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Shigeki Mizuno - One of the best experts on this subject based on the ideXlab platform.
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Specific chromomeres on the chicken W lampbrush chromosome contain specific repetitive DNA sequence families.
Chromosome research : an international journal on the molecular supramolecular and evolutionary aspects of chromosome biology, 1998Co-Authors: Irina Solovei, Shigeki Mizuno, Akira Ogawa, Mitsuru Naito, Herbert C. MacgregorAbstract:Chromomeres 1 and 3 of the chicken W lampbrush chromosome contain most of the EcoRI and XhoI repeat sequence families respectively. These chromomeres were stained with DAPI and their sizes relative to other W chromomeres were observed. Their relative contents of EcoRI and XhoI repeats were determined using fluorescence in situ hybridization with genomic probes for each of the two repeat families. There were two types of W chromosome in the chickens (White Leghorn and Rhode Island Red) used in this study with respect to the amount of EcoRI repeat. A high-copy-number type has about 4000 copies of the 1.2-kb repeat per genome and shows a large fluorescence signal on W chromomere 1. A low-copy-number type has about 700 copies per genome and does not have a detectable chromomere 1 on W chromosome, nor does it show FISH labelling in the region normally occupied by chromomere 1. The genome of Fayoumi chickens has about one-sixth the amount of the XhoI sequence family of White Leghorns. W lampbrush chromomere 3 is much smaller and its FISH labelling with the XhoI probe is much weaker in Fayoumis than in White Leghorns. These results demonstrate that in the chicken W chromosome, specific chomomeres are occupied by specific DNA repeat sequence families.
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distribution of XhoI and ecori family repetitive dna sequences into separate domains in the chicken w chromosome
Chromosoma, 1992Co-Authors: Yasushi Saitoh, Shigeki MizunoAbstract:Fluorescence in situ hybridization using as probes three biotinylated or digoxigenin-labeled chicken W chromosome-specific repeating DNA units (0.7 and 1.1 kb XhoI family and 1.2 kb EcoRI family units) suggested that a large fraction of one arm of the W chromosome was occupied by the EcoRI family sequences and that pericentromeric regions were widely occupied by the XhoI family sequences. A minor fraction of the EcoRI family was also present in a narrow region in the proximal half of the other arm. There was a region in the distal half of the latter arm where sequences from neither family hybridized. Evolutionary aspects of the presence of different domains occupied by different repetitive families and the significance of the unhybridized distal region are discussed.
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Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences
Chromosoma, 1991Co-Authors: Yasushi Saitoh, Hisato Saitoh, Hohei Ohtomo, Shigeki MizunoAbstract:Another family of repetitive sequences, designated the EcoRI family, was found in the DNA of the chicken W chromosome by hybridization with the W chromosome-specific XhoI family probe under conditions of low stringency. A 1.2 kb EcoRI fragment, the major repeating unit of the family, was cloned and sequenced. The 1.2 kb unit showed an overall sequence similarity of about 68% to the 0.7 kb XhoI family repeating unit and it consisted of tandem repeats of average length 21 bp, most of which contained (A)_3–5 and (T)_3–4 clusters separated by 6–8 G+C-rich sequences. These features and its behavior as a strongly bent molecule in solution were very similar to those found for other W chromosome-specific repetitive sequences in the order Galliformes: XhoI family of chicken, PstI family of turkey and TaqI family of pheasant. The cloned 1.2 kb unit contained 78 CpG dinucleotide sequences and those that were in HapII, HhaI and BstUI sites were shown to be extensively methylated in the genomic DNA. Repetition frequencies of the 1.2 kb unit among the female population of chicken fell into high- and low-level classes, which accounted for about 30% and 10%, respectively, of the DNa in the W chromosome. Thus, 70% to 90% of the DNA in the chicken W chromosome was shown to be occupied by bent-repetitive sequences. The EcoRI and XhoI family sequences were not intermingled over the short range but each family formed a unique domain ranging from one to several million base pairs.
Rintaro Sato - One of the best experts on this subject based on the ideXlab platform.
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Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: hub strains for giant DNA engineering.
Journal of biochemistry, 2019Co-Authors: Mitsuhiro Itaya, Mitsuru Sato, Masaru Tomita, Satoru Watanabe, Hirofumi Yoshikawa, Rintaro SatoAbstract:Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r-m+). It was demonstrated that the r-m+ strains can incorporate and transfer synthesized DNA with multiple XhoI sites. These should be of value as hub strains to integrate and disseminate giant DNA between B. subtilis 168 derivatives.
Yong Sheng Zong - One of the best experts on this subject based on the ideXlab platform.
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Analysis of Epstein-Barr virus with BamHI "f" variant and XhoI-loss of LMP1 gene in nasopharyngeal carcinoma
Zhonghua bing li xue za zhi = Chinese journal of pathology, 2003Co-Authors: An Jia Han, Yong Sheng Zong, Min Zhang, Su Mei Cao, Su Xia Lin, Ying Jie LiangAbstract:OBJECTIVE To investigate the genomic variation of Epstein-Barr virus (EBV) and its significance in nasopharyngeal carcinogenesis. METHODS Forty nasopharyngeal carcinoma (NPC) biopsy tissues were used for detection of EBV BamHI f variant and LMP1 XhoI-loss by polymerase chain reaction (PCR), nested PCR, and RFLP (restriction fragment length polymorphism). Forty-eight samples of peripheral blood mononuclear cells (PBMC) taken from apparently healthy adult individuals were used for detection of LMP1 XhoI-loss. Three samples of amplified LMP1 exon 1 DNA from B95-8 cell line and 2 NPC tissues (one having XhoI-loss and the other having Wt-XhoI/XhoI-loss) were sequenced. RESULTS Thirty out of the 40 NPC cases (30/40, 75%) harbored EBV BamHI f variant and the remaining 10 (10/40, 25%) harbored BamHI F prototype. Thirty out of the 39 NPCs (30/39, 76.9%) showed single EBV LMP1 XhoI-loss, 7 (7/39, 18.0%) showed single LMP1 Wt-XhoI (presence of a XhoI site in exon 1 of LMP1 gene, as in B95-8 cell line), and 2 (2/39, 5.1%) showed both LMP1 Wt-XhoI and XhoI-loss. Thirty-eight of the 39 NPCs (97.4%) showed EBV LMP1 XhoI-loss or/and BamHI F variant. In the NPC tissue (1 case only) showing the prototype of Wt-XhoI/BamHI "f", there were several base substitutions, including 5 missense mutations and 2 silent mutations present in LMP1 exon 3, on DNA sequencing. On the other hand, 10 out of the 48 samples of PBMC taken from apparently healthy individuals could be amplified successfully by nested PCR for detection of LMP1 XhoI site. All of these 10 samples carried the prototype of EBV LMP1 Wt-XhoI. CONCLUSIONS The majority of EBV present in neoplastic cells of NPC is of BamHI "f" variant and/or possesses LMP1 XhoI-loss, as compared with that in healthy individuals. This genomic variation of EBV may bear some roles in the development and progression of NPC.
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Loss of an XhoI-site within N-terminal region of Epstein-Barr virus LMP1 gene in nasopharyngeal carcinoma.
Ai zheng = Aizheng = Chinese journal of cancer, 2003Co-Authors: Su Xia Lin, An Jia Han, Yong Sheng Zong, Ying Jie LiangAbstract:BACKGROUND & OBJECTIVE: It is well known that Epstein-Barr virus(EBV) LMP1 gene is involved in nasopharyngeal carcinogenesis. This research was designed to investigate the loss of an Xho I-site within the N-terminus of Epstein-Barr virus(EBV) latent membrane protein 1(LMP1) gene isolated from nasopharyngeal carcinoma (NPC) in Guangdong for further understanding the sequence variation of LMP1 gene involved in carcinogenesis. METHODS: Sixty-three fresh nasopharyngeal biopsies taken from the patients with nasopharyngeal carcinoma were collected in Cancer Center of Sun Yat-sen University. The peripheral blood mononuclear cells (PBMCs) obtained from 10 healthy EBV carriers were as control. The QIAamp DNA Mini Kits were used for extracting the DNA of biopsies and PBMCs. The N-terminus of EBV LMP1 gene was amplified using nested polymerase chain reaction (PCR) and then followed by Xho I enzyme digestion. Bidirectional solid-phase sequencing of the PCR products was performed using four-colored fluorescence terminator sequencing method. RESULTS: No loss of an Xho I-site within N-terminus of EBV LMP1 gene (wt-Xho I) was detected in PBMCs of all 10 carriers. The loss of an Xho I-site (Xho I-loss) was demonstrated in 50 cases (50/63, 79.36%) and the partial loss was demonstrated in 4 cases (4/63, 6.35%). The loss of an Xho I-site was not found in 9 cases (9/63, 14.29%). Besides loss of an Xho I-site (nt:169423-169428; GAGCTC --> GATCTC), 4 additional missense point mutations were found. CONCLUSION: According to the results obtained from this investigation, the PBMCs of 10 EBV carriers residing in Guangdong merely contain EBV variant with wt-Xho I. On the contrary, the EBV variant with XhoI-loss becomes the predominant variant detected in NPC tissues. So, the genomic variation within N-terminus (loss of an Xho I-site and other missense point mutations) of EBV LMP1 gene might be developed in the process of nasopharyngeal carcinogenesis.
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Loss of an XhoI-site in N-terminal region of LMP1 gene of Epstein-Barr virus in nasopharyngeal carcinoma from Guangzhou
Guangdong Medical Journal, 2003Co-Authors: Su Xia Lin, Yong Sheng ZongAbstract:To investigate the loss of an XhoI-site within the N-terminal region of Epstein-Barr virus (EBV) LMP1 gene isolated from nasopharyngeal carcinoma (NPC) for the sake of understanding the sequence variation of EBV LMP1 gene involved in carcinogenesis. Sixty-three fresh nasopharyngeal biopsies taken from patients with NPC were collected from Cancer Center of Sun Yat-sen University. The mononuclear cells of 2-ml perpheral blood (PBMCs) taken from 10 healthy EBV carriers were as a control. The QIAamp DNA Mini Kit and QIAamp DNA Mini Blood Kit were used for extracting the DNA of biopsies and PBMCs, respectively. The N-terminal region of EBV LMP1 was amplified by using nested PCR and then followed by XhoI enzyme digestion. Bidirectional solid-phase sequencing of the PCR product was performed by using the four-coloured fluorescence terminator sequencing method. No loss of an XhoI-site within N-terminal region of EBV LMP1 (wt-XhoI) was detected in all 10 carriers' PBMCs.
Mitsuhiro Itaya - One of the best experts on this subject based on the ideXlab platform.
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Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: hub strains for giant DNA engineering.
Journal of biochemistry, 2019Co-Authors: Mitsuhiro Itaya, Mitsuru Sato, Masaru Tomita, Satoru Watanabe, Hirofumi Yoshikawa, Rintaro SatoAbstract:Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r-m+). It was demonstrated that the r-m+ strains can incorporate and transfer synthesized DNA with multiple XhoI sites. These should be of value as hub strains to integrate and disseminate giant DNA between B. subtilis 168 derivatives.
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Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168
Bioscience biotechnology and biochemistry, 2008Co-Authors: Naoto Ohtani, Mitsuru Sato, Masaru Tomita, Mitsuhiro ItayaAbstract:Conjugational transfer of pLS20 in Bacillus subtilis Marburg 168 is restricted by the BsuM restriction-modification system. Restriction efficiency was measured using pLS20 derivatives possessing various numbers of XhoI sites, which are known to be recognized by BsuM. An increase in XhoI sites clearly reduced the conjugational efficiency of pLS20 as compared with that of pUB110 plasmid lacking XhoI.
Yasushi Saitoh - One of the best experts on this subject based on the ideXlab platform.
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distribution of XhoI and ecori family repetitive dna sequences into separate domains in the chicken w chromosome
Chromosoma, 1992Co-Authors: Yasushi Saitoh, Shigeki MizunoAbstract:Fluorescence in situ hybridization using as probes three biotinylated or digoxigenin-labeled chicken W chromosome-specific repeating DNA units (0.7 and 1.1 kb XhoI family and 1.2 kb EcoRI family units) suggested that a large fraction of one arm of the W chromosome was occupied by the EcoRI family sequences and that pericentromeric regions were widely occupied by the XhoI family sequences. A minor fraction of the EcoRI family was also present in a narrow region in the proximal half of the other arm. There was a region in the distal half of the latter arm where sequences from neither family hybridized. Evolutionary aspects of the presence of different domains occupied by different repetitive families and the significance of the unhybridized distal region are discussed.
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Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences
Chromosoma, 1991Co-Authors: Yasushi Saitoh, Hisato Saitoh, Hohei Ohtomo, Shigeki MizunoAbstract:Another family of repetitive sequences, designated the EcoRI family, was found in the DNA of the chicken W chromosome by hybridization with the W chromosome-specific XhoI family probe under conditions of low stringency. A 1.2 kb EcoRI fragment, the major repeating unit of the family, was cloned and sequenced. The 1.2 kb unit showed an overall sequence similarity of about 68% to the 0.7 kb XhoI family repeating unit and it consisted of tandem repeats of average length 21 bp, most of which contained (A)_3–5 and (T)_3–4 clusters separated by 6–8 G+C-rich sequences. These features and its behavior as a strongly bent molecule in solution were very similar to those found for other W chromosome-specific repetitive sequences in the order Galliformes: XhoI family of chicken, PstI family of turkey and TaqI family of pheasant. The cloned 1.2 kb unit contained 78 CpG dinucleotide sequences and those that were in HapII, HhaI and BstUI sites were shown to be extensively methylated in the genomic DNA. Repetition frequencies of the 1.2 kb unit among the female population of chicken fell into high- and low-level classes, which accounted for about 30% and 10%, respectively, of the DNa in the W chromosome. Thus, 70% to 90% of the DNA in the chicken W chromosome was shown to be occupied by bent-repetitive sequences. The EcoRI and XhoI family sequences were not intermingled over the short range but each family formed a unique domain ranging from one to several million base pairs.
