title: The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects.
abstract: RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA 'specificity' design rules.
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom.|Safety Assessment, GlaxoSmithKline R&D, Ware, Hertfordshire, United Kingdom.|Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom.|Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, United Kingdom.
authors.forename: Piotr J
authors.initials: PJ
authors.lastname: Kamola
authors.affiliation: Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Nakano
authors.affiliation: Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Takahashi
authors.affiliation: Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Wilson
authors.affiliation: Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan.|Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
authors.forename: Kumiko
authors.initials: K
authors.lastname: Ui-Tei
mesh_terms: D020137:Base Pair Mismatch / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D020868:Gene Silencing; D018390:Gene Targeting / Q000379:methods*; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D034743:RNA-Induced Silencing Complex / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex