Science History of the Lab
      The lab was organized in 1978, when the late vice-president of the USSR Academy of Sciences asked Eugene D. Sverdlov, the researcher in the lab of Dr. Budovsky, to organize new group which was to implement the new direction of research in the Institute of Bioorganic Chemistry: applied and fundamental gene engineering studies. Since then our lab was involved in a number of research and development projects, the most notable being:
  • Development of chemical methods for modification of nucleic acids and development of chemical approaches to nucleic acids sequencing, secondary structure investigations and functioning.
  • Sequencing of the rpoBC operons encoding beta- and beta'- subunits of E. coli, S. typhimurium and P. putida RNA polymerases and localization of mutations in the rpoBC operon. Identification of the subunits of E. coli RNA polymerase involved in the initial stages of RNA synthesis.
  • Determination of primary structure of cDNA of alpha and beta- subunits of Na,K-ATPase from pig kidney. Identification of gene families corresponding to the alpha- and beta-subunits of Na,K- ATPase in human genome. Primary structure determination of the alpha-3 gene of alpha-subunit family and of a beta-subunit pseudogene. Study of the tissue-specificity of expression of alpha- and beta- subunits of the isoforms in human tissues and human cell lines. Detection of correlation between the ATPase subunits expression and tumor transformation of the cells.
  • Cloning and sequencing of the entire Hepatitis A virus cDNA (strain HAS15) and localization of the virus antigenic sites. Development of E. coli strains which overproduce human alpha- and gamma-interferon, interleukin 3, Hepatitis A antigenic determinants, HIV-1 and -2 antigenic determinants. Development of a technique for localization of new antigenic determinants in HIV viruses.
Since 1992 the fundamental research at the lab is mostly focused on comparative and structure-functional analyses of various genomes:
  • The functional mapping of the individual chromosomes. Chromosome-specific Expressed Sequenced Tag (EST) libraries were prepared for chromosomes 19, 20 and 21, EST map of human chromosome 19 was developed, LTRs of human endogenous retroviruses were mapped on the chromosome, the library of the nuclear Matrix Associated Regions (MAR) of chromosome 19 was prepared and the MARs were mapped on the chromosome.
  • The development of methods for mapping, sequencing and analysis of genomes, based on chemical techniques, in particular the application of oligonucleotide derivatives with increased affinity of complementary sequences binding were developed and shown to be useful for DNA sequencing as well as hybridization and PCR analyses. A new approach to systematic DNA sequencing based on the oligonucleotide application was proposed and applied to sequencing of DNA surrounding the LTRs on chromosome 19.
  • Techniques of subtractive hybridization for identification of differences between related genomes were developed and used for comparative analysis of human genomic and cDNAs from different tissues and also bacterial DNAs.
List of some most recent publications in English:
    Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, Sverdlov E
    A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3' terminus of L1.
  • Genomics 2002 80(4):402-6

     Khodosevich K, Lebedev Y, Sverdlov E
    Endogenous retroviruses and human evolution.
  • Comparative and Functional Genomics 2002; 3:494-8

     Komarova AV, Tchufistova LS, Supina EV, Boni IV
    Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation.
  • RNA 2002; 8(9):1137-1147

     Mamedov I, Batrak A, Buzdin A, Arzumanyan E, Lebedev Y, Sverdlov ED
    Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes.
  • Nucleic Acids Res 2002 15;30(14):e71

     Nikiforova NN, Velikodvorskaja TV, Kachko AV, Nikolaev LG, Monastyrskaya GS, Lukyanov SA, Konovalova SN, Protopopova EV, Svyatchenko VA, Kiselev NN, Loktev VB, Sverdlov ED
    Induction of alternatively spliced spermidine/spermine N1-acetyltransferase mRNA in the human kidney cells infected by venezuelan equine encephalitis and tick-borne encephalitis viruses.
  • Virology 2002 5;297(2):163-71.

     Domanskii A.N., Akopov S.B., Lebedev Y.B., Nikolaev L.G., Sverdlov E.D.
    Enhancer activity of solitary long terminal repeat of the human endogenous retrovirus of the HERV-K family.
  • Bioorg Khim 2002 Jul-Aug;28(4):341-5

     Buzdin A, Khodosevich K., Mamedov I., Vinogradova T., Lebedev Y., Hunsmann G., Sverdlov E.
    A Technique for Genome-Wide Identification of Differences in the Interspersed Repeats Integrations between Closely Related Genomes and Its Application to Detection of Human-Specific Integrations of HERV-K LTRs.
  • Genomics 2002 79(3): 413-22

     Chernov I. P., Akopov S. B., Nikolaev L. G., Sverdlov E. D.
    Indentification and mapping of nuclear matrix-attachment regions in a one megabase locus of human chromosome 19q13.12: long-range correlation of S/MARs and genes positions.
  • J Cell Biochem 2002 84(3): 590-600

     Vinogradova T, Leppik L, Kalinina E, Zhulidov P, Grzeschik KH, Sverdlov E.
    Selective Differential Display of RNAs containing interspersed repeats: analysis of changes in the transcription of HERV-K LTRs in germ cell tumors.
  • Mol Genet Genomics 2002 266(5):796-805

     Nadezhdin EV, Vinogradova TV, Sverdlov E. D.
    Interspecies subtractive hybridization of cDNA from human and chimpanzee brains.
  • Dokl Biochem Biophys 2001 381: 415-418

     Vinogradova T. V., Leppik L. P., Nikolaev L. G., Akopov S. B., Kleiman A. M., Senyuta N. B., Sverdlov E. D.
    Solitary human endogenous retroviruses-K LTRs retain transcriptional activity in vivo, the mode of which is different in different cell types.
  • Virology 2001 290: 83-90

     Kurdyukov SG, Lebedev YB, Artamonova II, Gorodentseva TN, Batrak AV, Mamedov IZ,
    Azhikina TL, Legchilina SP, Efimenko IG, Gardiner K, Sverdlov ED.
    Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history.
  • Gene 2001 273(1): 51-61

     Nadezhdin EV, Lebedev YB, Glazkova DV, Bornholdt D, Arman IP, Grzeschik K-H,
    Hunsmann G, Sverdlov ED.
    Identification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes.
  • Mol Genet Genomics 2001. 265:820-825
  • Domansky AN, Kopantzev EP, Snezhkov EV, Lebedev YB, Leib-Mosch C, Sverdlov ED.
    Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region.
    FEBS Lett. 2000 472(2-3):191-5.

  • Lebedev YB, Belonovitch OS, Zybrova NV, Khil PP, Kurdyukov SG, Vinogradova TV,
    Hunsmann G, Sverdlov ED.
    Differences in HERV-K LTR insertions in orthologous loci of humans and great apes.
    Gene. 2000; 247(1-2):265-77.

  • Sverdlov ED.
    Retroviruses and primate evolution.
    Bioessays. 2000; 22(2):161-71 (review)

  • Bogush ML, Velikodvorskaya TV, Lebedev YB, Nikolaev LG, Lukyanov SA, Fradkov AF,
    Pliyev BK, Boichenko MN, Usatova GN, Vorobiev AA, Andersen GL, Sverdlov ED.
    Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization.
    Mol Gen Genet. 1999; 262(4-5):721-9.

  • Lavrentieva I, et al.
    High polymorphism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats.
    FEBS Lett. 1999;443(3):341-7.

  • Akopyants NS, et al.
    PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori.
    Proc Natl Acad Sci U S A. 1998; 95(22):13108-13

  • Klinov DV, et al.
    High resolution mapping DNAs by R-loop atomic force microscopy.
    Nucleic Acids Res. 1998; 26(20):4603-10.

  • Sverdlov ED.
    Perpetually mobile footprints of ancient infections in human genome.
    FEBS Lett. 1998 ; 428(1-2):1-6. Review.

  • Lavrentieva I, et al.
    Subfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: physical neighbourhood does not correlate with identity level.
    Hum Genet. 1998; 102(1):107-16.

  • Akopov SB, et al.
    Long terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins.
    FEBS Lett. 1998 Jan 16;421(3):229-33.

  • Zavalova L, et al.
    Genes from the medicinal leech (Hirudo medicinalis) coding for unusual enzymes that specifically cleave endo-epsilon (gamma-Glu)-Lys isopeptide bonds and help to dissolve blood clots.
    Mol Gen Genet. 1996; 253(1-2):20-5.

  • Gurskaya NG, et al.
    Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate
    13-acetate.
    Anal Biochem. 1996; 240(1):90-7.

  • Fradkov A, et al.
    Enzyme from the medicinal leech (Hirudo medicinalis) that specifically splits
    endo-epsilon(-gamma-Glu)-Lys isopeptide bonds: cDNA cloning and protein primary structure.
    FEBS Lett. 1996; 390(2):145-8.

  • Ermolaeva OD, Sverdlov ED.
    Subtractive hybridization, a technique for extraction of DNA sequences distinguishing two closely related genomes: critical analysis.
    Genet Anal. 1996; 13(2):49-58. Review.

  • Diatchenko L, et al.
    Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries.
    Proc Natl Acad Sci U S A. 1996; 93(12):6025-30.

  • Nikolaev LG, et al.
    Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19.
    Nucleic Acids Res. 1996; 24(7):1330-6

  • Volik, S., Lebedev, Y., Nikolaev, L., Shevchenko, Y., Vinogradova, T., Kopantzev, E.,
    Kolesnik, T., Monastyrskaya, G., Kunz, U., Grzeschik, K.-H., Ashworth, L., Lennon, G.,
    Sverdlov, E.
    Mapping of transcribed sequences on human chromosome 19.
    DNA Sequence 1995;6:13-26

  • Borodin, A., Kopantsev, E., Wagner, L., Volik, S., Ermolaeva, O., Lebedev, Y.,
    Monastyrskaya, G., Kunz, J., Grzeschik, K.-H., Sverdlov, E.
    An arrayed library enriched in hncDNA corresponding to transcribed sequences of human chromosome 19: preparation and analysis.
    Genetic Analysis: Biomolecular Engineering 1995; 12:23-31

  • Lebedev, Y., Volik, S., Obradovich, D., Ermolaeva, O., Ashworth, L., Lennon, G., Sverdlov, E.
    Physical mapping of sequences homologous to an endogenous retrovirus LTR on human chromosome 19.
    Mol. and Gen. Genet. 1995; 247: 742-748

  • Prosnyak MI, et al.
    Substitution of 2-aminoadenine and 5-methylcytosine for adenine and cytosine in hybridization probes increases the sensitivity of DNA fingerprinting.
    Genomics. 1994;21(3):490-4

  • Lebedev YB, et al.
    Physical mapping of sequences homologous to an endogenous retrovirus LTR on human chromosome 19.
    Mol Gen Genet. 1995; 247(6):742-8
 

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