Title:
METHOD OF ESTIMATING AND IDENTIFYING TARGET mRNA CONTROLLED BY FUNCTIONAL RNA AND METHOD OF USING THE SAME
Document Type and Number:
WIPO Patent Application WO/2007/034977
Kind Code:
A1
Abstract:
It is intended to identify or estimate miRNAs and one or more target genes (target
mRNAs) targeted thereby. A method of estimating or identifying miRNAs and one
or more target mRNAs targeted thereby, which comprises calculating the most
stable secondary structures of double-stranded RNAs, which can be formed by
all partial sequences in all of the subject mRNAs with miRNAs, and the secondary
structure energies thereof to thereby search for all partial sequences capable
of having stable structures in the binding of miRNAs to mRNAs, and then calculating
the most stable secondary structure, which can be formed by a subject partial
sequence or the region in the vicinity of the subject partial sequence with the
partial sequence of a subject mRNA, and the secondary structure energy thereof
to thereby determine whether or not the partial sequence of the subject mRNA has
a structure enabling an interaction with the miRNA.
Inventors:
BARRERO ROBERTO ANTONIO (JP)
TAMURA TAKURO (JP)
GOJOBORI TAKASHI (JP)
IKEO KAZUHO (JP)
IMANISHI TADASHI (JP)
TAMURA TAKURO (JP)
GOJOBORI TAKASHI (JP)
IKEO KAZUHO (JP)
IMANISHI TADASHI (JP)
Application Number:
PCT/JP2006/319097
Publication Date:
March 29, 2007
Filing Date:
September 20, 2006
Export Citation:
Assignee:
BIOINFORMATICS INST FOR GLOBAL (JP)
NAT INST OF ADVANCED IND SCIEN (JP)
BITS CO LTD (JP)
BARRERO ROBERTO ANTONIO (JP)
TAMURA TAKURO (JP)
GOJOBORI TAKASHI (JP)
IKEO KAZUHO (JP)
IMANISHI TADASHI (JP)
NAT INST OF ADVANCED IND SCIEN (JP)
BITS CO LTD (JP)
BARRERO ROBERTO ANTONIO (JP)
TAMURA TAKURO (JP)
GOJOBORI TAKASHI (JP)
IKEO KAZUHO (JP)
IMANISHI TADASHI (JP)
International Classes:
C12Q1/68; A61K31/7088; A61K48/00; C12N15/09; G16B15/00; G16B20/20; G16B20/30; G16B20/50
Domestic Patent References:
| WO2005078096A2 | 2005-08-25 | |||
| WO2005056797A1 | 2005-06-23 | |||
| WO2005013901A2 | 2005-02-17 | |||
| WO2005103298A2 | 2005-11-03 | |||
| WO2006033928A2 | 2006-03-30 | |||
| WO2006115570A2 | 2006-11-02 | |||
| WO2006102309A2 | 2006-09-28 | |||
| WO2005098029A2 | 2005-10-20 |
Foreign References:
| JP2005503827A | 2005-02-10 | |||
| JP2005058235A | 2005-03-10 | |||
| US20050182005A1 | 2005-08-18 | |||
| US20060185027A1 | 2006-08-17 | |||
| JP2005296014A | 2005-10-27 | |||
| US20050266418A1 | 2005-12-01 | |||
| US20060003337A1 | 2006-01-05 |
Other References:
SUH M.-R. ET AL.: "Human embryonic stem cells express a unique set of microRNAs", DEV. BIOL., vol. 270, no. 2, 2004, pages 488 - 498, XP002404396
DOSTIE J. ET AL.: "Numerous microRNAs in neuronal cells containing novel microRNAs", RNA, vol. 9, 2003, pages 180 - 186, XP002354609
KIRIAKIDOU M. ET AL.: "A combined computational-experimental approach predicts human microRNA targets", GENES DEV., vol. 18, no. 10, 2004, pages 1165 - 1178, XP009032049
REHMSMEIER M. ET AL.: "Fast and effective prediction of microRNA/target duplexes", RNA, vol. 10, no. 10, 2004, pages 1507 - 1517, XP008044998
BURGLER C. ET AL.: "Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method", BMC GENOMICS, vol. 6, no. 1, 2005, pages 88, XP021002356
ZUKER M. ET AL.: "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information", NUCLEIC ACIDS. RES., vol. 9, no. 1, 1981, pages 133 - 148, XP003010680
WATANABE Y. ET AL.: "Computational analysis of microRNA targets in Caenorhabditis elegans", GENE, vol. 365, January 2006 (2006-01-01), pages 2 - 10, XP005280941
MUCKSTEIN U. ET AL.: "Thermodynamics of RNA-RNA binding", BIOINFORMATICS, vol. 22, no. 10, May 2006 (2006-05-01), pages 1177 - 1182, XP003010681
DOSTIE J. ET AL.: "Numerous microRNAs in neuronal cells containing novel microRNAs", RNA, vol. 9, 2003, pages 180 - 186, XP002354609
KIRIAKIDOU M. ET AL.: "A combined computational-experimental approach predicts human microRNA targets", GENES DEV., vol. 18, no. 10, 2004, pages 1165 - 1178, XP009032049
REHMSMEIER M. ET AL.: "Fast and effective prediction of microRNA/target duplexes", RNA, vol. 10, no. 10, 2004, pages 1507 - 1517, XP008044998
BURGLER C. ET AL.: "Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method", BMC GENOMICS, vol. 6, no. 1, 2005, pages 88, XP021002356
ZUKER M. ET AL.: "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information", NUCLEIC ACIDS. RES., vol. 9, no. 1, 1981, pages 133 - 148, XP003010680
WATANABE Y. ET AL.: "Computational analysis of microRNA targets in Caenorhabditis elegans", GENE, vol. 365, January 2006 (2006-01-01), pages 2 - 10, XP005280941
MUCKSTEIN U. ET AL.: "Thermodynamics of RNA-RNA binding", BIOINFORMATICS, vol. 22, no. 10, May 2006 (2006-05-01), pages 1177 - 1182, XP003010681
Attorney, Agent or Firm:
HIRAKI, Yusuke et al. (3-20 Toranomon 4-chome, Minato-k, Tokyo 01, JP)
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