PXD003622

PXD003622 is an original dataset announced via ProteomeXchange.

Title	Enhanced snoMEN vectors facilitate establishment of GFP–HIF-1α protein replacement human cell lines
Description	The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy.
HostingRepository	PRIDE
AnnounceDate	2016-05-06
AnnouncementXML	Submission_2016-05-06_05:06:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Vackar Afzal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-12 03:04:35	ID requested
⏵ 1	2016-05-06 05:06:07	announced

Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, Protein Replacement Human Cell Lines. PLoS One, 11(4):e0154759(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: snoMEN, snoRNA, RNA, human

Angus Lamond
contact affiliation	Principle Investigator
contact email	a.i.lamond@dundee.ac.uk
lab head
Vackar Afzal
contact affiliation	School of Life Sciences
contact email	v.z.afzal@dundee.ac.uk
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/2016/05/PXD003622

PRIDE project URI

• PRIDE
  1. PXD003622
     1. Label: PRIDE project
     2. Name: Enhanced snoMEN vectors facilitate establishment of GFP–HIF-1α protein replacement human cell lines