Browse > Article
http://dx.doi.org/10.7841/ksbbj.2011.26.2.131

Bioinformatics Approach to Direct Target Prediction for RNAi Function and Non-specific Cosuppression in Caenorhabditis elegans  

Kim, Tae-Ho (Laboratory of Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University)
Kim, Eui-Yong (Department of Physiology and Integrated Biosystems, College of Medicine, Inje University)
Joo, Hyun (Department of Physiology and Integrated Biosystems, College of Medicine, Inje University)
Publication Information
KSBB Journal / v.26, no.2, 2011 , pp. 131-138 More about this Journal
Abstract
Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.
Keywords
RNA interference (RNAi); Expressed Sequence Tag (EST); in silico Biology; Multiple Sequence Alignment; Cosuppression; dsRNA; Caenorhabditis elegans;
Citations & Related Records
연도 인용수 순위
  • Reference
1 OpenMosix Project. http://openmosix.sourceforge.net.(2008).
2 MPICH2. http://www.mcs.anl.gov/research/projects/mpich2/. (2010).
3 Serolis: Dot-plot software for literal and genetic sequences and DNA translation. http://www.code10.org.(2009)
4 Barak, A. and O. La'adan (1997) The MOSIX multicomputer operating system for high performance cluster computing, Future Gen. Comp. Sys. 13: 361-372.
5 Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.   DOI
6 Building a diskless Linux Cluster for high performance computations from a standard Linux distribution. http://www.uni-due.de/-bt0756/publications/2003-cluster/.(2003).
7 Dynamic Host Configuration Protocol. http://www.ietf.org/rfc/rfc2131.txt.(1997).
8 NFS version 3 Protocol Specification. http://www.ietf.org/rfc/rfc1813.txt.(1995).
9 Kamath, R. S., A. G. Fraser, Y. Dong, G. Poulin, R. Durbin, M. Gotta, A. Kanapin, N. Le Bot, S. Moreno, M. Sohrmann, D. P. Welchman, P. Zipperlen, and J. Ahringer (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.   DOI   ScienceOn
10 Hutvagner, G. and P. D. Zamore (2002) RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev. 12: 225-232.   DOI   ScienceOn
11 Smith, T. F. and M. S. Waterman (1981) Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197.   DOI
12 Kim, T. and H. Joo (2010) ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment. BMC Bioinformatics 11:467.   DOI
13 HPC (High Performance Computer) Linux Cluster How To. http://wiki.kldp.org/KoreanDoc/html/HPC-KLDP/index.html. (2003).
14 Schwarz, D. S., G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P. D. Zamore (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.   DOI   ScienceOn
15 Maeda, I., Y. Kohara, M. Yamamoto, and A. Sugimoto (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11: 171-176.   DOI   ScienceOn
16 Sijen, T., J. Fleenor, F. Simmer, K. L. Thijssen, S. Parrish, L. Timmons, R. H. Plasterk, and A. Fire (2001) On the role of the RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465-476.   DOI   ScienceOn
17 Cerutti, L., N. Mian, and A. Bateman (2000) Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the piwi domain. Trends Biochem. Sci. 25: 481-482.   DOI   ScienceOn
18 Ketting, R. F. and R. H. Plasterk (2000) A genetic link between co-suppression and RNA interference in C. elegans. Nature 404: 296-298.   DOI   ScienceOn
19 Dernburg, A. F., J. Zalevsky, M. P. Colaiacovo, and A. M.Villeneuve (2000) Transgene-mediated cosuppression in the C. elegans germ line. Genes Dev. 14: 1578-1583.
20 Zhong, W. and P. W. Sternberg (2006) Genome-wide prediction of C. elegans genetic interactions. Science 311: 1481-1484.   DOI
21 Montgomery, M. K., S. Xu, and A. Fire (1998) RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 95: 15502-15507.   DOI   ScienceOn
22 Arziman, Z., T. Horn, and M. Boutros (2005) E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res. 33: W582-W588.   DOI   ScienceOn
23 Fire, A., S. Xu, M. Montgomery, S. Kostas, S. Driver, and C. Mello (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.   DOI   ScienceOn
24 Hammond, S. M., A. A. Caudy, and G. J. Hannon (2001) Posttranscriptional Gene Silencing by Double-stranded RNA. Nature Rev. Gen. 2: 110-119.   DOI   ScienceOn
25 Chen, Y., A. Wan, and W. A. Liu (2006) Fast parallel algorithm for finding the longest common sequence of multiple biosequences. BMC Bioinformatics 4: S4.
26 Ashrafi, K., F. Y. Chang, J. L. Watts, A. G. Fraser, R. S. Kamath, J. Ahringer, and G. Ruvkun (2003) Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421: 268-272.   DOI   ScienceOn
27 Kamath, R. S., M. Martinez-Campos, P. Zipperlen, A. G. Fraser, and J. Ahringer (2000) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol. 2: 1-10.
28 Sijen, T., I. Vijn, A. Rebocho, R. van Blokland, D. Roelofs, J. N. M. Mol, and J. M. Kooter (2001) Transcriptional and posttranscriptional gene silencing are mechanistically related. Curr. Biol. 11: 436-440.   DOI   ScienceOn
29 Tijsterman, M., R. F. Kettling, O. L. Kristy, S. Titia, and R. H. Plasterk (2002) RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Science 295: 694-697.   DOI
30 Maeda, I., Y. Kohara, M. Yamamoto, and A. Sugimoto (2001) Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11: 171-176.   DOI   ScienceOn
31 Khan, S., G. Situ, K. Decker, and C. J. Schmidt (2003) GoFigure: automated gene ontology annotation. Bioinformatics 19: 2484-2485.   DOI   ScienceOn
32 Piano, F, A. J. Schetter, D. G. Morton, K. C. Gunsalus, V. Reinke, S. K. Kim, and K. J. Kemphues (2002) Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 12: 1959-1965.   DOI   ScienceOn
33 The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29.   DOI   ScienceOn