Kalmykova Alla Ivanovna | Institute of Molecular Genetics
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Academic degree:
Doctor of Biological Sciences
Academic title:
without academic rank
Division of IMG:
Laboratory of research of genomic repeats in eukaryotes
Position:
Head of Laboratory
Telephone:
+7-499-196-00-19
Е-mail: |
Main research interests
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.
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. Peculiarities of regulation of expression of telomeric retrotransposons in Drosophila. Antisense 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).
2011-2014. 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). Currently we are studying the structural organization of endogenous and transgene-associated piRNA clusters in Drosophila.
2012-2015. Studying of the genetic control of telomere dysfunction (fused telomeres) in early development of Drosophila (Morgunova et al 2015). Purification and analysis of the telomeric protein complex in the ovaries and embryos of Drosophila.
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. Peculiarities of regulation of expression of telomeric retrotransposons in Drosophila. Antisense 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).
2011-2014. 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). Currently we are studying the structural organization of endogenous and transgene-associated piRNA clusters in Drosophila.
2012-2015. Studying of the genetic control of telomere dysfunction (fused telomeres) in early development of Drosophila (Morgunova et al 2015). Purification and analysis of the telomeric protein complex in the ovaries and embryos of Drosophila.
Teaching activities
Supervisor of PhD students, graduate students
Publications
Main publications (2005-2015):
http://www.ncbi.nlm.nih.gov/pubmed/?term=Kalmykova+A+drosophila
1. Kalmykova A.I., Kwon D.A., Rozovsky Ya.M., Hueber N., Capy P., Maisonhaute C., and Gvozdev V.A. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21: 2281-2289, 2004.
2. Kalmykova A.I., Nurminsky D.I., Ryzhov D.V., Shevelyov Y.Y. Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster Nucl. Acids Res. 33: 1435-1444, 2005.
3. Kalmykova A.I., Klenov M.S., and Gvozdev V.A. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germ line. Nucl. Acids Res. 33: 2052-2059, 2005.
4. 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.
5. Shpiz SG, Kalmykova AI Structure of telomeric chromatin in Drosophila. Biochemistry (Mosc). 72(6):618-30, 2007.
6. 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.
7. 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.
8. S. Shpiz and A. Kalmykova Epigenetic transmission of piRNAs through the female germline Genome Biology 10: 208, 2009.
9. 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.
10. S. Shpiz and A. Kalmykova Control of telomere length in Drosophila, chapter for the book " "Reviews on Selected Topics of Telomere Biology", Bibo Li (Ed.), ISBN: 978-953-51-0849-8, pp. 31-56, InTech, 2012.
11. 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.Nucleic Acids Res. 41: 5757-68, 2013.
12. Olovnikov IA, Kalmykova AI. piRNA clusters as a main source of small RNAs in the animal germline. Biochemistry (Mosc). 78(6):572-84, 2013
13. 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.
14. 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. 2015 Aug 3. pii: gkv775.
http://www.ncbi.nlm.nih.gov/pubmed/?term=Kalmykova+A+drosophila
1. Kalmykova A.I., Kwon D.A., Rozovsky Ya.M., Hueber N., Capy P., Maisonhaute C., and Gvozdev V.A. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21: 2281-2289, 2004.
2. Kalmykova A.I., Nurminsky D.I., Ryzhov D.V., Shevelyov Y.Y. Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster Nucl. Acids Res. 33: 1435-1444, 2005.
3. Kalmykova A.I., Klenov M.S., and Gvozdev V.A. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germ line. Nucl. Acids Res. 33: 2052-2059, 2005.
4. 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.
5. Shpiz SG, Kalmykova AI Structure of telomeric chromatin in Drosophila. Biochemistry (Mosc). 72(6):618-30, 2007.
6. 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.
7. 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.
8. S. Shpiz and A. Kalmykova Epigenetic transmission of piRNAs through the female germline Genome Biology 10: 208, 2009.
9. 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.
10. S. Shpiz and A. Kalmykova Control of telomere length in Drosophila, chapter for the book " "Reviews on Selected Topics of Telomere Biology", Bibo Li (Ed.), ISBN: 978-953-51-0849-8, pp. 31-56, InTech, 2012.
11. 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.Nucleic Acids Res. 41: 5757-68, 2013.
12. Olovnikov IA, Kalmykova AI. piRNA clusters as a main source of small RNAs in the animal germline. Biochemistry (Mosc). 78(6):572-84, 2013
13. 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.
14. 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. 2015 Aug 3. pii: gkv775.