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Kashuba VI, Gizatullin RZ, Protopopov AI, Li J, Vorobieva NV, Fedorova L, Zabarovska VI, Muravenko OV, Kost-Alimova M, Domninsky DA, Kiss C, Allikmets R, Zakharyev VM, Braga EA, Sumegi J, Lerman M, Wahlestedt C, Zelenin AV, Sheer D, Winberg G, Grafodatsky A, Kisselev LL, Klein G, Zabarovsky ER. Analysis of NotI linking clones isolated from human chromosome 3 specific libraries. Gene 1999; 239:259-71. [PMID: 10548727 DOI: 10.1016/s0378-1119(99)00411-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have partially sequenced more than 1000 NotI linking clones isolated from human chromosome 3-specific libraries. Of these clones, 152 were unique chromosome 3-specific clones. The clones were precisely mapped using a combination of fluorescence in situ hybridization (FISH) and hybridization to somatic cell or radiation hybrids. Two- and three-color FISH was used to order the clones that mapped to the same chromosomal region, and in some cases, chromosome jumping was used to resolve ambiguous mapping. When this NotI restriction map was compared with the yeast artificial chromosome (YAC) based chromosome 3 map, significant differences in several chromosome 3 regions were observed. A search of the EMBL nucleotide database with these sequences revealed homologies (90-100%) to more than 100 different genes or expressed sequence tags (ESTs). Many of these homologies were used to map new genes to chromosome 3. These results suggest that sequencing NotI linking clones, and sequencing CpG islands in general, may complement the EST project and aid in the discovery of all human genes by sequencing random cDNAs. This method may also yield information that cannot be obtained by the EST project alone; namely, the identification of the 5' ends of genes, including potential promoter/enhancer regions and other regulatory sequences
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Affiliation(s)
- V I Kashuba
- Microbiology and Tumor Biology Center, Karolinska Institute, Stockholm, Sweden.
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Abstract
We have determined the nucleotide sequence of the 6868 bp full-size retrotransposon termed 'Tv1'. Tv1 was isolated from the DNA fraction of extracellular virus-like particles of Drosophila virilis culture cells. Tv1 has the typical structure for a gypsy-group retrotransposon. The Tv1 element was found to be flanked by 453 bp long terminal direct repeats identical to each other. The central part of the element contains three long open reading frames which resemble the gag, pol and env genes of retroviruses. ORF2 includes conservative motifs of protease, reverse transcriptase, RNase H and integrase in the order characteristic for the gypsy-group retrotransposons. Although most copies of Tv1 are located in pericentromeric heterochromatin, the amplification of this family demonstrated in the cell culture and site polymorphism observed in different Drosophila strains suggest functional activity of the Tv1 element.
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Affiliation(s)
- B V Andrianov
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow.
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Abstract
Migration of hematopoietic precursor cells to the thymus is shown to depend upon a novel molecule called Vanin-1 expressed by perivascular thymic stromal cells. An anti-Vanin-1 antibody blocks the binding of pro-T cells to thymic sections in vitro, the in vivo accumulation of bone marrow cells around cortical thymic vessels, and long-term thymic regeneration. Thus, it interferes with the entry, and not the differentiation, of hematopoietic precursor cells. The Vanin-1 gene codes for a GPI-anchored 70 kDa protein that shows homology only with human biotinidase. Transfection of thymic stromal cells with the Vanin-1 cDNA enhances thymocyte adhesion in vitro. These data suggest that Vanin-1 regulates late adhesion steps of thymus homing under physiological, noninflammatory conditions.
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Affiliation(s)
- M Aurrand-Lions
- Centre d'Immunologie, INSERM-Centre National de la Recherche Scientifique, Marseille, France
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Gizatullin RZ, Protopopov AI, Zabarovska V, Zakharyev VM, Kashuba VI, Klein G, Zabarovsky ER. Assignment of MOBP, encoding myelin-associated oligodendrocytic basic protein, to human chromosome bands 3p22-->p21.3 using somatic cell hybrids. Cytogenet Cell Genet 1996; 74:291-2. [PMID: 8976387 DOI: 10.1159/000134437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- R Z Gizatullin
- Microbiology and Tumor Biology Center, Karolinska Institute, Stockholm, Sweden
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Abstract
An integrated hepatitis B virus (HBV) DNA has been identified in a human neuroblastoma, cloned and sequenced. The integrated HBV DNA is not rearranged, although a 480-bp fragment is deleted. The integrated viral DNA covers the C gene fragment, the region of Pre-S and S, and the 3'-truncated X gene.
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Affiliation(s)
- N E Tagieva
- Engelhardt Institute of Molecular Biology, Moscow, Russia
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Allikmets RL, Kashuba VI, Pettersson B, Gizatullin R, Lebedeva T, Kholodnyuk ID, Bannikov VM, Petrov N, Zakharyev VM, Winberg G. NotI linking clones as a tool for joining physical and genetic maps of the human genome. Genomics 1994; 19:303-9. [PMID: 8188261 DOI: 10.1006/geno.1994.1062] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To study the connection among NotI linking clones, CpG islands, and genes, the sequence surrounding 143 NotI sites was determined. These NotI linking clones were isolated from human chromosome 3-specific libraries and contain an average C + G content of 65%. These clones represent sequence-tagged sites that can be positioned onto chromosome maps and used for generating a long-range NotI map of the human genome. A majority (about 90%) of these clones contain transcribed sequences, as detected by Northern blot hybridization, providing an efficient link between physical and functional (genetic) maps. The GenBank nucleotide database was searched with sequences from these NotI linking clones. For many clones, homology was found to human and other vertebrate genes. About 20 clones contained various repeats in their sequences and may represent microsatellite loci. Most of these NotI linking clones therefore represent evolutionarily conserved DNA fragments and also can be used for comparative genome mapping of other mammalian species. In addition, approximately 20% of all sequenced human CpG island-containing genes and more than 12% of all well-characterized human genes were found to possess NotI restriction sites. This is at least 2-5 times more than has been previously estimated and suggests that NotI sites have a much stronger association with genes.
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Affiliation(s)
- R L Allikmets
- Laboratory of Viral Carcinogenesis, National Cancer Institute, FCRDC, Frederick, Maryland 21702
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Schulga AA, Nurkiyanova KM, Zakharyev VM, Kirpichnikov MP, Skryabin KG. Cloning of the gene encoding RNase binase from Bacillus intermedius 7P. Nucleic Acids Res 1992; 20:2375. [PMID: 1594455 PMCID: PMC312358 DOI: 10.1093/nar/20.9.2375] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- A A Schulga
- Engelhardt Institute of Molecular Biology, Moscow, Russia
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Fehér A, Skryabin KG, Balázs E, Preiszner J, Shulga OA, Zakharyev VM, Dudits D. Expression of PVX coat protein gene under the control of extensin-gene promoter confers virus resistance on transgenic potato plants. Plant Cell Rep 1992; 11:48-52. [PMID: 24213037 DOI: 10.1007/bf00231839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/1991] [Revised: 12/05/1991] [Indexed: 06/02/2023]
Abstract
Tuber discs of potato (Solanum tuberosum L.) cultivars Desirée and Gracia were infected by Agrobacterium tumefaciens carrying a binary vector with the coat protein gene of potato virus X controlled by the carrot extensin gene long-transcript promoter. Several transgenic potato plants have been obtained by direct regeneration of shoots on culture medium with kanamycin used for selection. The presence of the coat protein gene was proved by Southern hybridization in several transformants. Its low but detectable expression level was shown by Northern and Western analysis. Ethephon treatment resulted in a five-fold increase in the amounts of the coat protein mRNA. The majority of transformants exhibited reduced accumulation of virus RNA in inoculated leaves. Potentials in the use of an ethylene-inducible promoter in the production of virus-resistant transgenic plants will be discussed.
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Affiliation(s)
- A Fehér
- Institute of Plant Physiology, Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, H-6701 Szeged, POB. 521, Hungary
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Georgiev OI, Nikolaev N, Hadjiolov AA, Skryabin KG, Zakharyev VM, Bayev AA. The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisae. Nucleic Acids Res 1981; 9:6953-8. [PMID: 6460984 PMCID: PMC327653 DOI: 10.1093/nar/9.24.6953] [Citation(s) in RCA: 190] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The complete nucleotide sequence of the 25 S rRNA gene from one rDNA repeating unit of Saccharomyces cerevisiae has been determined. The corresponding 25 S rRNA molecule contains 3392 nucleotides and has an estimated relative molecular mass (Mr, Na-salt) or 1.17 x 10(6). Striking sequence homology is observed with known 5'- and 3'-end terminal segments of L-rRNA from other eukaryotes. Possible models of interaction with 5.8 S rRNA are discussed.
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Bayev A, Georgiev OI, Hadjiolov AA, Nikolaev N, Skryabin KG, Zakharyev VM. The structure of the yeast ribosomal RNA genes. 3. Precise mapping of the 18 S and 25 S rRNA genes and structure of the adjacent regions. Nucleic Acids Res 1981; 9:789-99. [PMID: 7015285 PMCID: PMC326712 DOI: 10.1093/nar/9.4.789] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 5'-terminal of Saccharomyces cerevisiae 18 S and 25 S rRNA are precisely mapped within the sequence of the rDNA repeating unit. The 3'-terminal of 25 S rRNA and 37 S pre-rRNA are located within a 548 bp segment of the rDNA repeating unit by the use of a DNA polymerase I extension technique. The analysis of the rDNA sequences at the structural gene boundaries reveals the presence of oligonucleotide repeats which may be involved in transcription or processing control mechanisms. The sequence of rDNA in the transcription termination region is determined and possible mechanisms shaping the 3'-end of 25 S rRNA are discussed.
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Rubtsov PM, Musakhanov MM, Zakharyev VM, Krayev AS, Skryabin KG, Bayev AA. The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. Nucleic Acids Res 1980; 8:5779-94. [PMID: 7008030 PMCID: PMC324341 DOI: 10.1093/nar/8.23.5779] [Citation(s) in RCA: 264] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observed in the 3'-end region of the rRNA molecule. Comparison of the yeast 18 S rRNA sequences with partial sequence data, available for rRNAs of the other eucaryotes provides strong evidence that a substantial portion of the 18 S RNA sequence has been conserved in evolution.
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Bayev AA, Georgiev OI, Hadjiolov AA, Kermekchiev MB, Nikolaev N, Skryabin KG, Zakharyev VM. The structure of the yeast ribosomal RNA genes. 2. The nucleotide sequence of the initiation site for ribosomal RNA transcription. Nucleic Acids Res 1980; 8:4919-26. [PMID: 7003545 PMCID: PMC324269 DOI: 10.1093/nar/8.21.4919] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The 5'-terminal coding sequence for the 37 S precursor to rRNA of Saccharomyces cerevisiae is identified by reverse transcriptase extension and protection mapping with nuclease S1. The sequence of a 419 bp rDNA fragment containing the transcription initiation site and its adjacent region is determined.
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Ovchinnikov YA, Guryev SO, Krayev AS, Monastyrskaya GS, Skryabin KG, Sverdlov ED, Zakharyev VM, Bayev AA. Primary structure of an EcoRI fragment of lambda imm434 DNA containing regions cI-cro of phage 434 and cII-o of phage lambda. Gene X 1979; 6:235-49. [PMID: 478301 DOI: 10.1016/0378-1119(79)90060-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Digestion of phage lambda imm434 DNA with restriction endonuclease EcoRI yields 7 fragments. The shortest among them (1287 bp) contains the right part of the phage 434 immunity region and the phage DNA portion proximal to it. The complete primary structure of this fragment has been determined using the chemical method of DNA sequencing. Hypothetical amino-acid sequences of proteins coded by the cro gene of phage 434 and the cII gene of phage lambda, as well as NH2-terminal amino-acid sequences of the cI protein of phage 434 and the O protein of phage lambda, have been deduced solely on the basis of the DNA sequence. The fragment studied contains also the pR and probably prm promoters and the oR operator of phage 434. The sequence coding for them differs from the respective DNA sequence of phage lambda.
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