• Molecular & Cellular Toxicology
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• 제2권1호
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• pp.7-10
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• 2006

We performed comprehensive SNP validation and linkage disequilibrium (LD) analysis of the c-fos induced growth factor (Figf) gene in Korean population. Out of 32 SNPs, only 9 SNPs were polymorphic in Korean population. Validated SNPs formed a single extended haplotype block with strong LD through the entire length of the gene. Tagging SNP analysis picked only 2 SNPs to represent most of the genetic variation information of the Figf gene. Our results demonstrate the utility of LD block and tagging SNP analysis for an efficient way of performing a candidate gene based association study.

• BMB Reports
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• 제57권1호
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• pp.66-70
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• 2024

Prime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical studies using in-locus tagged plants. To promote genome-wide in-locus tagging, we also implemented a publicly available database that designs pegRNAs for in-locus tagging of all the Arabidopsis genes.

• The Plant Pathology Journal
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• 제15권3호
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• pp.137-143
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• 1999

A novel chromosomal gene tagging technique using a specific fragment of the fatty acid desaturase-like open reading frame (des-like ORF) from the tox-argK gene cluster of Pseudomonas syringae pv. phaseolicola was developed to identify Xanthomonas spp.released into the environment as biocontrol agents. X. campestris pv. convolvuli FB-635, a pathogen of Convolvulus arvensis L., (bindweed), was chosen as the organism in which to develop and test the system. A 0.52 kb DES fragment amplified from P. syringae pv. phaseolicola C-199 was inserted into pGX15, a cosmid clone containing a 10.3 kb Eco RI-HindIII fragment derived from the xanthomonadin biosynthetic gene cluster contained in plasmid pIG102, to create a pigG::DES insertion. The 10.8 kb EcoRI-BamHI fragment carrying the pigG:: DES insertion was cloned into pLAFR3 to generate pLXP22. pLXP22 was then conjugated into X. campestris pv. convolvuli FB-635 and the pigG::DES insertion integrated into the bacterial chromosome by marker exchange. Rifampicin resistant, tetracycline sensitive, starch hydrolyzing, white colonies were used to differentiate the marked strain from yellow pigmented wild-type ones. PCR primers specific for the unique DES fragment were used for direct detection of the marked strain. Result showed the marked strain could be detected at very low levels even in the presence of high levels of other closely related or competitive bacteria. This PCR-based DES-tagging system provides a rapid and specific tool for directly monitoring the dispersal and persistence of Xanthomonas spp.released into the environment.

• 식물조직배양학회지
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• 제22권5호
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• pp.241-260
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• 1995

Transposons, present in the genomes of all living organisms, are genetic element that can change positions, or transpose, within the genome. Most genomes contain several kinds of transposable elements and the molecular details of the mechanisms by which these transposons move have recently been uncovered in many families of transposable elements. Transposition is brought about by an enzyme known as transposaese encoded by the autonomous transposon itself, but, in the unautonomous transposon lacking the gene encoding the transposase, movement occurs only at the presence of the enzyme encoded by the autonomous one. There are two types of transposition events, conservative and replicative transposition. In the former the transposon moves without replication, both strands of the DNA moving together from one place to the other while in the latter the transposition frequently involves DNA replication, so one copy of transposon remains at its original site as another copy insole to a new site. The insertion of transposon into a gene can prevent it expression whereas excision from the gene may restore the ability of the gene to be expressed. There are marked similarities between transposons and certain viruses having single stranded Plus (+) RNA genomes. Retrotransposons, which differ from the ordinary transposons in that they transpose via an RNA-intermediate, behave much like retroviruses and have a structure of integrated retrovial DNA when they are inserted to a new target site. An insertional mutagenesis called transposon-tagging is now being used in a number of plant species to isolate genes involved in developmental and metabolic processes which have been proven difficult to approach by the traditional methods. Attempts to device a transposon-tagging system based on the maize Ac for use in heterologous species have been made by many research workers.

• 생명과학회지
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• 제28권9호
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• pp.1030-1041
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• 2018

환경 스트레스는 식물의 성장을 저해하며 작물의 생산량을 감소시키는 주요 원인이다. 식물은 다양한 유전자의 발현 변화를 통해 스트레스에 대한 저항성을 나타낸다. 본 연구에서는 activation tagging system을 이용하여 기존에 밝혀지지 않은 새로운 고염 스트레스 반응 유전자들을 분리하였다. 애기장대의 발아 단계에서 고염 스트레스에 저항성을 보이는 9개의 activation tagging 라인을 선별하였다. 그 중 TAIL-PCR 방법을 이용하여 AT7508, AT7512, AT7527, AT7544, AT7548, AT7556의 6개 라인에서 T-DNA가 삽입된 위치를 확인하였으며 각 라인에서 T-DNA가 삽입된 주변 유전자의 발현을 RT-PCR로 분석하였는데 AT7508, AT7512, AT7527, AT7544, AT7556에서 각각 ClpC2/HSP93-III (At3g48870), plant thionin family (At2g20605), anti-muellerian hormone type-2 receptor (At3g50685), vacuolar iron transporter family protein (At4g27870), microtubule-associated protein (At5g16730)이 activation 된 것으로 밝혀졌다. 더불어 AT7548에서는 T-DNA가 삽입된 곳의 양쪽에 위치하는 두 유전자인 Arabinogalactan protein 13 (AGP13) (At4g26320)과 F-box/RNI-like/FBD-like domains-containing protein (At4g26340)이 모두 activation 되었다. Activation 된 7개 유전자는 기존에 고염 스트레스 저항성과 관련된 기능이 알려지지 않은 유전자로 본 연구를 통해 새롭게 고염 스트레스 반응에 대한 기능이 밝혀졌다. 7개의 activation된 유전자 중 ClpC2/HSP93-III, AGP13, F-box/RNI-like/FBD-like domains-containing protein의 3개 유전자는 고염 스트레스에 의해 발현이 증가하였다. 또한 AT7508과 AT7527, AT7544 라인은 발아 단계뿐만 아니라 유식물체 발달 과정에서도 고염 스트레스 저항성을 보여 activation tagging 라인의 선별 결과의 타당성을 뒷받침 하였다. 본 연구의 결과를 통해 activation tagging system이 새로운 스트레스 반응 유전자를 찾아낼 수 있는 유용한 기술임을 확인할 수 있었다.

• Genomics & Informatics
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• 제6권2호
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• pp.64-67
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• 2008

The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.

• 식물조직배양학회지
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• 제21권6호
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• pp.319-326
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• 1994

십자화과 식물의 유용유전자를 cloning하기 위한 기초연구로서 십자화과 식물인 Armoracia rusicna의 재분화계와 형질전환계를 확립하고, gene tagging을 하기 위하여 binary vector에 삽입된 옥수수의 transposon 유전자 Ac/Ds를 도입한 결과, NAA 0.1 mg/L와 BA 1.0 mg/L를 함유한 MS 배지에서 최적의 shoot를 유기할 수 있었으며, MS 기본배지에 옮기면 쉽게 발근을 유도할 수 있었다. 옥수수의 Ac/Ds의 유전자를 잎에 형질전환시킨 결과 8-10%의 형질전환율을 보였으며, 엽병의 경우에도 4%의 형질전환 식물체가 얻어졌다. Kanamycin 100 mg/L 농도에서 선발한 개체를 PCR 분석 및 Southern blot분석을 행하였던 결과 PCR분석으로부터 Ds유전자가 식물에 도입된 것이 확인되었고, Southern blot 분석으로부터 Ac/Ds 모두가 도입된 것이 확인되었다.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.313-320
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• 2018

Rice is the staple food of more than 50% of the world population. Cultivated rice has the AA genome (diploid, 2n = 24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems have been utilized as main insertional mutagens in rice. The Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertional mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been conducted by collaborative works in Korea.

• Mycobiology
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• 제34권2호
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• pp.104-107
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• 2006

Flammulina velutipes was transformed efficiently by Agrobacterium-mediated transformation system. The transformation frequency was about 16% with the gill tissues of the fungal fruiting body. Southern hybridization and genetic analysis suggest that the introduced DNA was inserted onto different locations of the fungal genome, and inherited stably to the next generation via basidiospores. Transformation or gene tagging with Agrobacterium T-DNA based vector should be useful for wide ranges of genetic or molecular biological studies of the mushroom.

• Journal of Plant Biotechnology
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• 제37권2호
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• pp.125-132
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• 2010

Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.