• Animal cells and systems
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• 제1권4호
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• pp.629-635
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• 1997

Previously we reported the migration and rearrangement of a chloroplast gene cluster into mitochondria. The exact genomic locations of the clusters, modes of the gene rearrangement and mechanisms of the interorganellar migration of the clusters have yet to be understood. The detailed analysis needs to include a larger region of DNA surrounding each cluster. To study DNA rearrangement and migration in more detail a cosmid library was constructed using the total rice genomic DNA including nuclear, chloroplast and mitochondrial DNA. From this cosmid library, a sub-library was obtained by selecting the clones hybridized to various regions of chloroplast DNA. According to the hybridization pattern 136 clones from the sub-library were classified into 29 groups. Detailed analysis of these clones revealed that in addition to authentic chloroplast DNA, the clones contain its homologs resulted from rearrangement and mutation. We analyzed two clones in detail, which contain different rp12 homologs resulted from rearrangement and/or migration, respectively.

• Genomics & Informatics
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• 제8권2호
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• pp.86-89
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• 2010

Closely related species share large genomic segments called syntenic regions, where the genomic elements such as genes are arranged co-linearly among the species. While synteny is an important criteria in establishing orthologous regions between species, non-syntenic regions may display species-specific features. As the first step in cataloging human- or primate- specific genomic elements, we surveyed human genomic regions that are not syntenic with any other non-primate mammalian genomes sequenced so far. Based on the data compiled in Ensembl databases, we were able to identify 10 such regions located in eight different human chromosomes. Interestingly, most of these highly human- or primate- specific loci are concentrated in subtelomeric or pericentromeric regions. It has been reported that subtelomeric regions in human chromosomes are highly plastic and filled with recently shuffled genomic elements. Pericentromeric regions also show a great deal of segmental duplications. Such genomic rearrangements may have caused these large human- or primate- specific genome segments.

• 대한미생물학회지
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• 제34권6호
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Genomics & Informatics
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• 제14권3호
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• pp.70-77
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• 2016

Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.

• IMMUNE NETWORK
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• 제2권2호
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• pp.79-85
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• 2002

Background: In contrast to evidences of Ig H chain receptor editing in transformed cell lines and transgenic mouse models, there has been no direct evidence that this phenomenon occurs in human developing B cells. Methods: $V_HDJ_H$ rearrangements were obtained from genomic DNA of individual $IgM^-$ B cells from liver and $IgM^+B$ cells from bone marrow of 18 wk of gestation human fetus by PCR amplification and direct sequencing. Results: We found three examples of H chain receptor editing from $IgM^+$ and $IgM^-human$ fetal B cells. Two types of $V_H$ replacements were identified. The first involved $V_H$ hybrid formation, in which part of a $V_H$ gene from the initial VDJ rearrangement is replaced by part of an upstream $V_H$ gene at the site of cryptic RSS. The second involved a gene conversion like replacement of CDR2, in which another $V_H$ gene donated a portion of its CDR2 sequence to the initial VDJ rearrangement. Conclusion: These data provide evidence of receptor editing at the H chain loci in developing human B cells, and also the first evidence of a gene conversion event in human Ig genes.

• Asian Pacific Journal of Cancer Prevention
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• 제17권sup3호
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• pp.149-153
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• 2016

Breast cancer is the most common cancer in Iran. In the recent years an upward trend has been observed in the Iranian population. Early detection by molecular approaches may reduce breast cancer morbidity and mortality. We provided consultation to 3,782 women diagnosed with early onset breast cancer during the past 15 years (1999-2014). To establish a data set for BRCA gene alterations of the Iranian families at risk, two hundred and fifty four women who met our criteria were analyzed. A total number of 46 alterations including 18 variants with unknown clinical significance (39.1%), 18 missense mutations (39.1%), 7 Indels (15.2%) and 3 large rearrangement sequences (6%) were identified. Further scanning of affected families revealed that 49% of healthy relatives harbor identical causative mutations. This is the first report of comprehensive BRCA analysis in Iranian women with early onset breast cancer. Our findings provide valuable molecular data to support physicians as well as patients for the best decision making on disease management.

• 식물조직배양학회지
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• 제25권2호
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• pp.109-113
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• 1998

본 연구에서는 상처, 병원균의 침입 등에 의하여 발현양이 크게 증폭되는 토마토 PAL유전자의 promoter에 giant silk moth(Hyalophora cecropia)로부터 분리한 lytic gene의 genetic code를 일부 변경한 Shiva 유전자를 부착하여 담배, 감자 등의 작물에 형질전환을 시도하였다. 형질전환된 담배로부터 얻은 종자에 대한 kanamycin저항성 유전자의 유전분석, PCR 증폭 혹은 genomic Southern blot hybridization에 의하여 tPAL5 promoter-Shiva fusion gene의 염색체내로의 integration을 확인하였다. Kanamycin 저항성 유전자의 유전분석에서 선발된 7개체를 PCR 분석 실시한 결과 모든 개체가 positive임이 확인되었으나, genomic Southern blot Hybridization으로는 4개체가 negative로 나타났다. 특히 한 개체의 경우는 chromosome rearrangement 현상이 일어난 것으로 추정되었다. 감자의 경우는 남작(Irish Cobbler) 품종이 Zeatin 2.0 mg/L NAA 0.01 mg/L, GA$_3$ 0.1mg/L을 포함한 배지에서 callus형성율 및 shooting율이 가장 높아서 재분화된 형질전환체를 얻을 수 있었다. 한편 GUS 유전자는 Shiva 유전자의 3' 말단에 존재하는 NOS terminator 때문에 translation까지의 발현이 어려울 것으로 예상되었으나 형질 전환하지 않은 담배에서보다 10배 이상의 GUS활성을 나타내었다. 또한 감자 조직에 X-gluc을 사용하여 GUS($\beta$-glucuronidase)의 기질로 작용하게 하여 효소활성 자리를 염색한 결과 줄기, 잎, 뿌리 등의 도관 조직에 다량 발혈됨을 확인할 수 있었다.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.180-182
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• 2002

Substantial genomic diversity has been expected among clinical isolates of H. pylori. We have suggested that the two complete H. pylori genomes already sequenced may be insufficient for providing a discriminatory tool for typing clinical isolates as well as an insight into the genomic diversity, which enable to establish strategy for control of H. pylori infection. In this study, we determine the nucleotide sequence of the entire genome of Korean strain 51 and compare it with two reported genomic sequences to suggest validity for extensive genomic sequencing of H. pylori. The genome of H. pylori 51 consists of a circular chromosome with a size of 1,591,297 bp, which is corresponding to $95.4\%\;and\;96.8\%$ of the 26695 and J99 chromosome length, respectively. We predict that there are 1,454 open reading frames (ORFs) in 51, representing $91.4\%\;and\;97.2\%$ of the reported numbers of ORF of 26695 and J99, respectively. In contrast to 26695 and J99 that have 123 and 65 strain-specific genes, respectively, of the 1,454 genes, only 39 genes are unique to 51. Differences in genomic organization between 51 and each foreign strain were greater than between 2 foreign strains in pair wise entire sequence alignments by BLASTN. Particularly, the extent of genomic rearrangement observed between 51 and 26695 is higher than between 51 and J99. Multiple sequence alignment of orthologous genes among 3 strains showed that 51 is genetically closer to 26695 rather than J99. Phylogenetic analysis of nonsynonymous and synonymous mutation indicated J99 has the longest branch length in the unrooted phylogenetic tree, suggesting that J99 has higher mutation rate than the other 2 strains.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.183-192
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• 2003

With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.

• Molecules and Cells
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• 제24권2호
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• pp.215-223
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• 2007

The genes encoding non-specific lipid transfer proteins (nsLTPs), members of a small multigene family, show a complex pattern of expressional regulation, suggesting that some diversification may have resulted from changes in their expression after duplication. In this study, the evolution of nsLTP genes within the Poaceae family was characterized via a survey of the pseudogenes and unigenes encoding the nsLTP in rice pseudomolecules and the NCBI unigene database. nsLTP-rich regions were detected in the distal portions of rice chromosomes 11 and 12; these may have resulted from the most recent large segmental duplication in the rice genome. Two independent tandem duplications were shown to occur within the nsLTP-rich regions of rice. The genomic distribution of the nsLTP genes in the rice genome differs from that in wheat. This may be attributed to gene migration, chromosomal rearrangement, and/or differential gene loss. The genomic distribution pattern of nsLTP genes in the Poaceae family points to the existence of some differences among cereal nsLTP genes, all of which diverged from an ancient gene. The unigenes encoding nsLTPs in each cereal species are clustered into five groups. The somewhat different distribution of nsLTP-encoding EST clones between the groups across cereal species imply that independent duplication(s) followed by subfunctionalization (and/or neofunctionalization) of the nsLTP gene family in each species occurred during speciation.