식물 유전자 연구의 최근 동향

조용구,우희종,윤웅한,김홍식,우선희 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the highthroughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene’s role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.

식물 유전자 연구의 최근 동향

조용구,우희종,윤웅한,김홍식,우선희,Cho, Yong-Gu,Woo, Hee-Jong,Yoon, Ung-Han,Kim, Hong-Sig,Woo, Sun-Hee 한국식물생명공학회 2010 식물생명공학회지 Vol.37 No.2

As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the high-throughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene's role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.

The Insect Genomics in Future Pest Management

Woojin Kim,Yeon Ho Je 한국응용곤충학회 2012 한국응용곤충학회 학술대회논문집 Vol.2012 No.10

In 1990, the human genome project had begun with three billion dollars of budget, and the sequencing and analysis result of the three billion base pairs of human genome was finally published in 2000 to open a new era of genomics. Since the human genome project, many other genomes of eukaryotic model organisms, such as mouse, Drosophila, Arabidopsis, C. elegance, etc., became available, and this led the development of computational biology and comparative genomics. Also, during the last decade, the speed of the nucleotide sequencing increased significantly with lower cost by next generation sequencing technology, and the computational power to handle sequence information also has grown exponentially to make possible that a genomics approach is an affordable tool for many of the biological studies. In the entomology area, the 5000 insect genome project was launched in 2011 for understanding of the biology of insects in a new dimension. Based on the recent studies of functional genomics and the new discoveries in the biological sciences, such as innate immune system, RNAi technique, insect pathogens, etc., the information from the insect genomics study will make possible to improve our capability to manage insect pests in the future.

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Shin, Dong Hae,Hou, Jingtong,Chandonia, John-Marc,Das, Debanu,Choi, In-Geol,Kim, Rosalind,Kim, Sung-Hou 이화여자대학교 약학연구소 2008 藥學硏究論文集 Vol.- No.18

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

차세대 염기서열분석을 통한 밀 기능유전체 연구의 현황과 전망

최창현,윤영미,손재한,조성우,강천식 한국육종학회 2018 한국육종학회지 Vol.50 No.4

Hexaploid wheat (common wheat/bread wheat) is one of the most important cereal crops in the world and a model for research of an allopolyploid plant with a large, highly repetitive genome. In the heritability of agronomic traits, variation in gene presence/absence plays an important role. However, there have been relatively few studies on the variation in gene presence/absence in crop species, including common wheat. Recently, a reference genome sequence of common wheat has been fully annotated and published. In addition, advanced next-generation sequencing (NGS) technology provides high quality genome sequences with continually decreasing NGS prices, thereby dawning full-scale wheat functional genomic studies in other crops as well as common wheat, in spite of their large and complex genomes. In this review, we provide information about the available tools and methodologies for wheat functional genomics research supported by NGS technology. The use of the NGS and functional genomics technology is expected to be a powerful strategy to select elite lines for a number of germplasms.

가금 기능유전체 연구를 위한 메추리 모델의 활용

신상수(Sangsu Shin) 한국가금학회 2017 韓國家禽學會誌 Vol.44 No.2

The quail (Coturnix japonica) has been used as a model animal in many research fields and its application is still expanding in other fields. Compared to the chicken, the quail is quicker to reach sexually maturity, has short generation intervals, is easy to handle, requires less space and feed, and is sturdy. In addition, it produces many eggs and the research tools developed for chicken can be applied directly to quail or with some modifications. Due to recent advances in nextgeneration sequencing, abundant sequence data for the quail genome and transcripts have been generated. These sequence data are valuable sources for studying functional genomics using quail, which is one of the model animal used to investigate gene function and networks. Although there are some obstacles to be removed, the quail is the best optimized model to study the functional genomics of poultry. In many research fields, functional genomics study using the quail model will provide the best opportunity to understand the phenomena and principles of life. We review why, among many other birds, the quail is the best model for studying poultry functional genomics.

Functional Genomic Approaches Using the Nematode Caenorhabditis elegans as a Model System

Lee, Jun-Ho,Nam, Seung-Hee,Hwang, Soon-Baek,Hong, Min-Gi,Kwon, Jae-Young,Joeng, Kyu-Sang,Im, Seol-Hee,Shim, Ji-Won,Park, Moon-Cheol Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.1

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.

Functional Genomics Approach Using Mice

Sung, Young-Hoon,Song, Jae-Whan,Lee, Han-Woong Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.1

The rapid development and characterization of the mouse genome sequence, coupled with comparative sequence analysis of human, has been paralleled by a reinforced enthusiasm for mouse functional genomics. The way to uncover the in vivo function of genes is to analyze the phenotypes of the mutant animals. From this standpoint, the mouse is a suitable and valuable model organism in the studies of functional genomics. Therefore, there have been enormous efforts to enrich the list of the mutant mice. Such a trend emphasizes the random mutagenesis, including ENU mutagenesis and gene-trap mutagenesis, to obtain a large stock of mutant mice. However, since various mutant alleles are needed to precisely characterize the role of a gene in vivo, mutations should be designed. The simplicity and utility of transgenic technology can satisfy this demand. The combination of RNA interference with transgenic technology will provide more opportunities for researchers. Nevertheless, gene targeting can solely define the in vivo function of a gene without a doubt. Thus, transgenesis and gene targeting will be the major strategies in the field of functional genomics.

Functional Genomic Approaches Using the Nematode Caenorhabditis elegans as a Model System

Lee, Junho,Nam, Seunghee,Hwang, Soon Baek,Hong, Mingi,Kwon, Jae Young,Joeng, Kyu Sang,Im, Seol Hee,Shim, Jiwon,Park, Moon Cheol 한국생화학분자생물학회 2004 BMB Reports Vol.37 No.1

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.

A Review of Software for Predicting Gene Function

Swee Kuan Loha,Swee Thing Low,Mohd Saberi Mohamad,Safaai Deris,Shahreen Kasim,Choon Yee Wen,Zuwairie Ibrahim,Bambang Susilo,Yusuf Hendrawan,Agustin Krisna Wardani 보안공학연구지원센터 2015 International Journal of Bio-Science and Bio-Techn Vol.7 No.2

A rich resource of information on functional genomics data can be applied to annotating the thousands of unknown gene functions that can be retrieved from most sequenced. High-throughput sequencing can lead to increased understanding of proteins and genes. We can infer networks of functional couplings from direct and indirect interactions. The development of gene function prediction is one of the major recent advances in the bioinformatics fields. These methods explore genomic context by major recent advances in the bioinformatics fields rather than by sequence alignment. This paper reviews software related to predicting gene function. Most of these programs are freely available online. The advantages and disadvantages of each program are stated clearly in order for the reader to understand them in a simple way. Web links to the software are provided as well.