title: A detailed investigation of accessibilities around target sites of siRNAs and miRNAs.
abstract: BACKGROUND
  The importance of RNA sequence analysis has been increasing since the discovery of various types of non-coding RNAs transcribed in animal cells. Conventional RNA sequence analyses have mainly focused on structured regions, which are stabilized by the stacking energies acting on adjacent base pairs. On the other hand, recent findings regarding the mechanisms of small interfering RNAs (siRNAs) and transcription regulation by microRNAs (miRNAs) indicate the importance of analyzing accessible regions where no base pairs exist. So far, relatively few studies have investigated the nature of such regions.
  
  
  RESULTS
  We have conducted a detailed investigation of accessibilities around the target sites of siRNAs and miRNAs. We have exhaustively calculated the correlations between the accessibilities around the target sites and the repression levels of the corresponding mRNAs. We have computed the accessibilities with an originally developed software package, called 'Raccess', which computes the accessibility of all the segments of a fixed length for a given RNA sequence when the maximal distance between base pairs is limited to a fixed size W. We show that the computed accessibilities are relatively insensitive to the choice of the maximal span W. We have found that the efficacy of siRNAs depends strongly on the accessibility of the very 3'-end of their binding sites, which might reflect a target site recognition mechanism in the RNA-induced silencing complex. We also show that the efficacy of miRNAs has a similar dependence on the accessibilities, but some miRNAs also show positive correlations between the efficacy and the accessibilities in broad regions downstream of their putative binding sites, which might imply that the downstream regions of the target sites are bound by other proteins that allow the miRNAs to implement their functions. We have also investigated the off-target effects of an siRNA as a potential RNAi therapeutic. We show that the off-target effects of the siRNA have similar correlations to the miRNA repression, indicating that they are caused by the same mechanism.
  
  
  BACKGROUND
  The C++ source code of the Raccess software is available at http://www.ncrna.org/software/Raccess/ The microarray data on the measurements of the siRNA off-target effects are also available at the same site.
  
  
  BACKGROUND
  kiryu-h@k.u-tokyo.ac.jp
authors.affiliation: Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, Chiba 277-8561, Japan. kiryu-h@k.u-tokyo.ac.jp
authors.forename: Hisanori
authors.initials: H
authors.lastname: Kiryu
authors.forename: Goro
authors.initials: G
authors.lastname: Terai
authors.forename: Osamu
authors.initials: O
authors.lastname: Imamura
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Yoneyama
authors.forename: Kenji
authors.initials: K
authors.lastname: Suzuki
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000818:Animals; D005347:Fibroblasts / Q000378:metabolism; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000378:metabolism*; D034743:RNA-Induced Silencing Complex / Q000378:metabolism; D051381:Rats; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex