JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Bioinformatics Approach to Direct Target Prediction for RNAi Function and Non-specific Cosuppression in Caenorhabditis elegans
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
  • Journal title : KSBB Journal
  • Volume 26, Issue 2,  2011, pp.131-138
  • Publisher : Korean Society for Biotechnology and Bioengineering
  • DOI : 10.7841/ksbbj.2011.26.2.131
 Title & Authors
Bioinformatics Approach to Direct Target Prediction for RNAi Function and Non-specific Cosuppression in Caenorhabditis elegans
Kim, Tae-Ho; Kim, Eui-Yong; Joo, Hyun;
  PDF(new window)
 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;
 Language
Korean
 Cited by
 References
1.
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. crossref(new window)

2.
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. crossref(new window)

3.
Hammond, S. M., A. A. Caudy, and G. J. Hannon (2001) Posttranscriptional Gene Silencing by Double-stranded RNA. Nature Rev. Gen. 2: 110-119. crossref(new window)

4.
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. crossref(new window)

5.
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. crossref(new window)

6.
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.

7.
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. crossref(new window)

8.
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. crossref(new window)

9.
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. crossref(new window)

10.
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. crossref(new window)

11.
Ketting, R. F. and R. H. Plasterk (2000) A genetic link between co-suppression and RNA interference in C. elegans. Nature 404: 296-298. crossref(new window)

12.
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.

13.
Zhong, W. and P. W. Sternberg (2006) Genome-wide prediction of C. elegans genetic interactions. Science 311: 1481-1484. crossref(new window)

14.
Arziman, Z., T. Horn, and M. Boutros (2005) E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res. 33: W582-W588. crossref(new window)

15.
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. crossref(new window)

16.
Hutvagner, G. and P. D. Zamore (2002) RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev. 12: 225-232. crossref(new window)

17.
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. crossref(new window)

18.
Smith, T. F. and M. S. Waterman (1981) Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197. crossref(new window)

19.
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. crossref(new window)

20.
HPC (High Performance Computer) Linux Cluster How To. http://wiki.kldp.org/KoreanDoc/html/HPC-KLDP/index.html. (2003).

21.
Barak, A. and O. La'adan (1997) The MOSIX multicomputer operating system for high performance cluster computing, Future Gen. Comp. Sys. 13: 361-372.

22.
Building a diskless Linux Cluster for high performance computations from a standard Linux distribution. http://www.uni-due.de/-bt0756/publications/2003-cluster/.(2003).

23.
Dynamic Host Configuration Protocol. http://www.ietf.org/rfc/rfc2131.txt.(1997).

24.
NFS version 3 Protocol Specification. http://www.ietf.org/rfc/rfc1813.txt.(1995).

25.
OpenMosix Project. http://openmosix.sourceforge.net.(2008).

26.
MPICH2. http://www.mcs.anl.gov/research/projects/mpich2/. (2010).

27.
Serolis: Dot-plot software for literal and genetic sequences and DNA translation. http://www.code10.org.(2009)

28.
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.

29.
Khan, S., G. Situ, K. Decker, and C. J. Schmidt (2003) GoFigure: automated gene ontology annotation. Bioinformatics 19: 2484-2485. crossref(new window)

30.
The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29. crossref(new window)

31.
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. crossref(new window)

32.
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. crossref(new window)

33.
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. crossref(new window)