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Ayarpadikannan, Selvam,Kim, Heui-Soo Korea Genome Organization 2014 Genomics & informatics Vol.12 No.3
Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human Genome Project have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply "junk" DNA, but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability, and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the past two decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are a subject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionary tracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons are well studied, and their roles in these processes have been confirmed. In this review, we will give an overview of the importance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on the mechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.
Selvam Ayarpadikannan,김희수 한국유전체학회 2014 Genomics & informatics Vol.12 No.3
Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human GenomeProject have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply “junk” DNA,but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability,and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the pasttwo decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are asubject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionarytracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons arewell studied, and their roles in these processes have been confirmed. In this review, we will give an overview of theimportance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on themechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.
Functional analyses of the novel salt-inducible genes from Korean halophytes
Selvam Ayarpadikannan,Eunsook Chung,Hyun-A So,Kyoung-Mee Kim,Kenneth Ryan Schraufnagle,Ji Hae Park,Se Hyun Park,Jai-Heon Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Salinity stress severely affects plant growth and development causing crop loss worldwide. Suaeda asparagoides is a salt-marsh euhalophyte widely distributed in southwestern foreshore of Korea. To isolate salt tolerance genes from S. asparagoides, we constructed a cDNA library from leaf tissues of S. asparagoides that was treated with 200 mM NaCl. A total of 1,056 clones were randomly selected for EST sequencing, and 932 of them produced readable sequence. By sequence analysis, we identified 538 unigenes and registered each in National Center for Biotechnology Information. The 80 salt stress related genes were selected to study their differential expression. Reverse Transcriptase-PCR and Northern blot analysis revealed that 23 genes were differentially expressed under the high salinity stress conditions in S. asparagoides. They are functionally diverse including transport, signal transduction, transcription factor, metabolism and stress associated protein, and unknown function. Among them dehydrin (SaDhn) and RNA binding protein (SaRBP1) were examined for their abiotic stress tolerance in yeast (Saccharomyces cerevisiae). Yeast overexpressing SaDhn and SaRBP1 showed enhanced tolerance to osmotic, freezing and heat shock stresses. This study provides the evidence that SaRBP1 and SaDhn from S.asparagoides exert abiotic stress tolerance in yeast. Information of salt stress related genes from S. asparagoides will contribute for the accumulating genetic resources to improve osmotic tolerance in plants.
Functional analyses of the novel salt-inducible genes from Korean halophytes
Selvam Ayarpadikannan,Eunsook Chung,Hyun-A So,Kyoung-Mee Kim,Kenneth Ryan Schraufnagle,Kim Hyo Young,Jae-Sung Kwak,Hai Yang Yu,Soon-Ok Kim,Joo-Min Jeon,Myoung-HaeKwak,Jai-Heon Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Salinity stress severely affects plant growth and development causing crop loss worldwide. Suaeda asparagoides is a salt-marsh euhalophyte widely distributed in southwestern foreshore of Korea. To isolate salt tolerance genes from S. asparagoides, we constructed a cDNA library from leaf tissues of S. asparagoides that was treated with 200 mM NaCl. A total of 1,056 clones were randomly selected for EST sequencing, and 932 of them produced readable sequence. By sequence analysis, we identified 538 unigenes and registered each in National Center for Biotechnology Information. The 80 salt stress related genes were selected to study their differential expression. Reverse Transcriptase-PCR and Northern blot analysis revealed that 23 genes were differentially expressed under the high salinity stress conditions in S. asparagoides. They are functionally diverse including transport, signal transduction, transcription factor, metabolism and stress associated protein, and unknown function. Among them dehydrin (SaDhn) and RNA binding protein (SaRBP1) were examined for their abiotic stress tolerance in yeast (Saccharomyces cerevisiae). Yeast overexpressing SaDhn and SaRBP1 showed enhanced tolerance to osmotic, freezing and heat shock stresses. This study provides the evidence that SaRBP1 and SaDhn from S.asparagoides exert abiotic stress tolerance in yeast. Information of salt stress related genes from S. asparagoides will contribute for the accumulating genetic resources to improve osmotic tolerance in plants.
Eunsook Chung,Kyoung-Mee Kim,Selvam Ayarpadikannan,Hyun-A So,Kenneth Ryan Schraufnagle,Kim Hyo Young,Jae-Sung Kwak,Hai Yang Yu,Jai-Heon Lee 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07
Heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other important biological processes. In this study, a genome-wide analysis was carried out to identify all HSFs soybean genes. Twenty six nonredundant HSF genes (GmHsf) were identified in the latest soybean genome sequence. Chromosomal location, protein domain and motif organization of GmHsfs were analyzed in soybean genome. The phylogenetic relationships, gene duplications and expression profiles of GmHsf genes were also presented in this study. According to their structural features, the predicted members were divided into the previously defined classes A–C, as described in Arabidopsis. Using RT-PCR, the expression patterns of 26 GmHsf genes were investigated under heat stress. The data revealed that these genes presented different expression levels in response to heat stress conditions. Real-time (q)RT-PCR was performed to investigate transcript levels of five GmHsfs in response to multiple abiotic stresses. Differential expression of five GmHsfs implies their role during abiotic stresses. Subcellular localization using GFP-fusion protein demonstrated that GmHsf12 and GmHsf34 were restricted to the nucleus and GmHsf28 was localized in the nucleus and cytoplasm in plant. The results provide a fundamental clue for understanding of the complexity of the soybean HSF gene family and cloning specific function genes in further studies and applications.
Kyoung-Mee Kim,Eunsook Chung,Selvam Ayarpadikannan,Hyun-A So,Kenneth Ryan Schraufnagle,Ji Hae Park,Se Hyun Park,Jai-Heon Lee 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
Heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other important biological processes. In this study, a genome-wide analysis was carried out to identify all HSFs soybean genes. Twenty six nonredundant HSF genes (GmHsf) were identified in the latest soybean genome sequence. Chromosomal location, protein domain and motif organization of GmHsfs were analyzed in soybean genome. The phylogenetic relationships, gene duplications and expression profiles of GmHsf genes were also presented in this study. According to their structural features, the predicted members were divided into the previously defined classes A–C, as described in Arabidopsis. Using RT-PCR, the expression patterns of 26 GmHsf genes were investigated under heat stress. The data revealed that these genes presented different expression levels in response to heat stress conditions. Real-time (q)RT-PCR was performed to investigate transcript levels of five GmHsfs in response to multiple abiotic stresses. Differential expression of five GmHsfs implies their role during abiotic stresses. Subcellular localization using GFP-fusion protein demonstrated that GmHsf12 and GmHsf34 were restricted to the nucleus and GmHsf28 was localized in the nucleus and cytoplasm in plant. The results provide a fundamental clue for understanding of the complexity of the soybean HSF gene family and cloning specific function genes in further studies and applications.
Molecular cloning and characterization of RNA binding protein genes from the wild radish
정은숙,Selvam Ayarpadikannan,조창우,소현아,김경미,김순옥,곽명해,김기영,김도훈,이선우,이재헌 한국유전학회 2012 Genes & Genomics Vol.34 No.6
Two cDNA clones encoding RNA binding proteins (RBPs)were isolated from a cDNA library constructed from salt-treated leaf tissues of wild radish (Raphanus sativus var. hortensis for raphanistroide). The deduced amino acid sequence of either RsRBP1 or RsGRP1 contains an RNA-recognition motif (RRM) at the carboxy or amino terminal. Comparative sequence analysis of RsRBP1 reveals extensive homology (63-84%) to known RBPs from other plants. RsGRP1 was shown to be most homologous to AtGRP7 (93%) out of eight members of Arabidopsis glycine-rich RBPs. Transcript levels of RsRBP1 was up-regulated slowly and reached its maximum at 9 h during salt stress. On the other hand, RNA expression of RsGRP1 was up-regulated rapidly but significantly was reduced at 9 h after salt stress. The RsRBP1 and RsGRP1 proteins were detected in the nucleus and cytoplasm. Characterization of the transgenic Arabidopsis plants overexpressing RsRBP1 and RsGRP1 revealed that both transgenic lines displayed enhanced growth under the osmotic stress conditions. Overexpression of RsGRP1 resulted in delayed germination rates under the osmotic stress conditions, whereas RsRBP1 overexpression Arabidopsis did not display any dif-ference in germination rates during osmotic stress. These results suggest that RsRBP1 and RsGRP1 may be involved in the responses to osmotic stress in plant.