{"title":"RNA Dust: Where are the Genes?","authors":"P. Carninci","doi":"10.1093/dnares/dsq014","DOIUrl":"https://doi.org/10.1093/dnares/dsq014","url":null,"abstract":"","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"1 1","pages":"209 - 209"},"PeriodicalIF":0.0,"publicationDate":"2010-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82897330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest.
{"title":"Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome","authors":"Uttam Roymondal, S. Das, S. Sahoo","doi":"10.1093/dnares/dsn029","DOIUrl":"https://doi.org/10.1093/dnares/dsn029","url":null,"abstract":"We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"41 1","pages":"13 - 30"},"PeriodicalIF":0.0,"publicationDate":"2009-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88880064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome annotation produces a considerable number of putative proteins lacking sequence similarity to known proteins. These are referred to as "orphans." The proportion of orphan genes varies among genomes, and is independent of genome size. In the present study, we show that the proportion of orphan genes roughly correlates with the isolation index of organisms (IIO), an indicator introduced in the present study, which represents the degree of isolation of a given genome as measured by sequence similarity. However, there are outlier genomes with respect to the linear correlation, consisting of those genomes that may contain excess amounts of orphan genes. Comparisons of genome sequences among closely related strains revealed that some of the annotated genes are not conserved, suggesting that they are ORFs occurring by chance. Exclusion of these non-conserved ORFs within closely related genomes improved the correlation between the proportion of orphan genes and the IIO values. Assuming that the correlation holds in general, this relationship was used to estimate the number of "authentic" orphan genes in a genome. Using this definition of authentic orphan genes, the anomalies arising from over-assignments, e.g., the percentages of structural annotations, were corrected for 16 genomes, including those of five archaea.
{"title":"Estimation of the number of authentic orphan genes in bacterial genomes.","authors":"S. Fukuchi, K. Nishikawa","doi":"10.1093/DNARES/11.4.219","DOIUrl":"https://doi.org/10.1093/DNARES/11.4.219","url":null,"abstract":"Genome annotation produces a considerable number of putative proteins lacking sequence similarity to known proteins. These are referred to as \"orphans.\" The proportion of orphan genes varies among genomes, and is independent of genome size. In the present study, we show that the proportion of orphan genes roughly correlates with the isolation index of organisms (IIO), an indicator introduced in the present study, which represents the degree of isolation of a given genome as measured by sequence similarity. However, there are outlier genomes with respect to the linear correlation, consisting of those genomes that may contain excess amounts of orphan genes. Comparisons of genome sequences among closely related strains revealed that some of the annotated genes are not conserved, suggesting that they are ORFs occurring by chance. Exclusion of these non-conserved ORFs within closely related genomes improved the correlation between the proportion of orphan genes and the IIO values. Assuming that the correlation holds in general, this relationship was used to estimate the number of \"authentic\" orphan genes in a genome. Using this definition of authentic orphan genes, the anomalies arising from over-assignments, e.g., the percentages of structural annotations, were corrected for 16 genomes, including those of five archaea.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"96 1","pages":"219-31, 311-313"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87023403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. Ohara, T. Nagase, Gaku Mitsui, Hiroshi Kohga, R. Kikuno, S. Hiraoka, Yu Takahashi, S. Kitajima, Y. Saga, H. Koseki
We here modified a previously reported method for the construction of cDNA libraries by employing an in vitro recombination reaction to make it more suitable for comprehensive cDNA analysis. For the evaluation of the modified method, sets of size-selected cDNA libraries of four different mouse tissues and human brain were constructed and characterized. Clustering analysis of the 3' end sequence data of the mouse cDNA libraries indicated that each of the size-fractionated libraries was complex enough for comprehensive cDNA analysis and that the occurrence rates of unidentified cDNAs varied considerably depending on their size and on the tissue source. In addition, the end sequence data of human brain cDNAs thus generated showed that this method decreased the occurrence rates of chimeric clones by more than fivefold compared to conventional ligation-assisted methods when the cDNAs were larger than 5 kb. To further evaluate this method, we entirely sequenced 13 human unidentified cDNAs, named KIAA1990-KIAA2002, and characterized them in terms of the predicted protein sequences and their expression profiles. Taking all these results together, we here conclude that this new method for the construction of size-fractionated cDNA libraries makes it possible to analyze cDNAs efficiently and comprehensively.
{"title":"Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method.","authors":"O. Ohara, T. Nagase, Gaku Mitsui, Hiroshi Kohga, R. Kikuno, S. Hiraoka, Yu Takahashi, S. Kitajima, Y. Saga, H. Koseki","doi":"10.1093/DNARES/9.2.47","DOIUrl":"https://doi.org/10.1093/DNARES/9.2.47","url":null,"abstract":"We here modified a previously reported method for the construction of cDNA libraries by employing an in vitro recombination reaction to make it more suitable for comprehensive cDNA analysis. For the evaluation of the modified method, sets of size-selected cDNA libraries of four different mouse tissues and human brain were constructed and characterized. Clustering analysis of the 3' end sequence data of the mouse cDNA libraries indicated that each of the size-fractionated libraries was complex enough for comprehensive cDNA analysis and that the occurrence rates of unidentified cDNAs varied considerably depending on their size and on the tissue source. In addition, the end sequence data of human brain cDNAs thus generated showed that this method decreased the occurrence rates of chimeric clones by more than fivefold compared to conventional ligation-assisted methods when the cDNAs were larger than 5 kb. To further evaluate this method, we entirely sequenced 13 human unidentified cDNAs, named KIAA1990-KIAA2002, and characterized them in terms of the predicted protein sequences and their expression profiles. Taking all these results together, we here conclude that this new method for the construction of size-fractionated cDNA libraries makes it possible to analyze cDNAs efficiently and comprehensively.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"64 1","pages":"47-57"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87724588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
P. Sirithunya, S. Tragoonrung, A. Vanavichit, Nathinee Pa-In, Chanakarn Vongsaprom, T. Toojinda
Blast is an economically important disease of rice. To map genes controlling blast resistance, recombinant inbred lines (RIL) were developed from Khao Dawk Mali 105, an aromatic, blast-susceptible cultivar and the blast resistance donor, CT 9993-5-10-M (CT). A linkage map encompassing 2112 cM was constructed from 141 RILs using 90 restriction fragment length polymorphisms (RFLPs) and 31 simple sequence repeats (SSR). Virulent isolates of blast fungus were identified by screening differential host sets against 87 single-spore isolates collected from the north and northeast of Thailand. Fifteen virulent blast isolates were selected for leaf blast screening. Neck blast was evaluated both under natural conditions and controlled inoculations. Quantitative trait loci (QTLs) for broad resistance spectrum (BRS) to leaf blast were located on chromosomes 7 and 9. In particular, the QTL(ch9) was mapped near the Pi5(t) locus. The QTL(ch7) was located close to a previously mapped partial resistance QTL. Both loci showed significant allelic interaction. Genotypes having CT alleles at both QTL(ch7) and QTL(ch9) were the most resistant. Two neck-blast QTLs were mapped on chromosomes 5 and 6. The inconsistent map locations between the leaf and neck blast QTLs indicate the complexity of fixing both leaf and neck blast resistance. The coincidence of BRS and field resistance QTLs on chromosome 7 supports the idea that BRS may reflect the broad resistance spectrum to leaf blast in rice. These findings laid the foundation for the development of a marker-assisted scheme for improving Khoa Dawk Mali 105 and the majority of aromatic Thai rice varieties that are susceptible to blast.
稻瘟病是水稻重要的经济病害。为了定位稻瘟病抗性基因，以芳香型稻瘟病敏感品种“考多克马利105”和稻瘟病抗性供体CT 9993-5-10-M (CT)为材料，构建了重组自交系(RIL)。利用90个限制性片段长度多态性(RFLPs)和31个简单序列重复序列(SSR)，从141个rna中构建了包含2112 cM的连锁图谱。通过对从泰国北部和东北部收集的87株单孢子分离株进行差异寄主群筛选，鉴定出了毒力强的爆炸真菌分离株。选取15株毒力强的叶胚分离物进行叶胚筛选。在自然条件下和控制接种条件下对颈瘟进行了评价。叶片瘟病宽抗性谱(BRS)的数量性状位点(qtl)位于7号和9号染色体上。特别是，QTL(ch9)定位在Pi5(t)位点附近。该QTL(ch7)位于先前定位的部分抗性QTL附近。两个基因座均表现出显著的等位基因相互作用。在QTL(ch7)和QTL(ch9)上均有CT等位基因的基因型抗性最强。两个颈母细胞qtl分别定位在染色体5和6上。叶片与颈部抗风沙qtl图谱位置的不一致表明叶片与颈部抗风沙抗性的确定是复杂的。7号染色体上BRS和田间抗性qtl的重合支持了BRS可能反映水稻对叶瘟病的广泛抗性谱的观点。这些发现为开发一种标记辅助方案来改良Khoa Dawk Mali 105和大多数易患稻瘟病的泰国芳香水稻品种奠定了基础。
{"title":"Quantitative trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice (Oryza sativa).","authors":"P. Sirithunya, S. Tragoonrung, A. Vanavichit, Nathinee Pa-In, Chanakarn Vongsaprom, T. Toojinda","doi":"10.1093/DNARES/9.3.79","DOIUrl":"https://doi.org/10.1093/DNARES/9.3.79","url":null,"abstract":"Blast is an economically important disease of rice. To map genes controlling blast resistance, recombinant inbred lines (RIL) were developed from Khao Dawk Mali 105, an aromatic, blast-susceptible cultivar and the blast resistance donor, CT 9993-5-10-M (CT). A linkage map encompassing 2112 cM was constructed from 141 RILs using 90 restriction fragment length polymorphisms (RFLPs) and 31 simple sequence repeats (SSR). Virulent isolates of blast fungus were identified by screening differential host sets against 87 single-spore isolates collected from the north and northeast of Thailand. Fifteen virulent blast isolates were selected for leaf blast screening. Neck blast was evaluated both under natural conditions and controlled inoculations. Quantitative trait loci (QTLs) for broad resistance spectrum (BRS) to leaf blast were located on chromosomes 7 and 9. In particular, the QTL(ch9) was mapped near the Pi5(t) locus. The QTL(ch7) was located close to a previously mapped partial resistance QTL. Both loci showed significant allelic interaction. Genotypes having CT alleles at both QTL(ch7) and QTL(ch9) were the most resistant. Two neck-blast QTLs were mapped on chromosomes 5 and 6. The inconsistent map locations between the leaf and neck blast QTLs indicate the complexity of fixing both leaf and neck blast resistance. The coincidence of BRS and field resistance QTLs on chromosome 7 supports the idea that BRS may reflect the broad resistance spectrum to leaf blast in rice. These findings laid the foundation for the development of a marker-assisted scheme for improving Khoa Dawk Mali 105 and the majority of aromatic Thai rice varieties that are susceptible to blast.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"79 1","pages":"79-88"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86465827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kunihiko Takamatsu, K. Maekawa, T. Togashi, D. Choi, Yutaka Suzuki, T. Taylor, A. Toyoda, S. Sugano, A. Fujiyama, M. Hattori, Y. Sakaki, T. Takeda
We recently helped to complete the sequence of human chromosome 21 at a very high level of accuracy. Using this sequence we identified two novel genes, designated DSCR9 and DSCR10, in the so-called Down Syndrome Critical Region (DSCR) by computational gene prediction and subsequent cDNA cloning. Both DSCR9 and DSCR10 are expressed preferentially in testis and encode functionally unknown proteins with 149 and 87 amino acid residues, respectively. Zoo blot analysis suggested that both genes are exclusive to primate genomes such as chimpanzee, gorilla, orangutan, crab-eating monkey and African green monkey but are not present in other non-primate mammals including mouse, dog, cat, and chicken. Comparative genomic sequence analysis of DSCR9 and DSCR10 with the corresponding mouse syntenic region confirmed the lack of these genes in the mouse. These results strongly suggest that DSCR9 and DSCR10 have emerged as a new class of gene in the primate lineage during evolution.
{"title":"Identification of two novel primate-specific genes in DSCR.","authors":"Kunihiko Takamatsu, K. Maekawa, T. Togashi, D. Choi, Yutaka Suzuki, T. Taylor, A. Toyoda, S. Sugano, A. Fujiyama, M. Hattori, Y. Sakaki, T. Takeda","doi":"10.1093/DNARES/9.3.89","DOIUrl":"https://doi.org/10.1093/DNARES/9.3.89","url":null,"abstract":"We recently helped to complete the sequence of human chromosome 21 at a very high level of accuracy. Using this sequence we identified two novel genes, designated DSCR9 and DSCR10, in the so-called Down Syndrome Critical Region (DSCR) by computational gene prediction and subsequent cDNA cloning. Both DSCR9 and DSCR10 are expressed preferentially in testis and encode functionally unknown proteins with 149 and 87 amino acid residues, respectively. Zoo blot analysis suggested that both genes are exclusive to primate genomes such as chimpanzee, gorilla, orangutan, crab-eating monkey and African green monkey but are not present in other non-primate mammals including mouse, dog, cat, and chicken. Comparative genomic sequence analysis of DSCR9 and DSCR10 with the corresponding mouse syntenic region confirmed the lack of these genes in the mouse. These results strongly suggest that DSCR9 and DSCR10 have emerged as a new class of gene in the primate lineage during evolution.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"131 1","pages":"89-97"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85653719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Nakajima, N. Okazaki, H. Yamakawa, R. Kikuno, O. Ohara, T. Nagase
We have accumulated information on protein-coding sequences of uncharacterized human genes, which are known as KIAA genes, through cDNA sequencing. For comprehensive functional analysis of the KIAA genes, it is necessary to prepare a set of cDNA clones which direct the synthesis of functional KIAA gene products. However, since the KIAA cDNAs were derived from long mRNAs (> 4 kb), it was not expected that all of them were full-length. Thus, as the first step toward preparing these clones, we evaluated the integrity of protein-coding sequences of KIAA cDNA clones through comparison with homologous protein entries in the public database. As a result, 1141 KIAA cDNAs had at least one homologous entry in the database, and 619 of them (54%) were found to be truncated at the 5' and/or 3' ends. In this study, 290 KIAA cDNA clones were tailored to be full-length or have considerably longer sequences than the original clones by isolating additional cDNA clones and/or connected parts of additional cDNAs or PCR products of the missing portion to the original cDNA clone. Consequently, 265, 8, and 17 predicted CDSs of KIAA cDNA clones were increased in the amino-, carboxy-, and both terminal sequences, respectively. In addition, 40 cDNA clones were modified to remove spurious interruption of protein-coding sequences. The total length of the resultant extensions at amino- and carboxy-terminals of KIAA gene products reached 97,000 and 7,216 amino acid residues, respectively, and various protein domains were found in these extended portions.
{"title":"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.","authors":"D. Nakajima, N. Okazaki, H. Yamakawa, R. Kikuno, O. Ohara, T. Nagase","doi":"10.1093/DNARES/9.3.99","DOIUrl":"https://doi.org/10.1093/DNARES/9.3.99","url":null,"abstract":"We have accumulated information on protein-coding sequences of uncharacterized human genes, which are known as KIAA genes, through cDNA sequencing. For comprehensive functional analysis of the KIAA genes, it is necessary to prepare a set of cDNA clones which direct the synthesis of functional KIAA gene products. However, since the KIAA cDNAs were derived from long mRNAs (> 4 kb), it was not expected that all of them were full-length. Thus, as the first step toward preparing these clones, we evaluated the integrity of protein-coding sequences of KIAA cDNA clones through comparison with homologous protein entries in the public database. As a result, 1141 KIAA cDNAs had at least one homologous entry in the database, and 619 of them (54%) were found to be truncated at the 5' and/or 3' ends. In this study, 290 KIAA cDNA clones were tailored to be full-length or have considerably longer sequences than the original clones by isolating additional cDNA clones and/or connected parts of additional cDNAs or PCR products of the missing portion to the original cDNA clone. Consequently, 265, 8, and 17 predicted CDSs of KIAA cDNA clones were increased in the amino-, carboxy-, and both terminal sequences, respectively. In addition, 40 cDNA clones were modified to remove spurious interruption of protein-coding sequences. The total length of the resultant extensions at amino- and carboxy-terminals of KIAA gene products reached 97,000 and 7,216 amino acid residues, respectively, and various protein domains were found in these extended portions.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"22 1","pages":"99-106"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82751081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leaf trichome formation is known to be regulated by the TTG, GL1, GL2, and GL3 genes in Arabidopsis. GL1 and GL3 encode proteins with Myb and bHLH domains, respectively. Overexpression of the AtmybL2 gene, which encodes a single Myb-like DNA-binding domain, repressed trichome development in transgenic Arabidopsis plants. The amount of GL2 transcription was clearly reduced in the transgenic plants. Consistent with this, overexpression of AtmybL2 decreased beta-glucuronidase (GUS) activity in transgenic plants carrying a GUS-reporter gene regulated by the GL2 promoter. These findings, together with the results from our yeast two-hybrid analysis, suggest that GL3 gene function and overexpression of AtmybL2 act synergistically to inhibit trichome formation by negatively regulating GL2 expression.
{"title":"Overexpression of the AtmybL2 gene represses trichome development in Arabidopsis.","authors":"S. Sawa","doi":"10.1093/DNARES/9.2.31","DOIUrl":"https://doi.org/10.1093/DNARES/9.2.31","url":null,"abstract":"Leaf trichome formation is known to be regulated by the TTG, GL1, GL2, and GL3 genes in Arabidopsis. GL1 and GL3 encode proteins with Myb and bHLH domains, respectively. Overexpression of the AtmybL2 gene, which encodes a single Myb-like DNA-binding domain, repressed trichome development in transgenic Arabidopsis plants. The amount of GL2 transcription was clearly reduced in the transgenic plants. Consistent with this, overexpression of AtmybL2 decreased beta-glucuronidase (GUS) activity in transgenic plants carrying a GUS-reporter gene regulated by the GL2 promoter. These findings, together with the results from our yeast two-hybrid analysis, suggest that GL3 gene function and overexpression of AtmybL2 act synergistically to inhibit trichome formation by negatively regulating GL2 expression.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"32 1","pages":"31-4"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84994163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. Iwasaki, Y. Ezura, R. Ishida, M. Kajita, M. Kodaira, J. Knight, S. Daniel, M. Shi, M. Emi
Advances in technologies for identifying genetic polymorphisms rapidly and accurately will dramatically accelerate the discovery of disease-related genes. Among a variety of newly described methods for rapid typing of single-nucleotide polymorphisms (SNPs), gene detection using DNA microarrays is gradually achieving widespread use. This method involves the use of short (11- to 13-mer) allele-specific oligonucleotides. This method allows simultaneous analysis of many SNPs in DNAs from a large number of individuals, in a single experiment. In this work, we evaluated the accuracy of a new microarray-based short allele-specific oligonucleotide (ASO) hybridization method. There is a 96-well formatted array on a single plate, in which up to 256 spots are included in each well. Fluorescent probes for our experiments were produced by multiplex PCR amplification often target SNP-containing regions. We genotyped 192 individuals across a panel of ten single base variations, which included an insertion/deletion polymorphism. For comparison, we genotyped the same individuals for the same SNPs by the method of single-base extension with fluorescence detection. The typing accuracies of the microarray-based PCR-ASO and single-base extension methods were calculated as 99.9% and 99.1%, respectively, on the basis of genotyping results determined by direct sequencing. We conclude that the microarray-based hybridization method using short ASO probes represents a potential breakthrough technology for typing large numbers of SNPs rapidly and efficiently.
{"title":"Accuracy of genotyping for single nucleotide polymorphisms by a microarray-based single nucleotide polymorphism typing method involving hybridization of short allele-specific oligonucleotides.","authors":"H. Iwasaki, Y. Ezura, R. Ishida, M. Kajita, M. Kodaira, J. Knight, S. Daniel, M. Shi, M. Emi","doi":"10.1093/DNARES/9.2.59","DOIUrl":"https://doi.org/10.1093/DNARES/9.2.59","url":null,"abstract":"Advances in technologies for identifying genetic polymorphisms rapidly and accurately will dramatically accelerate the discovery of disease-related genes. Among a variety of newly described methods for rapid typing of single-nucleotide polymorphisms (SNPs), gene detection using DNA microarrays is gradually achieving widespread use. This method involves the use of short (11- to 13-mer) allele-specific oligonucleotides. This method allows simultaneous analysis of many SNPs in DNAs from a large number of individuals, in a single experiment. In this work, we evaluated the accuracy of a new microarray-based short allele-specific oligonucleotide (ASO) hybridization method. There is a 96-well formatted array on a single plate, in which up to 256 spots are included in each well. Fluorescent probes for our experiments were produced by multiplex PCR amplification often target SNP-containing regions. We genotyped 192 individuals across a panel of ten single base variations, which included an insertion/deletion polymorphism. For comparison, we genotyped the same individuals for the same SNPs by the method of single-base extension with fluorescence detection. The typing accuracies of the microarray-based PCR-ASO and single-base extension methods were calculated as 99.9% and 99.1%, respectively, on the basis of genotyping results determined by direct sequencing. We conclude that the microarray-based hybridization method using short ASO probes represents a potential breakthrough technology for typing large numbers of SNPs rapidly and efficiently.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"8 1","pages":"59-62"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82849488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Monna, Noriyuki Kitazawa, R. Yoshino, Junko Suzuki, Haruka Masuda, Y. Maehara, M. Tanji, Mizuho Sato, S. Nasu, Y. Minobe
A rice semidwarfing gene, sd-1, known as the "green revolution gene," was isolated by positional cloning and revealed to encode gibberellin 20-oxidase, the key enzyme in the gibberellin biosynthesis pathway. Analysis of 3477 segregants using several PCR-based marker technologies, including cleaved amplified polymorphic sequence, derived-CAPS, and single nucleotide polymorphisms revealed 1 ORF in a 6-kb candidate interval. Normal-type rice cultivars have an identical sequence in this region, consisting of 3 exons (558, 318, and 291 bp) and 2 introns (105 and 1471 bp). Dee-Geo-Woo-Gen-type sd-1 mutants have a 383-bp deletion from the genome (278-bp deletion from the expressed sequence), from the middle of exon 1 to upstream of exon 2, including a 105-bp intron, resulting in a frame-shift that produces a termination codon after the deletion site. The radiation-induced sd-1 mutant Calrose 76 has a 1-bp substitution in exon 2, causing an amino acid substitution (Leu [CTC] to Phe [TTC]). Expression analysis suggests the existence of at least one more locus of gibberellin 20-oxidase which may prevent severe dwarfism from developing in sd-1 mutants.
{"title":"Positional cloning of rice semidwarfing gene, sd-1: rice \"green revolution gene\" encodes a mutant enzyme involved in gibberellin synthesis.","authors":"L. Monna, Noriyuki Kitazawa, R. Yoshino, Junko Suzuki, Haruka Masuda, Y. Maehara, M. Tanji, Mizuho Sato, S. Nasu, Y. Minobe","doi":"10.1093/DNARES/9.1.11","DOIUrl":"https://doi.org/10.1093/DNARES/9.1.11","url":null,"abstract":"A rice semidwarfing gene, sd-1, known as the \"green revolution gene,\" was isolated by positional cloning and revealed to encode gibberellin 20-oxidase, the key enzyme in the gibberellin biosynthesis pathway. Analysis of 3477 segregants using several PCR-based marker technologies, including cleaved amplified polymorphic sequence, derived-CAPS, and single nucleotide polymorphisms revealed 1 ORF in a 6-kb candidate interval. Normal-type rice cultivars have an identical sequence in this region, consisting of 3 exons (558, 318, and 291 bp) and 2 introns (105 and 1471 bp). Dee-Geo-Woo-Gen-type sd-1 mutants have a 383-bp deletion from the genome (278-bp deletion from the expressed sequence), from the middle of exon 1 to upstream of exon 2, including a 105-bp intron, resulting in a frame-shift that produces a termination codon after the deletion site. The radiation-induced sd-1 mutant Calrose 76 has a 1-bp substitution in exon 2, causing an amino acid substitution (Leu [CTC] to Phe [TTC]). Expression analysis suggests the existence of at least one more locus of gibberellin 20-oxidase which may prevent severe dwarfism from developing in sd-1 mutants.","PeriodicalId":11212,"journal":{"name":"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes","volume":"46 1","pages":"11-7"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75353653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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