title	Copy number variation in tRNA isodecoders impairs mammalian development and balanced translation
Description	The number of tRNA isodecoder genes has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-seq, RNA-seq and proteomics we observed distinct molecular consequences of individual tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoders compensate for the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least four tRNA-Phe isodecoders is required for embryonic development and survival. The loss of tRNA-Phe-1-1 and any other three tRNA-Phe genes causes embryonic lethality indicating that tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA isodecoder genes is required to buffer translation and viability in mammals.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:44:48.346.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Timothy McCubbin
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-11 05:33:07	ID requested
1	2023-04-18 18:21:00	announced
2	2023-11-14 08:54:25	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:44:48	announced	2024-10-22: Updated project metadata.

10.1038/S41467-023-37843-9;

submitter keyword: brain,Mouse, liver

Aleksandra Filipovska
contact affiliation	Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
contact email	aleksandra.filipovska@uwa.edu.au
lab head
Timothy McCubbin
contact affiliation	University of Queensland
contact email	t.mccubbin@uq.edu.au
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/04/PXD029684

PRIDE project URI

• PRIDE
  1. PXD029684
     1. Label: PRIDE project
     2. Name: Copy number variation in tRNA isodecoders impairs mammalian development and balanced translation