PXD017893-3

PXD017893 is an original dataset announced via ProteomeXchange.

Title	NAD capping of mRNAs is abundant but strongly guarded against in yeast
Description	The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5'-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG motif for this purpose. Most NAD-RNAs are 3'-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:11:48.657.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yaqing Zhang
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-05 01:47:04	ID requested
1	2020-09-02 07:47:20	announced
2	2020-11-04 23:06:18	announced	2020-11-05: Updated publication reference for PubMed record(s): 33139726.
⏵ 3	2024-10-22 05:11:54	announced	2024-10-22: Updated project metadata.

10.1038/s41467-020-19326-3;

Zhang Y, Kuster D, Schmidt T, Kirrmaier D, N, ü, bel G, Ibberson D, Benes V, Hombauer H, Knop M, J, ä, schke A, Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast. Nat Commun, 11(1):5508(2020) [pubmed]

submitter keyword: NAD-RNA,S.cerevisiae, RNA surveillance, npy1, decapping

Andres Jäschke
contact affiliation	Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University
contact email	jaeschke@uni-hd.de
lab head
Yaqing Zhang
contact affiliation	Institute of Pharmacy and Molecular Biotechnology, Heidelberg University
contact email	yaqing.zhang@uni-heidelberg.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/2020/09/PXD017893

PRIDE project URI

• PRIDE
  1. PXD017893
     1. Label: PRIDE project
     2. Name: NAD capping of mRNAs is abundant but strongly guarded against in yeast