RNAi Screening

Simplified Illustration of RNAi

Simplified Illustration of RNAi

RNAi continues to be a very important tool for performing genetic analyses. It is particularly attractive because it can be used in many insect systems. However, it works better in some than in others.

Of course, this technology has been developed in a number of ways by those working on Drosophila melanogaster and its use in genetic screens both in Drosophila cells and in vivo has reach lofty levels of sophistication.

Insect scientists with an interest in the use and application of genetic technologies should be aware of these advanced capabilities and applications so they can cherry-pick what may work in their insects of interest or what might be modified so it can work in their system.

Basic in vivo F1 RNAi screen. photo: http://jcggdb.jp/GlycoPOD/protocolShow.action?nodeId=t32

Basic in vivo F1 RNAi screen.
photo: http://jcggdb.jp/GlycoPOD/protocolShow.action?nodeId=t32

Fortunately, Mohr (2014) has provided a concise summary of RNAi screening in Drosophila that is worth reading and is a good source of references on the topic.

Particularly helpful is her aggregation of various online resources in two tables (an excerpt of Table 1 is shown below).   Some of these resources can be helpful to anyone wishing to use RNAi as a functional genomics tool.

In vivo RNAi screens typically rely on large collections of transgenic fly lines each capable of expressing a single shRNA using a Gal4 –responsive promoter in essentially any cells of the insect at any developmental stage by making use of large existing collections of Gal4 enhancer-trap lines.  On a (much) smaller scale, similar approaches could be taken in a number of insects with up-and-running Gal4/UAS systems.

While most screens tend to be large and dependent on transgenic RNAi, this is not always the case and “large-scale screens have been performed in which dsRNA was injected into embryos, followed by time-lapse confocal microscopy…” Mohr (2014)    see Jankovics et al (2011)

Where there’s a will there’s a way.

FlyRNAi is a blog from the Director of the Drosophila RNAi Screening Center

FlyRNAi is a blog from the Director of the Drosophila RNAi Screening Center

Finally, the author, Dr. Stephanie Mohr is Director of the Drosophila RNAi Screening Center and, in additon,  has a useful blog called FlyRNAi where she tracks and comments on developments and applications of RNAi and RNAi screening in Drosophila.

 
Data from Mohr (2014)
Selected online resources for Drosophila cell-based and in vivo RNAi screening.
(See Mohr (2014) for references associated with each resource)
Resource type/name URL(s)
General information, external links and data access
Drosophila RNAi Screening Center (DRSC) http://www.flyrnai.org/
FlyBase resources list http://flybase.org
Genome RNAi http://www.genomernai.org/
RNAi fly stock collections and information
Bloomington Drosophila Stock Center http://flystocks.bio.indiana.edu/
NIG-Japan http://www.shigen.nig.ac.jp/fly/nigfly/
RNAi Stock Validation and Phenotypes (RSVP) http://www.flyrnai.org/rsvp
Transgenic RNAi Project (TRiP) http://www.flyrnai.org/trip
Vienna Drosophila RNAi Center (VDRC) http://stockcenter.vdrc.at/control/main
Drosophila cultured cell lines and information
Drosophila Genome Resource Center (DGRC) https://dgrc.cgb.indiana.edu/Home
Cell-based and in vivo fly RNAi collections search tool
Updated Targets of RNAi Reagents (UP-TORR) http://www.flyrnai.org/up-torr/
Cross-species RNAi rescue
DRSC RNAi rescue search tool http://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl
FlyFos collection search tool http://transgeneome-old.mpi-cbg.de/index.php?id=42

A Functional Genomic Screen Combined with Time-Lapse Microscopy Uncovers a Novel Set of Genes Involved in Dorsal Closure of Drosophila Embryos Ferenc Jankovics, László Henn, Ágnes Bujna, Péter Vilmos, Nóra Kiss, Miklós Erdélyi Research Article | published 20 Jul 2011 | PLOS ONE 10.1371/journal.pone.0022229

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