Nature Methods
- 4, 337 - 344 (2007)
Published online: 11 March 2007; | doi:10.1038/nmeth1025
Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studiesRalf Kittler1, 7, 8, Vineeth Surendranath1, 2, 8, Anne-Kristin Heninger1, Mikolaj Slabicki1, Mirko Theis1, Gabriele Putz1, Kristin Franke1, Antonio Caldarelli1, Hannes Grabner1, 3, Karol Kozak1, 3, Jan Wagner1, 3, Effi Rees4, Bernd Korn4, Corina Frenzel5, Christoph Sachse5, Birte Sönnichsen5, Jie Guo6, Janell Schelter6, Julja Burchard6, Peter S Linsley6, Aimee L Jackson6, Bianca Habermann1, 2 & Frank Buchholz11
Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany. 2
Scionics Computer Innovation, GmbH, Tatzberg 47-51, D-01307 Dresden, Germany. 3
Technology Development Studio, Pfotenhauerstrasse 108, D-01307 Dresden, Germany. 4
RZPD-Ressourcenzentrum für Genomforschung, Im Neuenheimer Feld 506, D-69120 Heidelberg, Germany. 5
Cenix BioScience GmbH, Tatzberg 47, Dresden 01307, Germany. 6
Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, Washington 98034, USA. 7
Present address: Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA. 8
These authors contributed equally to this work.
Correspondence should be addressed to Bianca Habermann habermann@mpi-cbg.de or Frank Buchholz buchholz@mpi-cbg.de RNA interference (RNAi) has become an important technique for loss-of-gene-function studies in mammalian cells. To achieve reliable results in an RNAi experiment, efficient and specific silencing triggers are required. Here we present genome-wide data sets for the production of endoribonuclease-prepared short interfering RNAs (esiRNAs) for human, mouse and rat. We used an algorithm to predict the optimal region for esiRNA synthesis for every protein-coding gene of these three species. We created a database, RiDDLE, for retrieval of target sequences and primer information. To test this in silico resource experimentally, we generated 16,242 esiRNAs that can be used for RNAi screening in human cells. Comparative analyses with chemically synthesized siRNAs demonstrated a high silencing efficacy of esiRNAs and a 12-fold reduction of downregulated off-target transcripts as detected by microarray analysis. Hence, the presented esiRNA libraries offer an efficient, cost-effective and specific alternative to presently available mammalian RNAi resources.
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