KSBB Journal

The Korean Society for Biotechnology and Bioengineering (한국생물공학회)
권호 표지
DOI QR코드

DOI QR Code

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

생물정보학적 접근을 통한 Caenorhabditis elegans 모델시스템의 생체내 RNAi 기능예측 및 비특이적 공동발현억제 현상 분석

  • 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)
  • 김태호 (일본 오사카대학교 WPI 면역선도연구센터) ;
  • 김의용 (인제의대 생리학교실) ;
  • 주현 (인제의대 생리학교실)
  • Received : 2010.12.22
  • Accepted : 2011.03.21
  • Published : 2011.04.30
Download PDF
⟨ Previous Next ⟩

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

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. https://doi.org/10.1016/S0960-9822(01)00116-6
  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. https://doi.org/10.1038/35888
  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. https://doi.org/10.1038/35052556
  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. https://doi.org/10.1073/pnas.95.26.15502
  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. https://doi.org/10.1038/nature01279
  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. https://doi.org/10.1016/S0960-9822(01)00052-5
  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. https://doi.org/10.1016/S0092-8674(01)00576-1
  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. https://doi.org/10.1016/S0968-0004(00)01641-8
  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. https://doi.org/10.1016/S0092-8674(03)00759-1
  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. https://doi.org/10.1038/35005113
  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. https://doi.org/10.1126/science.1123287
  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. https://doi.org/10.1093/nar/gki468
  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. https://doi.org/10.1038/nature01278
  16. Hutvagner, G. and P. D. Zamore (2002) RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev. 12: 225-232. https://doi.org/10.1016/S0959-437X(02)00290-3
  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. https://doi.org/10.1093/nar/25.17.3389
  18. Smith, T. F. and M. S. Waterman (1981) Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197. https://doi.org/10.1016/0022-2836(81)90087-5
  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. https://doi.org/10.1186/1471-2105-11-467
  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. https://doi.org/10.1093/bioinformatics/btg338
  30. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25: 25-29. https://doi.org/10.1038/75556
  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. https://doi.org/10.1016/S0960-9822(02)01301-5
  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. https://doi.org/10.1126/science.1067534
  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. https://doi.org/10.1016/S0960-9822(01)00052-5