PXD012613

PXD012613 is an original dataset announced via ProteomeXchange.

Title	TRIM21-mediated protein depletion recapitulates mutant gene phenotype in early mouse embryos
Description	It is often desirable to be able to regulate or impair the expression of specific genes to study early developmental events in the mammalian embryo. While DNA and RNA methods are routine, methods using proteins are still in their infancy. When proteins in the cell encounter a specific antibody and the ubiquitin-protein ligase TRIM21, a ternary complex forms with the target protein, leading to its rapid and acute degradation – hence the name ‘Trim-Away'. However, there are many unknowns in this new endeavour. First and foremost, the extent to which endogenous proteins can be depleted depends on their amount in relation to the amount of exogenous antibody, which is limited by the microinjection procedure. Secondly, the depletion of the protein must be sustained over days. Using mass spectrometry and the iBAQ algorithm, we estimate the amount of proteins found in preimplantation mouse embryos. Most of these amounts are tractable with the microinjection method presented here, which supplies 10E-4 picomoles of antibody contained in 100 picolitres, before incurring toxic effects on mouse development. Building on these data, we demonstrate the feasibility of protein knock-down for a gene which is essential in the preimplantation mouse embryo, namely TEA domain family member 4 (Tead4). Knock-down persists long enough to result in a phenotype which is entirely consistent with that of the null mutation and the RNA interference: significantly reduced mRNA expression of TEAD4 target genes Cdx2 and Gata3, failure of CDX2 nuclear translocation and the embryo’s inability to implant. We conclude that at least for a time window of 3-4 days of preimplantation development, protein depletion is on the rise as a valid alternative to DNA and RNA methods.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:52:54.863.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannes Drexler
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-07 03:54:09	ID requested
1	2019-09-11 08:48:03	announced
2	2019-10-25 04:12:14	announced	2019-10-25: Updated publication reference for PubMed record(s): 31638890.
⏵ 3	2024-10-22 04:53:03	announced	2024-10-22: Updated project metadata.

Israel S, Casser E, Drexler HCA, Fuellen G, Boiani M, A framework for TRIM21-mediated protein depletion in early mouse embryos: recapitulation of Tead4 null phenotype over three days. BMC Genomics, 20(1):755(2019) [pubmed]

10.1186/s12864-019-6106-2;

curator keyword: Biological

submitter keyword: mouse, embryo, early development, SILAC, iBAQ, oocyte, proteome

Hannes C. A. Drexler
contact affiliation	Max Planck Institut for Molecular Biomedicine Bioanalytical Mass Spectrometry Röntgenstr. 20 48159 Münster Germany
contact email	hannes.drexler@mpi-muenster.mpg.de
lab head
Hannes Drexler
contact affiliation	Bioanalytical Mass Spectrometry, Max Planck Insitute for Molecular Biomedicine, Roentgenstr. 20, 48149 Münster, Germany
contact email	hannes.drexler@mpi-muenster.mpg.de
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/2019/09/PXD012613

PRIDE project URI

• PRIDE
  1. PXD012613
     1. Label: PRIDE project
     2. Name: TRIM21-mediated protein depletion recapitulates mutant gene phenotype in early mouse embryos