PXD050738-3

PXD050738 is an original dataset announced via ProteomeXchange.

Title	Complexome profiling of nuclear lysates from control and USP39-depleted HeLa cells
Description	RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic 5′ splice sites. To explore the interactions of USP39 and the effect of its depletion in HeLa cells, we performed complexome profiling of nuclear lysates. We observed most USP39 stably integrated into the tri-snRNP complex and there is almost no free nuclear protein. More importantly, the relative abundance of tri-snRNP spliceosome complex was impaired in USP39-depleted cells. As previous reports indicated, USP39 is a regulator of tri-snRNP stability and its depletion decreased the levels of assembled U4/U6.U5 complexes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:59:42.796.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD050738
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alfredo Cabrera-Orefice
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-18 16:05:03	ID requested
1	2024-09-25 10:12:44	announced
2	2024-09-27 02:34:26	announced	2024-09-27: Updated project metadata.
⏵ 3	2024-10-22 06:59:43	announced	2024-10-22: Updated project metadata.

10.6019/PXD050738;

submitter keyword: HeLa cells,Complexome profiling, USP39, Nucleus, Spliceosome

Alfredo Cabrera-Orefice
contact affiliation	Functional Proteomics Center, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
contact email	alfredbiomed@gmail.com
lab head
Alfredo Cabrera-Orefice
contact affiliation	Goethe University Frankfurt
contact email	alfredbiomed@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050738
     1. Label: PRIDE project
     2. Name: Complexome profiling of nuclear lysates from control and USP39-depleted HeLa cells