title: Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies.
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.
authors.affiliation: Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Kittler
authors.forename: Vineeth
authors.initials: V
authors.lastname: Surendranath
authors.forename: Anne-Kristin
authors.initials: AK
authors.lastname: Heninger
authors.forename: Mikolaj
authors.initials: M
authors.lastname: Slabicki
authors.forename: Mirko
authors.initials: M
authors.lastname: Theis
authors.forename: Gabriele
authors.initials: G
authors.lastname: Putz
authors.forename: Kristin
authors.initials: K
authors.lastname: Franke
authors.forename: Antonio
authors.initials: A
authors.lastname: Caldarelli
authors.forename: Hannes
authors.initials: H
authors.lastname: Grabner
authors.forename: Karol
authors.initials: K
authors.lastname: Kozak
authors.forename: Jan
authors.initials: J
authors.lastname: Wagner
authors.forename: Effi
authors.initials: E
authors.lastname: Rees
authors.forename: Bernd
authors.initials: B
authors.lastname: Korn
authors.forename: Corina
authors.initials: C
authors.lastname: Frenzel
authors.forename: Christoph
authors.initials: C
authors.lastname: Sachse
authors.forename: Birte
authors.initials: B
authors.lastname: Sönnichsen
authors.forename: Jie
authors.initials: J
authors.lastname: Guo
authors.forename: Janell
authors.initials: J
authors.lastname: Schelter
authors.forename: Julja
authors.initials: J
authors.lastname: Burchard
authors.forename: Peter S
authors.initials: PS
authors.lastname: Linsley
authors.forename: Aimee L
authors.initials: AL
authors.lastname: Jackson
authors.forename: Bianca
authors.initials: B
authors.lastname: Habermann
authors.forename: Frank
authors.initials: F
authors.lastname: Buchholz
mesh_terms: D000818:Animals; D004722:Endoribonucleases / Q000235:genetics*; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D006801:Humans; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D014158:Transcription, Genetic; D014162:Transfection; D020506:Untranslated Regions; D014584:User-Computer Interface
chemical_list: D034741:RNA, Small Interfering; D020506:Untranslated Regions; D004722:Endoribonucleases