title: An effective method for selecting siRNA target sequences in mammalian cells.
abstract: RNA interference is a gene-silencing phenomenon triggered by dsRNA (double-stranded RNA) and has been widely used for studying gene functions. The short interfering RNA (siRNA) responsible for RNA interference, however, varies markedly in its gene-silencing efficacy. Because this efficacy depends on the selected target sequences, we developed an effective selection method based on the gene degradation measure (priority score) defined by positional features of individual nucleotides. We tested this method experimentally by using it to select new siRNA target sequences in the homo sapiens cyclin B1 gene (CCNB1) and confirmed that it selected highly effective gene-silencing sequences. The proposed method will therefore be useful for selecting new siRNA target sequences in mammalian cells.
authors.affiliation: RIKEN Genomic Sciences Center (GSC), Tsurumi-ku, Yokohama, Kanagawa, Japan. takasaki@gsc.riken.jp
authors.forename: Shigeru
authors.initials: S
authors.lastname: Takasaki
authors.forename: Shuji
authors.initials: S
authors.lastname: Kotani
authors.forename: Akihiko
authors.initials: A
authors.lastname: Konagaya
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000502:physiology; D045744:Cell Line, Tumor; D019926:Cyclin B / Q000235:genetics; D056744:Cyclin B1; D015971:Gene Expression Regulation, Enzymologic / Q000502:physiology; D020868:Gene Silencing / Q000502:physiology; D006367:HeLa Cells / Q000737:chemistry / Q000201:enzymology / Q000378:metabolism; D006801:Humans; D034741:RNA, Small Interfering / Q000502:physiology*
chemical_list: C534699:CCNB1 protein, human; D019926:Cyclin B; D056744:Cyclin B1; D034741:RNA, Small Interfering