PXD026774

PXD026774 is an original dataset announced via ProteomeXchange.

Title	Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation
Description	Turnover of nucleoplasmic transcripts by the multi-subunit RNA exosome is mediated by two adaptors; the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely been based on long-term factor depletion strategies. Here, we rapidly deplete a NEXT, a PAXT and a core-exosome component, uncovering direct consequences of their losses. Global proteome analyses displayed only minor changes, yet exposed the immediate co-depletion of exosome and adaptor subunits, reflecting possible sub-complex compositions. Parallel high-resolution 3’end sequencing of newly synthesized RNA confirmed earlier established long-term depletion phenotypes. Still, rapid NEXT depletion displayed a narrower phenotype, illustrated by its restricted effect on snoRNA-hosting introns, whereas long-term NEXT depletion data had suggested a more general role of the complex in mediating intron turnover. While this validates snoRNA-hosting introns as primary NEXT targets, our data suggest that nuclear 5’-3’ RNA decay is altered after prolonged NEXT depletion, obscuring interpretation. Further analysis of snoRNA-hosting introns also uncovered an unusual mode of core exosome-independent RNA decay. Due to its non-processive nature, we speculate that this reflects a hitherto undisclosed exosome-independent activity of the EXOSC10 ribonuclease.
HostingRepository	PRIDE
AnnounceDate	2022-01-13
AnnouncementXML	Submission_2022-01-13_07:30:57.340.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD026774
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jens Andersen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-18 01:33:38	ID requested
⏵ 1	2022-01-13 07:30:57	announced

Dataset with its publication pending

submitter keyword: RNA exosome, NEXT, PAXT, degron tag, TMTpro

Jens S. Andersen
contact affiliation	Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
contact email	jens.andersen@bmb.sdu.dk
lab head
Jens Andersen
contact affiliation	University of Southern Denmark, Department og Biochemistry and Molecular Biology
contact email	jens.andersen@bmb.sdu.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026774
     1. Label: PRIDE project
     2. Name: Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation