OnTarget: in silico design of MiniPromoters for targeted delivery of expression

Abstract MiniPromoters, or compact promoters, are short DNA sequences that can drive expression in specific cells and tissues. While broadly useful, they are of high relevance to gene therapy due to their role in enabling precise control of where a therapeutic gene will be expressed. Here, we presen...

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Bibliographic Details
Published in:Nucleic acids research 2023-07, Vol.51 (W1), p.W379-W386
Main Authors: Fornes, Oriol, Av-Shalom, Tamar V, Korecki, Andrea J, Farkas, Rachelle A, Arenillas, David J, Mathelier, Anthony, Simpson, Elizabeth M, Wasserman, Wyeth W
Format: Article
Language:English
Subjects:
Computational Biology - instrumentation
Computational Biology - methods
Computer Simulation
Enhancer Elements, Genetic - genetics
Genome
Genomics
Internet
Promoter Regions, Genetic - genetics
Software
Web Server Issue
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Summary:Abstract MiniPromoters, or compact promoters, are short DNA sequences that can drive expression in specific cells and tissues. While broadly useful, they are of high relevance to gene therapy due to their role in enabling precise control of where a therapeutic gene will be expressed. Here, we present OnTarget (http://ontarget.cmmt.ubc.ca), a webserver that streamlines the MiniPromoter design process. Users only need to specify a gene of interest or custom genomic coordinates on which to focus the identification of promoters and enhancers, and can also provide relevant cell-type-specific genomic evidence (e.g. accessible chromatin regions, histone modifications, etc.). OnTarget combines the provided data with internal data to identify candidate promoters and enhancers and design MiniPromoters. To illustrate the utility of OnTarget, we designed and characterized two MiniPromoters targeting different cell populations relevant to Parkinson Disease. Graphical Abstract Graphical Abstract OnTarget (http://ontarget.cmmt.ubc.ca) is a webserver for the design of cell-type-specific MiniPromoters from genomic evidence provided by users. MiniP, MiniPromoter.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad375