복부 초음파에서 신우암으로 오인된 신동맥류 1예

황인철,김영주,이충현,장성구,김진일,이선주 경희대학교 2000 慶熙醫學 Vol.16 No.3-4

Analysis of transcriptome change in high level of VitE accumulating rice mutant induced by in vitro mutagenesis

Jung Eun Hwang,Sun-Hee Kim,Kang-ie Lee,Sun-Goo Hwang,Jin-Baek Kim,Sang Hoon Kim,Bo-Keun Ha,Si-Yong Kang,Dong Sub Kim 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

VitE (tocotrienols and tocopherols) are micronutrients with antioxidant properties synthesized by photosynthetic bacteria and plants that play important roles in animal and human nutrition. A new mutant line, T1001-1, was isolated from in vitro mutagenized population by ionizing radiation and shown to have increased VitE contents. The total VitE content was 26% increased in the T1001-1 mutant seeds compare with cv. Dongan (wild-type). In addition, we showed that the mutant confers retarded seedling growth during the early seedling growth stage in rice. To study the molecular mechanism of VitE biosynthesis, we used the rice microarray to identify genes that are upor down-regulated in T1001-1 mutant. In addition, we identified differentially regulated pathway using MapMan analysis, which provides deep insight into changes in transcript and metabolites. Our results enhanced the transcription of genes involved in starch and lipid metabolism in T1001-1 mutant. To identify the molecular mechanisms of the events involving transcription factors in tocopherol accumulation, we compared the expression patterns of transcription factors. The AP2-EREBP, WRKY, C2H2 transcription factor were up-regulated, whereas the MYB family was down-regulated in T1001-1 mutant. Our results demonstrate change of important transcript in high level of VitE accumulating rice mutant.

Gene expression profiles during ionizing radiations and co-expression network analysis of radio marker gene in rice (Oryza sativa L.)

Jung Eun Hwang,Sun-Hee Kim,Sun-Goo Hwang,Cheol Seong Jang,Jin-Baek Kim,Sang Hoon Kim,Bo-Keun Ha,Si-Yong Kang,Dong Sub Kim 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and affects gene expression within the plant genome. To monitor the genome-wide transcriptome changes by ionizing radiation, we used rice Affimetrix GeneChip microarray to identify genes that are up- or down regulated by gamma-ray (200 Gy, 60Co source), cosmic-ray and ion beam (40 Gy, 220 MeV carbon ion). The overall expression patterns between gamma-ray and ion beam were similar but cosmic-ray was regulated differently. Combined results from all 3 radiations identified 27 up-regulated genes and 188 down regulated genes. These results mean the induction of similar mechanism changes in treatments of gamma ray and ion beam. However the different expression in treatment of cosmic-ray might be due to the other environmental conditions. Among the commonly up- or down- regulated genes, we chose highly up- or down- regulated several genes and confirmed its regulation in response to ionizing radiation exposure by RT-PCR analysis. Moreover, we showed that specific co-expression networks of candidate radio marker genes by ARACNE algorithm. Our results present profiles of gene expression related to different ionizing radiation and marker gene to predict sensitivity to ionizing radiation, such as GS (glutelin subunit) and FBX322.

Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis

Sun-Goo Hwang,Dong sub Kim,A-Reum Han,Cheol Seong Jang 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

In order to better understand the biological systems that are affected in response to cosmic ray, we conducted the weighted gene co-expression network analysis with module detection method. By using the Pearson’s correlation coefficient value, we were evaluated the complex gene-gene functional interactions between 680 CR-response probes from integrated microarray datasets, which included large-scale transcriptional profiling of 918 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched function such as oxidoreductase activity, response to stimulus and stress, and hydrolase activity. Especially, module 1 and 2 commonly showed the enriched annotation categories such as oxidoreductase activity, including the enriched cis-regulatory elements known as ROS specific regulator. These results suggest in module1 and 2 that ROS-mediated irradiation response pathway are affected by CR. We found the 243 irradiation-dependent probes, which were exhibited the similarities of differentially expressed patterns in various irradiation microarray datasets, and RT-PCR for confirmations of several irradiation-dependent genes were exhibited the similar expressed patterns in rice by CR, gamma ray and Ion beam treatments. Interestingly, these genes were differentially expressed by non-gravity. Moreover, we were identified the co-regulations between several irradiation-dependent genes and functional interacted genes in the CR-responsive network by various GA treatments such as different conditions of dose and treatment time. These results of network-based analysis might provide a clue to understanding the complex biological system of CR.

Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis.

Hwang, Sun-Goo,Kim, Dong Sub,Jang, Cheol Seong Kluwer Academic 2011 Genetica. Vol.139 No.8

<P>The leucine-rich repeat (LRR) receptor kinase (RLK) proteins constitute a large superfamily in the plant genome, and carry out key functions in a variety of biological pathways. In an effort to determine the evolutionary fate of members of a large gene family such as plant LRR RLK proteins we conducted in silico analysis using complete genome sequencing datasets, genome-wide transcriptome databases, and bioinformatics tools. A total of 292 and 165 LRR RLK genes were retrieved from the rice and Arabidopsis genomes, respectively, formed by diverse duplication events for gene expansion. The phylogenic analyses of the LRR RLK genes suggested combinations of LRR domains and RLK domains in the ancient plant genome prior to the divergence of rice and Arabidopsis, followed by massive independent expansions during speciation. The somewhat high frequencies (50-73%) of expressional divergence of members of duplicate gene pairs formed by whole/segmental genome duplication (W/SGD) and tandem duplication (TD) events of Arabidopsis and TD events of rice support the idea of their functional diversity for gene retention. By contrast, a relatively low degree (at least 20%) of members of rice LRR RLK gene pairs formed by W/SGD appear to be divergent in expression following the duplication event. At least 7 pairs of co-expressed gene clusters, including each of the tentative orthologous LRR RLK genes between rice and Arabidopsis, were enriched to an orthologous set between members of each of the pairs as compared to those of the random pairs, suggesting some degree of functional conservation of individual genes. These results may shed some light on the crucial functions of the plant LRR RLK genes with regard to a variety of biological processes.</P>

Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant

Hwang, Sun-Goo,Hwang, Jin Gyu,Kim, Dong Sub,Jang, Cheol Seong Springer-Verlag 2014 Genetica. Vol.142 No.1

Identifications of DNA polymorphism associated with signaling pathway in arsenic tolerance rice mutants

Sun-Goo Hwang,Hyeon Mi Park,A-Reum Han,Cheol Seong Jang 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

In order to select a rice population with useful trait such as arsenic tolerance for crop improvement, we have developed 3000 M7 Targeting Induced Local Lesions IN Genomes (TILLING) lines by gamma ray (GR) irradiation treatment to a rice variety (cv. Donganbyeo). A total of 2 M7 lines exhibited the arsenic (AsV) tolerant phenotype (hereafter, named Arsenic Tolerant TILLING line 1 and 2, and designed as ATT1 and 2), in which the shoots and roots length of ATT lines were significantly longer than those of wild type (WT) during As(V) treatment. To survey the DNA polymorphism of these plants, we conducted the Whole genome resequencing with 10x coverage in ATT lines. By comparative analysis among ATT lines, we have identified the common DNA polymorphism such as 11,817 SNPs (49.83% in ATT1 and 48.35% in ATT2) and 30,618 InDels (86.72% in ATT1 and 86.23% in ATT2). Also, these mutants were showed the close relationships more than WT. To further study the changed amino acids of genes, we commonly identified the 758 genes for non-synonymous SNPs and 249 genes for changed codon InDels. These genes were mainly exhibited the enriched GO functions such as catalytic activity, nucleic acid binding and transferring phosphorus-containing groups. To determine the genes associated with arsenic-related mechanism in DNA polymorphism of ATT lines, we have retrieved the two structurally altered genes (Os11g47870 and Os03g19900) for metalloid As(V) detoxification toward induced genes in response to arsenic treatments by public microarray datasets. We suggest that As(V) tolerant phenotypes of ATT lines are certainly affected by structurally altered genes associated with phosphorus transferring and As(V) detoxification during GR treatment

Whole-genome resequencing of a Korean rice cultivar (cv. Donganbyeo) for DNA polymorphism discovery

Sun-Goo Hwang,Cheol Seong Jang 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

The application of next generation sequencing technologies allows us to discover the high levels of DNA polymorphism throughout a genome, e.g., single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels). We performed whole-genome resequencing of a Korean rice cultivar (cv. Donganbyeo) and then obtained the sequences of covered 366,042,872 bp (96.63%) with average mapped read depth of 34.17 on 382,788,128 bp of the Japanese cultivar genome (cv. Nipponbare). We characterized the polymorphisms of 173,711 SNPs, 295,334 insertions and 40,642 deletions based on the comparison of both genomes. About 11.5% and 17.8% of the annotated total SNPs were presented in the regions of 1kb upstreams and genes, respectively. The annotated InDels in gene regions were similar with 15.5% insertion (4,588) and 15.9% (5,100) deletions, but not in 1kb upstream regions with 9.0% insertion (2,662) and 14.3% deletions (5,100). In addition, the Korea rice genome sequences were mapped on individual chromosome, resulted that SNPs were shown with different frequencies from each chromosome. The InDels distributions on individual chromosomes exhibited similar pattern as compared to those of SNPs. Some gene families such as NB-ARC (NB-LRR), F-box, RLK (serine/threonine protein kinase) and Zinc-finger (RING) for SNPs occurred the similar pattern with those of Arabidopsis. These results might be useful for better understanding the genome structure and genetic diversity of the Korean rice cultivars.

Genome-wide transcriptome profiling of genes associated with arsenate toxicity in an arsenic-tolerant rice mutant

Hwang, Sun-Goo,Chapagain, Sandeep,Lee, Jae Woo,Han, A-Reum,Jang, Cheol Seong Elsevier Science B.V., Amsterdam. 2017 Plant Physiology and Biochemistry Vol. No.

<P><B>Abstract</B></P> <P>The presence of arsenic (As) in polluted environments, such as ground water, affects the accumulation of As in rice grains and causes a serious threat to human health. However, the precise molecular regulations related to As toxicity and tolerance in rice remain largely unknown. In the present study, we developed an arsenic-tolerant type 1 (ATT1) rice mutant by γ-irradiation mutagenesis and performed genome-wide transcriptome analysis for the characterization of As-responsive genes. Toxicity inhibited transcriptional regulation of putative genes involved in photosynthesis, mitochondrial electron transport, and lipid biosynthesis metabolism in wild-type (WT) and ATT1 rice mutant. However, many cysteine biosynthesis-related genes were significantly upregulated in both plants. We also attempted to elucidate the putative genes associated with As tolerance by comparing transcriptomes and identified ATT1-specific transcriptional regulation of genes involved in stress and RNA-protein synthesis. This analysis identified 50 genes that had DNA polymorphisms in upstream regions that differed from those in the exon regions, which suggested that genetic variations in the upstream regions might enhance As tolerance in the mutants. Therefore, the expression profiles of the genes evaluated in this study may improve understanding of the functional roles of As-related genes in response to As tolerance mechanisms and could potentially be used in molecular breeding to limit As accumulation in rice grains.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The arsenic-tolerant type 1 (ATT1) rice mutant showed increased shoot length and decreased H<SUB>2</SUB>O<SUB>2</SUB> accumulation in roots during As(V) stress compared with wild type (WT). </LI> <LI> AsV toxicity inhibited the transcriptional regulation of genes associated with photosynthesis, mitochondrial electron transport, and lipid biosynthesis metabolism. </LI> <LI> Co-expression network analysis significantly exhibited the high-abundance transcript levels of AsV stress response. </LI> <LI> Tissue-specific transcript levels revealed that several genes involved in abiotic stress and RNA-protein synthesis pathways showed distinct expression patterns between WT and ATT1. </LI> </UL> </P>

Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice

Hwang, Jung Eun,Hwang, Sun‐,Goo,Kim, Sun‐,Hee,Lee, Kyung Jun,Jang, Cheol Seong,Kim, Jin‐,Baek,Kim, Sang Hoon,Ha, Bo‐,Keun,Ahn, Joon‐,Woo,Kang, Si‐,Yong,Kim, Dong Su Blackwell Publishing Ltd 2014 Physiologia plantarum Vol.150 No.4

<P>Ionizing radiation (IR) affects gene expression from plant genomes. To monitor the genome‐wide transcriptional changes induced by three types of IR, we used the rice Affymetrix GeneChip microarray to identify genes that are up‐ or down‐regulated by gamma rays (GAs), cosmic rays (CRs) and ion beams (IBs). The overall expression patterns in rice seedlings generated from seeds exposed to GAs and IBs were similar but differed for CRs exposure. Expression profiles of genes involved in metabolic pathways and cellular response were identified using <SMALL>MapMan</SMALL> analysis. This result revealed that IRs induced gene expression related to sucrose–starch metabolisms; sugar and starch accumulation was significantly increased in response to three types of IR in rice. In addition, we compared the genes commonly up‐ or down‐regulated by exposure to three types of IR and identified 53 candidate radio marker genes (RMGs) that were differentially regulated by radiation exposure but not by other stresses. Among these genes, we selected six RMGs commonly applicable to different types of IR by specific coexpression networks using the algorithm for the reconstruction of accurate cellular networks (<SMALL>aracne)</SMALL> and confirmed the expression of these genes by reverse transcription‐polymerase chain reaction (RT‐PCR) analysis. Our results provided insight into the mechanisms of the responses to different types of IR and identified multiple marker genes to predict sensitivity to three types of IR.</P>