PXD028636

PXD028636 is an original dataset announced via ProteomeXchange.

Title	2'-O-methylation of the second transcribed nucleotide in eukaryotic RNA 5’ cap impacts protein production levels and susceptibility to DXO-mediated transcript degradation
Description	Eukaryotic mRNA 5’ end is decorated with cap structure which plays multiple roles in the cell. Most importantly, protects transcript from exonucleolytic degradation and enables translation of encoded protein conducted by cap-dependent machinery. This is also a key feature in the process of recognizing RNA as self or non-self molecule by cellular innate immune system. Cap is composed of 7-methylguanosine linked by a 5′,5′-triphosphate chain to the first transcribed nucleotide, and is formed enzymatically during transcription. This m7GpppN structure, called cap0, can be further modified by CMTR1 methyltransferase to cap1 (m7GpppNm), which predominates in eukaryotic cells. Cap2, with additional 2′-O-methylation at the second transcribed nucleotide (m7GpppNmpNm) added by another methyltransferase CMTR2, also can be found at mRNA 5’ end. We present new tools allowing for in vitro synthesis of RNAs possessing cap2, i.e tetranucleotide cap analogues. Utilizing these for in vitro transcription reactions we obtained RNAs with 2′-O-methylation present at the second transcribed nucleotide. Due to that we investigated the role of cap2 in protein production from reporter mRNA protected with this structure in different conditions, normal or stress ones, or with CMTR1/2 down regulated level. We also assessed the affinity of eIF4E protein to differentially capped RNAs. Furthermore, we verified whether an additional 2′-O-methylation presence in capped RNA makes transcript more resistant to decapping enzyme action.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:27.995.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD028636
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Dominik Cysewski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-19 22:21:25	ID requested
1	2022-09-08 06:08:47	announced
⏵ 2	2023-11-14 08:53:28	announced	2023-11-14: Updated project metadata.

10.6019/PXD028636;

submitter keyword: cap,A549, mRNA

Paweł Sikorski
contact affiliation	Centre of New Technology University of Warsaw Banacha 2C 02-097 Warsaw, Poland
contact email	p.sikorski@cent.uw.edu.pl
lab head
Dominik Cysewski
contact affiliation	Medical University of Bialystok
contact email	dominikcysewski@gmail.com
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/2022/09/PXD028636

PRIDE project URI

• PRIDE
  1. PXD028636
     1. Label: PRIDE project
     2. Name: 2'-O-methylation of the second transcribed nucleotide in eukaryotic RNA 5’ cap impacts protein production levels and susceptibility to DXO-mediated transcript degradation