PXD028571-1

PXD028571 is an original dataset announced via ProteomeXchange.

Title	Internal Ribosome Entry Site RNAs act in trans through an antisense sequence
Description	SINEUPs are antisense long non-coding RNAs (lncRNAs) that increase translation of overlapping mRNAs through the activity of two domains: an embedded SINEB2 sequence UP-regulates translation (Effector Domain) while the antisense region provides target specificity (Binding Domain). In this study, we show that the invSINEB2 sequence from the natural SINEUP AS Uchl1 RNA exhibits the functions of an Internal Ribosomal Entry Site (IRES), while viral and cellular IRES sequences act as Effector Domains, promoting protein expression in trans. We demonstrate that the Stem Loop1 of AS Uchl1 SINEB2 is functionally equivalent to the IIId loop of Hepatitis C Virus IRES. The natural circ5533, a circular RNA at the c-myc locus, up-regulates the protein expression in trans of specific target mRNAs through an IRES sequence serving as Effector Domain and antisense regions as Binding Domains. This work shows a new function for embedded transposable elements in lncRNAs, proves that an IRES sequence can work in trans enhancing the translation of a target mRNA and identify a new class of regulatory circRNAs.
HostingRepository	PRIDE
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-24_17:25:51.549.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrea Armirotti
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-16 07:41:18	ID requested
⏵ 1	2025-08-24 17:25:52	announced

D'Agostino S, Tettey-Matey A, Volpe M, Pierattini B, D'Agostino M, Sm, ě, l, á D, Ansaloni F, Broglia L, Lau P, Peruzzo O, Braccia C, Armirotti A, Scarpato M, Damiani D, Ros G, Di Carlo V, Maniscalco F, Bechara E, Tartaglia GG, Carninci P, Santoro C, Persichetti F, Pandolfini L, Simonetti A, Espinoza S, Zucchelli S, Sanges R, Bon C, Gustincich S, Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs. Nucleic Acids Res, 53(15):(2025) [pubmed]

10.1093/nar/gkaf788;

submitter keyword: proteomics, circ5533, pxk, binding domain,SINEUPs

Andrea Armirotti
contact affiliation	Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
contact email	andrea.armirotti@iit.it
lab head
Andrea Armirotti
contact affiliation	Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia
contact email	andrea.armirotti@iit.it
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/2025/08/PXD028571

PRIDE project URI

• PRIDE
  1. PXD028571
     1. Label: PRIDE project
     2. Name: Internal Ribosome Entry Site RNAs act in trans through an antisense sequence