WO2003106672A3 - METHOD OF USING THE 5 'END OF THE MRNA FOR CLONING AND ANALYSIS - Google Patents

METHOD OF USING THE 5 'END OF THE MRNA FOR CLONING AND ANALYSIS Download PDF

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Publication number
WO2003106672A3
WO2003106672A3 PCT/JP2003/007514 JP0307514W WO03106672A3 WO 2003106672 A3 WO2003106672 A3 WO 2003106672A3 JP 0307514 W JP0307514 W JP 0307514W WO 03106672 A3 WO03106672 A3 WO 03106672A3
Authority
WO
WIPO (PCT)
Prior art keywords
analysis
mrna
cloning
concatemers
transcriptome
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/JP2003/007514
Other languages
French (fr)
Other versions
WO2003106672A2 (en
Inventor
Yoshihide Hayashizaki
Piero Carninci
Matthias T Harbers
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Dnaform KK
RIKEN
Original Assignee
Dnaform KK
RIKEN
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Dnaform KK, RIKEN filed Critical Dnaform KK
Priority to JP2004513485A priority Critical patent/JP4403069B2/en
Priority to EP03733397A priority patent/EP1523554A2/en
Priority to AU2003238702A priority patent/AU2003238702A1/en
Priority to US10/517,544 priority patent/US20050250100A1/en
Publication of WO2003106672A2 publication Critical patent/WO2003106672A2/en
Publication of WO2003106672A3 publication Critical patent/WO2003106672A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR

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  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne une méthode permettant d'obtenir les extrémités 5' de régions transcrites d'une pluralité de fragments d'acide nucléique obtenus à partir de matières biologiques ou de fractions groupées synthétiques. Les fragments d'ADN codant pour les extrémités 5' sont enrichis pour leur analyse individuelle ou pour l'analyse de leurs concatémères. Les informations de séquence dérivées des extrémités 5' peuvent servir à la caractérisation et au clonage du transcriptome.The invention relates to a method for obtaining the 5 'ends of transcribed regions of a plurality of nucleic acid fragments obtained from biological materials or from synthetic grouped fractions. The DNA fragments coding for the 5 ′ ends are enriched for their individual analysis or for the analysis of their concatemers. Sequence information derived from the 5 'ends can be used to characterize and clone the transcriptome.

PCT/JP2003/007514 2002-06-12 2003-06-12 METHOD FOR UTILIZING THE 5'END OF mRNA FOR CLONING AND ANALYSIS Ceased WO2003106672A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2004513485A JP4403069B2 (en) 2002-08-12 2003-06-12 Methods for using the 5 'end of mRNA for cloning and analysis
EP03733397A EP1523554A2 (en) 2002-06-12 2003-06-12 Method of utilizing the 5' end of transcribed nucleic acid regions for cloning and analysis
AU2003238702A AU2003238702A1 (en) 2002-06-12 2003-06-12 Method of utilizing the 5'end of transcribed nucleic acid regions for cloning and analysis
US10/517,544 US20050250100A1 (en) 2002-06-12 2003-06-12 Method of utilizing the 5'end of transcribed nucleic acid regions for cloning and analysis

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
JP2002-171851 2002-06-12
JP2002171851 2002-06-12
JP2002-235294 2002-08-12
JP2002235294 2002-08-12

Publications (2)

Publication Number Publication Date
WO2003106672A2 WO2003106672A2 (en) 2003-12-24
WO2003106672A3 true WO2003106672A3 (en) 2004-07-01

Family

ID=29738376

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/JP2003/007514 Ceased WO2003106672A2 (en) 2002-06-12 2003-06-12 METHOD FOR UTILIZING THE 5'END OF mRNA FOR CLONING AND ANALYSIS

Country Status (4)

Country Link
US (1) US20050250100A1 (en)
EP (1) EP1523554A2 (en)
AU (1) AU2003238702A1 (en)
WO (1) WO2003106672A2 (en)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB0228289D0 (en) 2002-12-04 2003-01-08 Genome Inst Of Singapore Nat U Method
US8222005B2 (en) 2003-09-17 2012-07-17 Agency For Science, Technology And Research Method for gene identification signature (GIS) analysis
JP3845416B2 (en) * 2003-12-01 2006-11-15 株式会社ポストゲノム研究所 Gene tag acquisition method
US20080096255A1 (en) * 2004-07-02 2008-04-24 Matthias Harbers Method for Preparing Sequence Tags
BRPI0706353B1 (en) * 2006-01-05 2023-01-24 Interdigital Patent Holdings, Inc METHOD FOR ALLOCING RADIO RESOURCES IN A MOBILE COMMUNICATION SYSTEM
WO2009107816A1 (en) * 2008-02-29 2009-09-03 独立行政法人理化学研究所 Method for increasing enzymatic reactivity
US9052304B2 (en) 2009-03-13 2015-06-09 Terrasep, Llc Methods and apparatus for centrifugal liquid chromatography
EP2475988B1 (en) 2009-09-09 2018-11-14 The General Hospital Corporation Use of microvesicles in analyzing nucleic acid profiles
US20130029339A1 (en) 2009-09-09 2013-01-31 The General Hospital Corporation Use of microvesicles in analyzing kras mutations
WO2012031008A2 (en) 2010-08-31 2012-03-08 The General Hospital Corporation Cancer-related biological materials in microvesicles
WO2012051622A2 (en) * 2010-10-15 2012-04-19 The General Hospital Corporation Microvesicle-based assays
CA2817111C (en) 2010-11-10 2019-03-05 Exosome Diagnostics, Inc. Method for isolation of nucleic acid containing particles and extraction of nucleic acids therefrom
US11312991B2 (en) 2016-01-27 2022-04-26 Kabushiki Kaisha Dnaform Method for decoding base sequence of nucleic acid corresponding to end region of RNA and method for analyzing DNA element
CN106636063A (en) * 2016-09-27 2017-05-10 广州精科医学检验所有限公司 Primer compound, application thereof and method for establishing library and confirming nucleotide sequence

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002010438A2 (en) * 2000-07-28 2002-02-07 The Johns Hopkins University Serial analysis of transcript expression using long tags
US6352828B1 (en) * 1994-10-13 2002-03-05 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
EP1197552A2 (en) * 2000-08-25 2002-04-17 Riken Method of preparing normalized and/or subtracted cDNA
WO2003091416A2 (en) * 2002-04-26 2003-11-06 Lynx Therapeutics, Inc. Constant length signatures for parallel sequencing of polynucleotides

Family Cites Families (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4683195A (en) * 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
WO1991011533A1 (en) * 1990-01-26 1991-08-08 E.I. Du Pont De Nemours And Company Method for isolating primer extension products from template-directed dna polymerase reactions
US5695934A (en) * 1994-10-13 1997-12-09 Lynx Therapeutics, Inc. Massively parallel sequencing of sorted polynucleotides
US6280935B1 (en) * 1994-10-13 2001-08-28 Lynx Therapeutics, Inc. Method of detecting the presence or absence of a plurality of target sequences using oligonucleotide tags
US5750341A (en) * 1995-04-17 1998-05-12 Lynx Therapeutics, Inc. DNA sequencing by parallel oligonucleotide extensions
FR2733762B1 (en) * 1995-05-02 1997-08-01 Genset Sa METHOD FOR THE SPECIFIC COUPLING OF THE HAIR OF THE 5 'END OF A RNAM FRAGMENT AND PREPARATION OF RNAM AND COMPLETE DNA
US5866330A (en) * 1995-09-12 1999-02-02 The Johns Hopkins University School Of Medicine Method for serial analysis of gene expression
US5695937A (en) * 1995-09-12 1997-12-09 The Johns Hopkins University School Of Medicine Method for serial analysis of gene expression
US5962271A (en) * 1996-01-03 1999-10-05 Cloutech Laboratories, Inc. Methods and compositions for generating full-length cDNA having arbitrary nucleotide sequence at the 3'-end
US6013488A (en) * 1996-07-25 2000-01-11 The Institute Of Physical And Chemical Research Method for reverse transcription
JP3441899B2 (en) * 1996-11-01 2003-09-02 理化学研究所 How to make a full-length cDNA library
US6265163B1 (en) * 1998-01-09 2001-07-24 Lynx Therapeutics, Inc. Solid phase selection of differentially expressed genes
WO2001012855A2 (en) * 1999-08-13 2001-02-22 Yale University Binary encoded sequence tags
US6958217B2 (en) * 2001-01-24 2005-10-25 Genomic Expression Aps Single-stranded polynucleotide tags
US20030190618A1 (en) * 2002-03-06 2003-10-09 Babru Samal Method for generating five prime biased tandem tag libraries of cDNAs

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6352828B1 (en) * 1994-10-13 2002-03-05 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
WO2002010438A2 (en) * 2000-07-28 2002-02-07 The Johns Hopkins University Serial analysis of transcript expression using long tags
EP1197552A2 (en) * 2000-08-25 2002-04-17 Riken Method of preparing normalized and/or subtracted cDNA
WO2003091416A2 (en) * 2002-04-26 2003-11-06 Lynx Therapeutics, Inc. Constant length signatures for parallel sequencing of polynucleotides

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
CARNINCI, P. & HAYASHIZAKI, Y.: "High-Efficiency Full-Length cDNA Cloning", METHODS IN ENZYMOLOGY, vol. 303, 1999, pages 19 - 44, XP001022979 *
EDERY, I. ET AL.: "An Efficient Strategy To Isolate Full-Length cDNAs Based on an mRNA Cap Retention Procedure (CAPture)", MOLECULAR AND CELLULAR BIOLOGY, vol. 15, no. 6, June 1995 (1995-06-01), pages 3363 - 3371, XP002915963 *
MARUYAMA, K. & SUGANO, S.: "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides", GENE, vol. 138, no. 1-2, 28 January 1994 (1994-01-28), pages 171 - 174, XP001008855 *
See also references of EP1523554A2 *
SHIBATA, Y. ET AL.: "Cloning Full-Length, Cap-Trapper-Selected cDNAs by Using the Single-Strand Linker Ligation Method", BIOTECHNIQUES, vol. 30, no. 6, June 2001 (2001-06-01), pages 1250 - 1254, XP002197302 *
SHIRAKI, T. ET AL.: "Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, vol. 100, no. 26, 23 December 2003 (2003-12-23), pages 15776 - 15781, XP001161070 *
SUZUKI, Y. ET AL.: "Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites", EMBO REPORTS, vol. 2, no. 5, May 2001 (2001-05-01), pages 388 - 393, XP001176665 *
THEISSEN, H. ET AL.: "Cloning of the human cDNA for the U1 RNA-associated 70K protein", EMBO JOURNAL, vol. 5, no. 12, 1 December 1986 (1986-12-01), pages 3209 - 3217, XP009002534 *

Also Published As

Publication number Publication date
EP1523554A2 (en) 2005-04-20
US20050250100A1 (en) 2005-11-10
WO2003106672A2 (en) 2003-12-24
AU2003238702A8 (en) 2003-12-31
AU2003238702A1 (en) 2003-12-31

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