Laboratory of Eukaryotic Genomic Repeats | Institute of Molecular Genetics

Kalmykova Alla Ivanovna


List of staff

Kalmykova Alla I., PhD, Dr. Sci.;
Sokolova Olesya A., PhD, scientist;
Kordyukova Mariya Yu., junior scientist;
Radion Elizaveta I., PhD, junior scientist;
Morgunova Valeriya V., junior scientist;
Solovyova Anastasiya Y., graduate student;
Gonchar Atastasiya D., graduate student.


Main directions of research

Our research is focused on fundamental problems in genomics of higher eukaryotes, such as the study of the structure, evolution and functioning of heterochromatic sequences and the role of small RNAs in regulating the activity of transposable elements in Drosophila. We explore various aspects of the piRNA (PIWI interacting RNA) pathway in the Drosophila germline and early embryogenesis, including the role of small RNAs in maternal epigenetic silencing mechanism. Another topic of our research is the study of the structure of telomeric complex in germ line tissues and early development, as well as the role of piRNAs in telomere biology.

Main scientific results

Since 2005, when the Group of Eukaryotic Genomic Repeats was established, the following main results were obtained:
2005-2007. The role of the piRNA silencing in the control of telomere length in Drosophila (Savitsky et al. 2006; Shpiz et al. 2007)
2008-2011. Regulation of expression of telomeric retrotransposons in Drosophila. Divergent promoter of telomeric retroelement HeT-A was described. It was shown that small RNAs inhibit expression of telomeric and other retrotransposons on transcriptional level (Shpiz et al 2009; Shpiz et al. 2011; Radion et al. 2017).
2010-2018. The relationship between the efficiency of primary piRNA production and variable response to transposon invasions in natural populations was established (Ryazansky et al. 2017).
2011-2018. The phenomenon of the formation of de novo piRNA clusters associated with transgenic constructs and the endogenous copies of transposable elements in euchromatin was described (Olovnikov et al 2013; Shpiz et al. 2014). Prerequisites of de novo formation of transgenic piRNA clusters are studied (Akulenko et al. 2018).
2012-2018. Studying of the genetic control of telomere dysfunction in early development of Drosophila (Morgunova et al 2015). Purification and analysis of the telomeric protein complex in the ovaries and embryos of Drosophila. Subcellular localization of telomeric retrotransposon HeT-A ribonucleoprotein particles in the Drosophila germline and early embryogenesis (Olovnikov et al.2016).
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  1. M. Savitsky, D. Kwon, P. Georgiev, A. Kalmykova, V. Gvozdev Telomere elongation is under the control of the RNAi-based mechanism in the Drosophila germline. Genes Dev. 20: 345-354, 2006.
  2. S. Shpiz , D. Kwon, A. Uneva, M. Kim, M. Klenov, Y. Rozovsky, P.. Georgiev , M. Savitsky , A. Kalmykova Characterization of Drosophila telomeric retroelement TAHRE: transcription, transpositions and RNAi-based regulation of expression.. Mol. Biol. Evol. 24:2535-45, 2007.
  3. S. Shpiz , D. Kwon, Y. Rozovsky, A. Kalmykova rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus  Nucl. Acids Res. 37: 268-278, 2009.
  4. Shpiz S, Olovnikov I, Sergeeva A, Lavrov S, Abramov Y, Savitsky M, Kalmykova A. Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons. Nucleic Acids Res. 39: 8703-8711, 2011.
  5. Olovnikov I, Ryazansky S, Shpiz S, Lavrov S, Abramov Y, Vaury C, Jensen S, Kalmykova A. De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment.ucleic Acids Res. 2013  41: 5757-68, 2013.
  6. S. Shpiz, S. Ryazansky, I. Olovnikov, Y. Abramov, A Kalmykova. Euchromatic transposon insertions trigger production of novel pi- and endo-siRNAs at the target sites in the Drosophila germline, PLOS Genetics, 10:e1004138, 2014.
  7.  Morgunova V, Akulenko N, Radion E, Olovnikov I, Abramov Y, Olenina LV, Shpiz S, Kopytova DV, Georgieva SG, Kalmykova A. Telomeric repeat silencing in germ cells is essential for early development in Drosophila. Nucleic Acids Res. 43: 8762–8773б, 2015.
  8.  Olovnikov IA, Morgunova VV, Mironova AA, Kordyukova MY, Radion EI, Olenkina OM, Akulenko NV, Kalmykova AI. Interaction of Telomeric Retroelement HeT-A Transcripts and Their Protein Product Gag in Early Embryogenesis of Drosophila. Biochemistry (Mosc). 2016 81:1023-30.
  9. E. Radion, S. Ryazansky, N. Akulenko, Y. Rozovsky, D. Kwon, V. Morgunova, I. Olovnikov, A. Kalmykova Telomeric retrotransposon HeT-A contains a bidirectional promoter that initiates divergent transcription of piRNA precursors in Drosophila germline. J. of Mol. Biol. 2017, 429, 3280–3289.
  10. S. Ryazansky, E. Radion, A Mironova, N Akulenko, Y. Abramov, V. Morgunova, M. Kordyukova, I. Olovnikov, A. Kalmykova (2017) Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet 13(4): e1006731.  
  11. N. Akulenko, S. Ryazansky, V. Morgunova, P.A. Komarov, I. Olovnikov, C. Vaury, S. Jensen and A. Kalmykova Transcriptional and chromatin changes accompanying de novo formation of transgenic piRNA clusters. RNA, 24: 574-584, 2018. DOI: 10.1261/rna.062851.117.
  12. M. Kordyukova, I. Olovnikov, A. Kalmykova. Transposon control mechanisms in telomere biology. Current Opinion in Genetics & Development, 49:56-62, 2018.