PXD021678-1

PXD021678 is an original dataset announced via ProteomeXchange.

Title	Gene- and species-specific Hox mRNA translation by ribosome expansion segments
Description	Ribosomes have been suggested to directly control gene regulation, however regulatory roles for ribosomal RNA (rRNA) remain largely unexplored. Expansion segments (ESs) consist of multitudes of tentacle-like rRNA structures extending from the core ribosome in eukaryotes. ESs are remarkably variable in sequence and size across eukaryotic evolution with a largely unknown function. In characterizing ribosome binding to a regulatory element within a Homeobox (Hox) 5’ UTR, we unexpectedly identify a modular stem-loop within this element that binds to a single ES, ES9S. Here, we described the raw data of the relative quantification proteomic analysis using tandem mass tag mass spectrometry of the ribonucleoprotein (RNP) complexes enriched from affinity pulldown of the 4xS1m-aptamer fusion constructs with the lysate components of C3H/10T1/2 cells and mouse embryo. 4xS1m pulldown is performed by combining mouse Hoxa9 mRNA elements (P3 and P4) with C3H/10T1/2 cell lysates, and by combining a9 IRES180 and an unrelated viral IRES with E11.5 FVB mouse embryo lysates. The aptamer alone served as a negative control. RNPs in the eluate were released by RNAse A treatment and were subjected to TMT 6plex labelling.
HostingRepository	PRIDE
AnnounceDate	2020-11-19
AnnouncementXML	Submission_2020-11-19_06:33:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Teodorus Theo Susanto
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-24 22:50:22	ID requested
⏵ 1	2020-11-19 06:33:29	announced

Leppek K, Fujii K, Quade N, Susanto TT, Boehringer D, Lenar, č, i, č T, Xue S, Genuth NR, Ban N, Barna M, Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments. Mol Cell, 80(6):980-995.e13(2020) [pubmed]

submitter keyword: RNA structure, mRNA translation, ribosome, internal initiation, internal ribosome entry site, stem-loop, Hox cluster, Hoxa9, RNA-protein interaction, ribosomal RNA, 4xS1m aptamer, affinity purification, LC MSMS, 6plex TMT, mouse FVB embryo E11.5, C3H/10T1/2

Maria Barna
contact affiliation	Department of Genetics, Stanford University
contact email	mbarna@stanford.edu
lab head
Teodorus Theo Susanto
contact affiliation	Graduate student
contact email	tsusanto@stanford.edu
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/2020/11/PXD021678

PRIDE project URI

• PRIDE
  1. PXD021678
     1. Label: PRIDE project
     2. Name: Gene- and species-specific Hox mRNA translation by ribosome expansion segments