Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies

Ralf Kittler, Vineeth Surendranath, Anne Kristin Heninger, Mikolaj Slabicki, Mirko Theis, Gabriele Putz, Kristin Franke, Antonio Caldarelli, Hannes Grabner, Karol Kozak, Jan Wagner, Effi Rees, Bernd Korn, Corina Frenzel, Christoph Sachse, Birte Sönnichsen, Jie Guo, Janell Schelter, Julja Burchard, Peter S. LinsleyAimee L. Jackson, Bianca Habermann, Frank Buchholz

Research output: Contribution to journalArticle

139 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)337-344
Number of pages8
JournalNature Methods
Volume4
Issue number4
DOIs
StatePublished - Apr 2007

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Endoribonucleases
RNA Interference
Small Interfering RNA
Genes
Genome
RNA
Cells
Microarray Analysis
Microarrays
Computer Simulation
Libraries
Rats
Screening
Down-Regulation
Databases
Costs and Cost Analysis
Costs
Proteins
Experiments

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Cell Biology

Cite this

Kittler, R., Surendranath, V., Heninger, A. K., Slabicki, M., Theis, M., Putz, G., ... Buchholz, F. (2007). Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nature Methods, 4(4), 337-344. https://doi.org/10.1038/nmeth1025

Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. / Kittler, Ralf; Surendranath, Vineeth; Heninger, Anne Kristin; Slabicki, Mikolaj; Theis, Mirko; Putz, Gabriele; Franke, Kristin; Caldarelli, Antonio; Grabner, Hannes; Kozak, Karol; Wagner, Jan; Rees, Effi; Korn, Bernd; Frenzel, Corina; Sachse, Christoph; Sönnichsen, Birte; Guo, Jie; Schelter, Janell; Burchard, Julja; Linsley, Peter S.; Jackson, Aimee L.; Habermann, Bianca; Buchholz, Frank.

In: Nature Methods, Vol. 4, No. 4, 04.2007, p. 337-344.

Research output: Contribution to journalArticle

Kittler, R, Surendranath, V, Heninger, AK, Slabicki, M, Theis, M, Putz, G, Franke, K, Caldarelli, A, Grabner, H, Kozak, K, Wagner, J, Rees, E, Korn, B, Frenzel, C, Sachse, C, Sönnichsen, B, Guo, J, Schelter, J, Burchard, J, Linsley, PS, Jackson, AL, Habermann, B & Buchholz, F 2007, 'Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies', Nature Methods, vol. 4, no. 4, pp. 337-344. https://doi.org/10.1038/nmeth1025
Kittler, Ralf ; Surendranath, Vineeth ; Heninger, Anne Kristin ; Slabicki, Mikolaj ; Theis, Mirko ; Putz, Gabriele ; Franke, Kristin ; Caldarelli, Antonio ; Grabner, Hannes ; Kozak, Karol ; Wagner, Jan ; Rees, Effi ; Korn, Bernd ; Frenzel, Corina ; Sachse, Christoph ; Sönnichsen, Birte ; Guo, Jie ; Schelter, Janell ; Burchard, Julja ; Linsley, Peter S. ; Jackson, Aimee L. ; Habermann, Bianca ; Buchholz, Frank. / Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. In: Nature Methods. 2007 ; Vol. 4, No. 4. pp. 337-344.
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