AR106636A1 - Métodos y sistemas para pronosticar el riesgo del silenciamiento del transgén - Google Patents

Métodos y sistemas para pronosticar el riesgo del silenciamiento del transgén

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Publication number
AR106636A1
AR106636A1 ARP160103417A ARP160103417A AR106636A1 AR 106636 A1 AR106636 A1 AR 106636A1 AR P160103417 A ARP160103417 A AR P160103417A AR P160103417 A ARP160103417 A AR P160103417A AR 106636 A1 AR106636 A1 AR 106636A1
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AR
Argentina
Prior art keywords
transgene
acetylation
silencing
methylation
risk
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ARP160103417A
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English (en)
Inventor
Sastry Dent Lakshmi
Sriram Shreedharan
Wang Pohao
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Dow Agrosciences Llc
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Publication date
Application filed by Dow Agrosciences Llc filed Critical Dow Agrosciences Llc
Publication of AR106636A1 publication Critical patent/AR106636A1/es

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    • G—PHYSICS
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • 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
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Cell Biology (AREA)
  • Plant Pathology (AREA)
  • Botany (AREA)
  • Mycology (AREA)
  • Breeding Of Plants And Reproduction By Means Of Culturing (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La presente se basa en el uso de los niveles de metilación de H3K9me2 en los genomas de las plantas para pronosticar el silenciamiento del transgén, la estabilidad del transgén, y/o el nivel de expresión del transgén. Se proporcionan procedimientos y/o sistemas para la generación de mapas de H3K9me2 de todo el genoma y su uso con un valor de umbral asignado para pronosticar el silenciamiento de los genes. Los métodos y/o los sistemas proporcionados en este documento se pueden utilizar en la configuración de alto rendimiento para la evaluación de gran un número de eventos transformados en un período relativamente corto de tiempo en comparación con las tecnologías existentes. Reivindicación 1: Un método para pronosticar el riesgo del silenciamiento del transgén, que comprende, (a) generar los datos del perfil de metilación de histonas / acetilación en el genoma de una planta; (b) ensamblar los datos del perfil de metilación de histonas / acetilación de la etapa (a) en una base de datos de metilación / acetilación de histonas que muestra los números de los picos de los perfiles de metilación / acetilación de histonas; (c) analizar las secuencias de, por lo menos, un sitio de inserción de un transgén; y (d) comparar las secuencias del sitio de inserción del transgén de la etapa (c) con la base de datos de metilación / acetilación de histonas de la etapa (b); en donde (i) si el sitio de inserción del transgén cae en pico cero o pico uno de los perfiles de metilación / acetilación de histonas, no hay riesgo del silenciamiento del transgén, o (ii) si el sitio de inserción del transgén cae en perfiles de picos de dos o más de la metilación / acetilación de histonas, existe un riesgo significativo de silenciamiento del transgén.
ARP160103417A 2015-11-10 2016-11-10 Métodos y sistemas para pronosticar el riesgo del silenciamiento del transgén AR106636A1 (es)

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US201562253213P 2015-11-10 2015-11-10

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AR106636A1 true AR106636A1 (es) 2018-01-31

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US (2) US10633703B2 (es)
EP (1) EP3374907B1 (es)
CN (1) CN108292328B (es)
AR (1) AR106636A1 (es)
TW (1) TW201723480A (es)
WO (1) WO2017083092A1 (es)

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109192244A (zh) * 2018-09-07 2019-01-11 福建省农业科学院水稻研究所 一种水稻耐储藏特性的快速评价方法
CN114634982A (zh) * 2020-12-15 2022-06-17 广州市基准医疗有限责任公司 一种检测多核苷酸变异的方法

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Publication number Publication date
CN108292328A (zh) 2018-07-17
WO2017083092A1 (en) 2017-05-18
US20200224269A1 (en) 2020-07-16
EP3374907B1 (en) 2022-10-19
TW201723480A (zh) 2017-07-01
CN108292328B (zh) 2022-04-19
EP3374907A1 (en) 2018-09-19
BR112018006884A2 (pt) 2018-10-16
EP3374907A4 (en) 2019-07-03
US20170130266A1 (en) 2017-05-11
US10633703B2 (en) 2020-04-28

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