Group for Studying the Non-Coding DNA

        Group leader

        Olga Podgornaya

        Professor, D.Sci., Ph.D.


Staff Members

Dr. N. Enukashvily

Dr. A. Voronin

Dr. I. Kuznetsova

Dr. I. Matveev

PhD Students

A. Komissarov

E. Gavrilova

N. Galaktionov

L. Adonin


1. Classification of the tandem repeats (TR) in the mouse genome databases (in silico) and checking of the bioinformatic prediction of TR positions (in situ) by florescent in situ hybridization (FISH). Chromosome specific TR is found.

Fig. 1. A - The graph of tandem repeat arrays distribution was done in program Mathemetica 6.0. Each circle represents one array of 941 in total. The circle size reflects the size of the array itself in log scale. Each family colored: A1 - MiSat (red); B2 - MaSat (blue); C3 - TRPC-21A (orange light); C4 - multi locus (ML, violet); C5 - single locus (SL, yellow); C6 - WGS only (whole genome shotgun database; orange dark); D7,8 - transposon related tandem repeats (TE, green). X axis - monomer length (unit, bp) up to 2 kb; Y axis - GC content in % normalized to 1; Z axis - % of homology between monomers, of which arrays built.
B - In situ FISH with TRPC-21A long probe (1) and short probe (2) with signal mapped on karyotype (3). Metaphase spreads from bone marrow are used. Chromosome numbers are indicated. DAPI is blue, FISH signal is green. Bar - 5 μm. On (3) chromosomes, which bear signal according to in silico prediction are marked; karyotype assembled from metaphase plate shown on (2). TRPC-21A is shown in orange light on Fig. 1, A.

2. Satellite DNA (satDNA) transcription is under investigation. Our results demonstrate the involvement of satDNA in associations between human chromosomes and intermingling of chromosome territories. The invading satDNA can undergo decondensation to a certain level. This process is accompanied by demethylation and transcription. We found that pericentromeric satellites entered chromocenters only some days after induction of E-14 and IOUD2 mouse embryonic stem cells. The redistribution was accompanied by association with HP1a and transcription from pericentromeric (but not centromeric) satDNA. RNA was polyadenylated and transcribed from the forward chain. Probes made from the cDNA hybridized to all chromosomes. In differentiating cells, the transcript was found exclusively in chromocenters while in differentiated cultured L929 cells it formed 1-2 large clusters outside chromocenters. Using ChIP and immunostaining, we demonstrated that in induced cells pericentromeric DNA interacted with RNA-helicase p68 that was previously shown to be involved in transcription regulation and to be involved in differentiation processes.

3. New protein - mesoglein, is found and its' gene cloned. Body of the scyphoid jellyfish Aurelia aurita consists of 2 epithelia - epidermis and gastroderm. The layers are separated by a thick layer of extracellular matrix - mesoglea. A. aurita has a lot of cells in the mesoglea unlike many other Cnidarians. The major protein of the mesoglea with apparent molecular mass of 47 kDa was detected by SDS-PAGE. A partial mRNA of the protein 1421 bp long was cloned and sequenced. The search for homologous nucleotide and protein sequences shows that the mRNA sequence is novel. Deduced amino acid sequence of 416 aa contains zona pellucida (ZP) domain and Delta/Serrate/Lag-2 (DSL) domain. The protein was named mesoglein. According to reverse transcription PCR mesoglein is expressed in the mature medusa exclusively in the mesogleal cells. Mesoglein belongs to the lowest phyla among ZP domain-containing proteins. The protein is a structural element of the mesoglea extracellular matrix and the component of the new structure - contact plate of the A.aurita oocyte.

Fig. 2. A - Oocytes at successive stages of maturation (I-VII) were immunostained (serum dilution 1:2000). Immunofluorescence with antibodies against mesoglein (bottom row, red) and DAPI (bottom row, blue) combined with phase contrast (upper row) demonstrate that the material in the forming contact plate contains the antigenic determinants same as mesoglein. Arrows on both rows indicates precursor granules of the contact plate. Bar - 10 μm.
B - Diagrammatic reconstruction of A. aurita oocyte maturation. Adapted from Eckelbarger and Larson, 1988. Stages of oogenesis are indicated by numbers I-VII (in Roman according to Adonin et al., 2009) and in Arabic (according to the Eckelbarger and Larson, 1988): (1) Oocyte begins moving into mesoglea from germinal epithelium; (2) endodermal cells in germinal epithelium begin differentiating into trophocytes, and oocyte begins forming parallel arrays of membranes resembling smooth endoplasmic reticulum; (3) oocyte completes movement into mesoglea but retains association with trophocytes, the germinal vesicle migrates closer to the trophocytes and yolk synthesis begins; (4) oocyte involved in synthesis of yolk through activity of Golgi complex and uptake of precursors through endocytosis; (5) late-stage vitellogenic oocyte containing large quantity of yolk. Granules and the contact plate are added to the scheme. The sea flow, i.e. the direction of spermatozoids to come is marked by an arrow and it is obvious that the contact plate is exposed in this direction.


Komissarov AS, Gavrilova EV, Demin S.Ju, Ishov A.M., Podgornaya OI. 2011. The tandemly repeated DNA families in the mouse genome. BMC Genomics (Submitted).

Matveev I.V., Adonin L.S., Shaposhnikova T.G. Podgornaya O.I. 2011. Aurelia aurita – Cnidarian with a prominent medusiod stage. J Exp Zool B Mol Dev Evol. (Submitted).

Komissarov A, Kuznetsova I, Podgornaya O. 2010. Mouse Centromeric Tandem Repeats in silico and in situ. Russian Journal of Genetics, 46 (9) : 1080-1083.

Adonin L., Podgornaya O., Matveev I., Shaposhnikova T. 2009. Plate in the zone of oocyte and germinal epithelium contact in scyphomedusa Aurelia aurita binds antibodies to ZP-domain protein mesoglein. Cell and Tissue Biology. 3 (3) : 283-288.

Kukalev A.S., Lobov I.B, Percipalle P., Podgornaya O.I. 2009. SAF-A/hnRNP-U localization in interphase and metaphase. Cytogenet Genome Res. 124 : 288-297.

Enukashvily N. I., Malashicheva A. B., Waisertreiger I. S-R. 2009. Satellite DNA spatial localisation and transcriptional activity in mouse embryonic E-14 and IOUD2 stem cells. Cytogenet Genome Res. 124 : 277-287.

Enukashvily N. I., Donev R., Waisertreiger I. S., Podgornaya O. I. 2007. Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells. Cytogenet Genome Res. 118 (1) : 42-54.

Matveev I.V., Shaposhnikova T.G, Podgornaya O.I. 2007. A novel Aurelia aurita protein mesoglein contains DSL and ZP domains. Gene. 399 : 20-25.

Kuznetsova I, Podgornaya O, Ferguson-Smith M.A. 2006. High-resolution organization of mouse centromeric and pericentromeric DNA. Cytogenet Genome Res. 112 : 248-255.

Kuznetsova I.S, Voronin A.P, Podgornaya O.I. 2006. Telomere and TRF2/MTBP localization in respect to satellite DNA during cell cycle of the mouse cell line. Rejuvenation Research. 9 (3) : 391-401.

Shaposhnikova T., Matveev I, Napara T, Podgornaya O. 2005. Mesogleal cells of the jellyfish Aurelia aurita produce the fibres of the mesoglea. Cell Biol Internat. 29 : 952-958.

Kuznetsova I.S., Prusov A.N., Enukashvily N.I., Podgornaya O.I. 2005. New types of mouse centromeric satellite DNAs. Chrom Res. 12 : 9-25.

Enukashvily N., Donev R., Sheer D., Podgornaya O. 2005. Satellite DNA binding and cellular localisation of RNA helicase p68. J Cell Sci. 118 : 611-622.

Podgornaya O.I., Voronin A.P., Enukashvily N.I., Matveev I.V., Lobov I.B. 2003. Structure-specific DNA-binding proteins as the foundation for 3-dimensional chromatin organization. Int Rev Cytol. 224 : 227-296.

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