Filtering of Ineffective siRNAs and Improved siRNA Design Tool

MOTIVATION Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs. RESULTS The contribution of this paper is 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective. AVAILABILITY The siRNA design software tool can be found in the website http://www.cs.hku.hk/~sirna/ CONTACT smyiu@cs.hku.hk

[1]  T. Hennet,et al.  Biosynthesis of the Linkage Region of Glycosaminoglycans , 2001, The Journal of Biological Chemistry.

[2]  D. Weidner,et al.  Physical and Functional Interaction between Myeloid Cell Leukemia 1 Protein (MCL1) and Fortilin , 2002, The Journal of Biological Chemistry.

[3]  A. Fire,et al.  Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Hong-Gang Wang,et al.  A Role of the C-terminal Region of Human Rad9 (hRad9) in Nuclear Transport of the hRad9 Checkpoint Complex* , 2002, The Journal of Biological Chemistry.

[5]  Myles Brown,et al.  Molecular Determinants for the Tissue Specificity of SERMs , 2002, Science.

[6]  S. Narumiya,et al.  The Rho-associated protein kinase p160ROCK is required for centrosome positioning , 2002, The Journal of cell biology.

[7]  C. Haass,et al.  Presenilin and nicastrin regulate each other and determine amyloid β-peptide production via complex formation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Stephen J. Elledge,et al.  Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes , 2003, Science.

[9]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[10]  Jun Qin,et al.  ATR and ATRIP: Partners in Checkpoint Signaling , 2001, Science.

[11]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[12]  M. Stevenson,et al.  Modulation of HIV-1 replication by RNA interference , 2002, Nature.

[13]  Dianqing Wu,et al.  Second Cysteine-rich Domain of Dickkopf-2 Activates Canonical Wnt Signaling Pathway via LRP-6 Independently of Dishevelled* , 2002, The Journal of Biological Chemistry.

[14]  Juhana E. Heinonen,et al.  Silencing of Bruton's tyrosine kinase (Btk) using short interfering RNA duplexes (siRNA) , 2002, FEBS letters.

[15]  K Weber,et al.  Identification of essential genes in cultured mammalian cells using small interfering RNAs. , 2001, Journal of cell science.

[16]  W. Nelson,et al.  Methyl-CpG Binding Domain Protein 2 Represses Transcription from Hypermethylated π-Class Glutathione S-Transferase Gene Promoters in Hepatocellular Carcinoma Cells* , 2002, The Journal of Biological Chemistry.

[17]  S. Chae,et al.  Extracellular Export of Sphingosine Kinase-1 Enzyme , 2002, The Journal of Biological Chemistry.

[18]  Fran Lewitter,et al.  siRNA Selection Server: an automated siRNA oligonucleotide prediction server , 2004, Nucleic Acids Res..

[19]  J. Kofron,et al.  Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway. , 2003, Science.

[20]  J. Downward,et al.  The Serine Protease Omi/HtrA2 Regulates Apoptosis by Binding XIAP through a Reaper-like Motif* , 2002, The Journal of Biological Chemistry.

[21]  N. Mailand,et al.  Deregulated human Cdc14A phosphatase disrupts centrosome separation and chromosome segregation , 2002, Nature Cell Biology.

[22]  E. Eide,et al.  The Circadian Regulatory Proteins BMAL1 and Cryptochromes Are Substrates of Casein Kinase Iε* , 2002, The Journal of Biological Chemistry.

[23]  Malgorzata Kisielow,et al.  Isoform-specific knockdown and expression of adaptor protein ShcA using small interfering RNA. , 2002, The Biochemical journal.

[24]  J. Kofron,et al.  Distinctive Roles of PHAP Proteins and Prothymosin-α in a Death Regulatory Pathway , 2003, Science.

[25]  Anton Buzdin,et al.  Improving specificity of DNA hybridization-based methods. , 2004, Nucleic acids research.

[26]  Susan R. Wilson.  INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .

[27]  Shaheynoor Talukder,et al.  Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo , 2010, The EMBO journal.

[29]  B. Stillman,et al.  Orc6 Involved in DNA Replication, Chromosome Segregation, and Cytokinesis , 2002, Science.

[30]  S. Elledge,et al.  Phosphorylation-Dependent Ubiquitination of Cyclin E by the SCFFbw7 Ubiquitin Ligase , 2001, Science.

[31]  W. Trimble,et al.  The mammalian septin MSF localizes with microtubules and is required for completion of cytokinesis. , 2002, Molecular biology of the cell.

[32]  M. Tsuneoka,et al.  A Novel Myc Target Gene, mina53, That Is Involved in Cell Proliferation* , 2002, The Journal of Biological Chemistry.

[33]  Wenwu Cui,et al.  OptiRNAi, a Web-based program to select siRNA sequences , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[34]  E. Nigg,et al.  Role of Hec1 in Spindle Checkpoint Signaling and Kinetochore Recruitment of Mad1/Mad2 , 2002, Science.

[35]  Xiaoqi Liu,et al.  Activation of Cdc2/cyclin B and inhibition of centrosome amplification in cells depleted of Plk1 by siRNA , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  E. Nabel,et al.  A growth factor‐dependent nuclear kinase phosphorylates p27Kip1 and regulates cell cycle progression , 2002, The EMBO journal.

[37]  Ximena Opitz-Araya,et al.  Requirement for Caspase-2 in Stress-Induced Apoptosis Before Mitochondrial Permeabilization , 2002, Science.

[38]  Thorsten Joachims,et al.  Making large scale SVM learning practical , 1998 .

[39]  Russell L Finley,et al.  Mediation of the DCC Apoptotic Signal by DIP13α* , 2002, The Journal of Biological Chemistry.

[40]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[41]  T. Tuschl,et al.  RNA interference is mediated by 21- and 22-nucleotide RNAs. , 2001, Genes & development.

[42]  P. Lehner,et al.  Ubiquitylation of MHC class I by the K3 viral protein signals internalization and TSG101‐dependent degradation , 2002, The EMBO journal.

[43]  M. Amarzguioui,et al.  Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. , 2002, Nucleic acids research.