PXD005761

PXD005761 is an original dataset announced via ProteomeXchange.

Title	Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5’ UTR of tumor-associated mRNAs
Description	G-quadruplex structures in the 5’ UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). The identified ribosomal proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. In addition, several proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the set of candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions may be relevant to the regulation of mRNA maturation and may play an important role in tumor biology.
HostingRepository	PRIDE
AnnounceDate	2017-11-14
AnnouncementXML	Submission_2017-11-14_09:35:21.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jens Kurreck
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-01-23 01:35:10	ID requested
⏵ 1	2017-11-14 09:35:22	announced

Serikawa T, Spanos C, von Hacht A, Budisa N, Rappsilber J, Kurreck J, Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs. Biochimie, 144():169-184(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Shotgun proteomics, SILAC, RNA, G-quadruplexes, Bcl-2, NRAS, MMP16, ARPC2, RBPs, post-transcriptional regulation, translational regulation, cancer

Jens Kurreck
contact affiliation	Technische Universität Berlin
contact email	jens.kurreck@tu-berlin.de
lab head
Jens Kurreck
contact affiliation	Technische Universität Berlin
contact email	jens.kurreck@tu-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005761
     1. Label: PRIDE project
     2. Name: Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5’ UTR of tumor-associated mRNAs