Alla Krasikova

Personal information

Education & Qualifications

Current Position

Recent Honours

2008 - the Award for the best oral talk on the 18th European Colloquium on Animal Cytogenetics and Gene Mapping (Bucharest, Romany)
2009-2010 - Research Grant from the President of Russia for young scientists No.1.11.328.2009
2010 - the Award from the Saint-Petersburg Government for the scientific and educational achievements (Diploma No. 10027)
2011 - National L'Oreal-UNESCO fellowship within the programme "For Women in Science"
2014-2015 - Research Grant from the President of Russia for young scientists No.1.11.337.2014
2015 - Leonhard Euler Prize for outstanding scientific achievements in the field of Science and Technology from the Government of St. - Petersburg and St. - Petersburg Scientific Center RAS
2016 - Saint-Petersburg State University Award "Young scientists' contribution to science" for the scientific publications on the genome architecture and functional compartmentalization of oocyte and somatic cell nucleus

Current research interests

Our current research is focusing on the investigation of functional compartmentalization and 3D-architecture of the oocyte nucleus (germinal vesicle). Nowadays, the role of intranuclear actin in the regulation of transcription and spatial genome organization in amphibian and avian growing oocytes has been studied in details. Molecular composition and 3-dimentional organization of meiotic chromosomes and intranuclear domains, such as amplified nucleoli and Cajal bodies, have been investigated by using of microinjections of fluorescently labeled molecules, modern techniques of confocal laser scanning microscopy and computational image-processing procedures, such as iso-surfacing and building the 3D-reconstructions. We also pay a special attention to establishment a link between the formation of various intranuclear domains and the expression of long non-coding RNA molecules. Giant lampbrush chromosomes from growing oocytes are been using as an adequate tool for exploration of genome expression. Fate and functions of non-coding RNA transcripts accumulating during the lampbrush stage of oogenesis are also under our investigation.

3D reconstruction of the giant nucleus isolated from growing oocyte of domestic chicken (Gallus gallus domesticus), scanned by using of confocal fluorescent microscope Leica TCS SP5 (Alla Krasikova, Antonina Maslova).

Other Qualifications

2005 - Practical Course on DNA-Microarrays Application in Comparative Cytogenetics, Leiden, Netherlands
2012 - "ENGAGE/GEUVADIS RNA-seq Workshop", European Bioinformatics Institute, Cambridge, UK
2013 - "Laboratory Management Course for Group Leaders", European Molecular Biology Organization, Heidelberg, Germany
2013 - "Fifth International Course on Fluorescence in situ Hybridization (FISH+array-CGH+microdissection)", University of Yena, Germany
2014 - "Writing in the Sciences", Stanford University Online Courses
2019-2020 - "Blackboard Learn Basics for teachers", Saint-Petersburg State University Online Courses
2020 - "Digital teacher. Practices and tools for organizing effective distance learning", Academy of National Economy and Public Administration, Online Course

Interships

Teaching activity

Author's lecture course "Genome architecture and nuclear compartmentalization"

Lectures within the course "Presentation of scientific data and the art of preparing an application for a grant"

Author's lecture course "Functions of non-coding RNA"

Students and trainees: Elena Vasilevskaya, Tatiana Khodyuchenko, Antonina Maslova, Dmitrij Dedukh, Darya Popova

Practical course "Structural and molecular analysis of biological systems"

Current Research Grants

2009-2011 Federal Grant-in-Aid Program "Human Capital for Science and Education in Innovative Russia" (Governmental Contract No. P1299);
2010-2012 Federal Grant-in-Aid Program "Human Capital for Science and Education in Innovative Russia" (Governmental Contract No. P1367);
2011-2013 Federal Grant-in-Aid Program "Human Capital for Science and Education in Innovative Russia" (Grant # 8122);
2011-2013 Research Grant from the Saint-Petersburg University No. 1.38.66.2011;
2013-2015 Research Grant from the Saint-Petersburg University for leading scientists;
2014-2015 Research Grant from the President of Russia for young scientists No.1.11.337.2014;
2014-2016 Research Grant from the Russian Science Foundation (# 14-14-00131);
2015-2016 Research Grant from the Russian Foundation for Basic Research (# 15-34-2102)
2019 Publishing Grant from the Russian Foundation for Basic Research (# 978-5-288-05984-1)
2019-2022 Research Grant from the Russian Science Foundation (# 19-74-20075)

Other activities

2011 - 2017 Member of the Scientific Board of the Biological Faculty (St Petersburg State University) (http://www.bio.spbu.ru/science/sciencecom.php);
2014 - 2022 Member of the Editorial Board of the "Biological Communications" Journal (https://biocomm.spbu.ru/);
2013 - 2017 Chair of the Council of Young Scientists of Saint-Petersburg State University (http://english.spbu.ru/science-4/sovetmu);
2015 - 2017 Member of the youth section of the Council for Science under the Ministry of Education and Science of the Russian Federation;
2015 - up to now Member of the European Cytogeneticists Association (http://www.e-c-a.eu/en/)
2017 - 2022 Deputy Editor-in-Chief of the "Biological Communications" Journal (https://biocomm.spbu.ru/);
2021 - up to now Associate Editor in Genome Organization and Dynamics (specialty section of Frontiers in Molecular Biosciences)

Major Publications

1. A. Krasikova, T. Kulikova, M. Schelkunov, N. Makarova, A. Fedotova, V. Plotnikov, V. Berngardt, A. Maslova, A. Fedorov.
   The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic Acids Research (2024). DOI:10.1093/nar/gkae941
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2. Dedukh D., Maslova A., Al-Rikabi A., Padutsch N., Liehr T., Krasikova A.
   Karyotypes of water frogs from the Pelophylax esculentus complex: results of cross-species chromosomal painting. Chromosoma (2023). DOI:10.1007/s00412-023-00812-8
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3. Krasikova, A., Kulikova, T., Rodriguez Ramos, J.S., Maslova, A.
   Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes.
   Epigenetics & Chromatin 16, 24 (2023). DOI: 10.1186/s13072-023-00499-2.
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4. Krasikova, A., Fishman V., Kulikova T.
   Lampbrush chromosome studies in the post-genomic era.
   Bioessays: News and Reviews in Molecular, Cellular and Developmental Biology. (2023) DOI:10.1002/bies.202200250
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5. Maslova A., Plotnikov V., Nuriddinov M. Gridina M., Fishman V.,Krasikova, A.
   Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line.
   BMC Genomics. (2023) DOI:10.1186/s12864-023-09158-y
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6. Nurislamov, A.; Lagunov, T.; Gridina, M.; Krasikova, A.; Fishman, V.
   Single-cell DNA methylation analysis of chicken lampbrush chromosomes.
   International Journal of Molecular Sciences. (2022) DOI:10.3390/ijms232012601
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7. Gridina M., Taskina A., Lagunov T., Nurislamov A., Kulikova T., Krasikova A., Fishman V.
   Comparison and critical assessment of single-cell Hi-C protocols.
   Heliyon. (2022) DOI:10.1016/j.heliyon.2022.e11023
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8. Kulikova T., Maslova A., Starshova P., Rodriguez Ramos J.S., Krasikova A.
   Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes.
   Chromosoma. (2022) DOI:10.1007/s00412-022-00780-5.
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9. Kulikova, T., Krasikova, A.
   RNA-FISH on Lampbrush Chromosomes: Visualization of Individual Transcription Units
   In: Cytogenetics and Molecular Cytogenetics, T. Liehr (Editor), CRC Press, Boca Raton, 2022, ISBN: 978-1003223658, (pp. 307-317).
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10. Dedukh D., Riumin S., Kolenda K., Chmielewska M., Rozenblut-Koscisty B., Kazmierczak M., Ogielska M., Krasikova A.
    Maintenance of pure hybridogenetic water frog populations: Genotypic variability in progeny of diploid and triploid parents.
    PLOS ONE 17(7):e0268574 (2022) DOI:10.1371/journal.pone.0268574.
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11. A. Maslova, Krasikova A.
    FISH going meso-scale: a microscopic search for chromatin domains.
    Frontiers in Cell and Developmental Biology.9:753097 (2021) DOI: 10.3389/fcell.2021.753097
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12. Dedukh D., Krasikova A.
    Delete and survive: strategies of programmed genetic material elimination in eukaryotes.
    Biological Reviews. 2021 DOI:10.1111/brv.12796
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13. Dedukh D, Riumin S, Chmielewska M, Rozenblut-Koscisty B, Kolenda K, Kazmierczak M, Dudzik A, Ogielska M, Krasikova A.
    Micronuclei in germ cells of hybrid frogs from Pelophylax esculentus complex contain gradually eliminated chromosomes.
    Scientific Reports. 10, 8720 (2020) DOI: 10.1038/s41598-020-64977-3
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14. Zlotina A., Maslova A., Pavlova O., Kosyakova N., Al-Rikabi A.,Liehr T., Krasikova A.
    Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing.
    Frontiers in Genetics. 11:57 (2020) DOI: 10.3389/fgene.2020.00057
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15. Kulikova T, Surkova A, Zlotina A, Krasikova A.
    Mapping epigenetic modifications on chicken lampbrush chromosomes.
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16. Krasikova A.V. Kulikova T.V.
    Lampbrush chromosomes: current concepts and research perspectives.
    St Petersburg University Publishing House, 2019. 104 p. ISBN 978-5-288-05984-1 [In Russian].
    Read more
17. Dedukh D., Litvinchuk J., Svinin A., Litvinchuk S., Rosanov J.and Krasikova A.
    Variation in hybridogenetic hybrid emergence between populations of water frogs from the Pelophylax esculentus complex.
    PloS One. 14(11) (2019) DOI: 10.1371/journal.pone.0224759
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18. Krasikova A, Kulikova T.
    Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes.
    Noncoding RNA. 6(1):1 (2019) DOI: 10.3390/ncrna6010001
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19. Fishman, V., Battulin, N., Nuriddinov, M., Maslova, A., Zlotina, A., Strunov, A., Chervyakova, D., Korablev, A., Serov, O., Krasikova, A.
    3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin.
    Nucleic Acids Research. DOI: 10.1093/nar/gky1103 (2018)
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20. Chmielewska, M., Dedukh, D., Haczkiewicz, K., Rozenblut-Kościsty, B., Kaźmierczak, M., Kolenda, K., Serwa, E., Pietras-Lebioda, A., Krasikova, A., Ogielska, M.
    The programmed DNA elimination and formation of micronuclei in germ line cells of the natural hybridogenetic water frog Pelophylax esculentus.
    Scientific Reports, 8 (1) 7870 (2018)
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21. Zlotina A., Dedukh D., Krasikova A.
    Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies.
    Genes (2017). V.8(11). doi: 10.3390/genes8110311
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22. D. Dedukh, S. Litvinchuk, J. Rosanov, D. Shabanov, A. Krasikova
    Mutual maintenance of di- and triploid Pelophylax esculentus hybrids in R-E systems: results from artificial crossings experiments.
    BMC Evolutionary Biology 17:220 (2017).
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23. A. V. Krasikova, T. V. Kulikova
    Distribution of heterochromatin markers in lampbrush chromosomes in birds.
    Russian Journal of Genetics 53(9): 1022–1029 (2017)
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24. Dedukh, D.V., Krasikova, A.V.
    Methodological approaches for studying the european water frog Pelophylax esculentus complex.
    Russ J Genet (2017) 53: 843.
    
25. Kulikova T., Khodychenko T., Petrov Y., Krasikova A.
    Low-voltage scanning electron microscopy study of lampbrush chromosomes and nuclear bodies in avian and amphibian oocytes.
    Scientific Reports - 2016.- V.6 (36878). - doi: 10.1038/srep36878
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26. I. Trofimova, A. Krasikova.
    Transcription of highly repetitive tandemly organized DNA in amphibians and birds: a historical overview and modern concepts.
    RNA Biology, 2016. DOI: 10.1080/15476286.2016.1240142
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27. A.Zlotina, A. Krasikova.
    FISH in Lampbrush Chromosomes.
    In: Fluorescence in situ Hybridization (FISH)-Application Guide, T Liehr (Editor), 2nd Ed., Springer, Berlin, 2017, ISBN: 978-3662529577, pp. 445-458.
    
28. Krasikova A., Kulikova T.
    Atomic Force Microscopy of the avian and amphibian lampbrush chromosome.
    The Russian Journal of Ornithology. - 2016. - V. 25 (1338) - P. 3457-3463.
    Free full text [In Russian]
29. Krasikova A., Kulikova T., Zlotina A.
    Lampbrush chromosomes as a model for exploration into loci of nuclear domains formation.
    Cell and Tissue Biology. - 2016. - V. 58 (4) - P. 277-280.
    
30. Zlotina A., Kulikova T., Kosyakova N., Liehr T., Krasikova A.
    Microdissection of lampbrush chromosomes as an approach for generation of locus-specific FISH-probes and samples for high-throughput sequencing.
    BMC Genomics. 2016. 17:126
    DOI: 10.1186/s12864-016-2437-4
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31. Kulikova T., Chervyakova D., Zlotina A., Krasikova A., Gaginskaya E.
    Giant poly (A)-rich RNP aggregates form at terminal regions of avian lampbrush chromosomes.
    Chromosoma. 2015. 1-16
    DOI:10.1007/s00412-015-0563-4
    
32. Trofimova I., Chervyakova D., Krasikova A.
    Transcription of subtelomere tandemly repetitive DNA in chicken embryogenesis.
    Chromosome Research. 2015.
    DOI: 10.1007/s10577-015-9487-3.
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33. Maslova A., Zlotina A., Kosyakova N., Sidorova M., Krasikova A.
    Three-dimensional architecture of tandem repeats in chicken interphase nucleus.
    Chromosome Research. 2015.
    DOI: 10.1007/s10577-015-9485-5.
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34. Krasikova A., Fedorov A.
    Expression Profiles of Long and Short RNAs in the Cytoplasm and Nuclei of Growing Chicken (Gallus gallus domesticus) Oocytes.
    Russian Journal of Genetics. Applied Research - 2015. - V. 6(3) - P. 307-313.
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35. Dedukh D., Litvinchuk S., Rosanov J., Mazepa G., Saifitdinova A., Shabanov D., Krasikova A.
    Optional Endoreplication and Selective Elimination of Parental Genomes during Oogenesis in Diploid and Triploid Hybrid European Water Frogs.
    PLoS ONE. 2015. V. 10(4).
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36. Trofimova I., Popova D., Vasilevskaya E., Krasikova A.
    Non-coding RNA derived from a conservative subtelomeric tandem repeat in chicken and Japanese quail somatic cells.
    Molecular Cytogenetics. 2014. V. 7:102. P. 1-13
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37. Khodyuchenko T., Krasikova A.
    Cajal bodies and histone locus bodies: Molecular composition and function.
    Russian Journal of Developmental Biology. 2014. V. 45:6. P. 297 312
    Abstract
38. Dedukh D., Mazepa G., Shabanov D., Rosanov J., Litvinchuk S., Borkin L., Saifitdinova A., Krasikova A.
    Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine.
    BMC Genetics. 2013. V. 14. 26
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39. Maslova A., Krasikova A.
    Nuclear actin depolymerization in transcriptionally active avian and amphibian oocytes leads to collapse of intranuclear structures.
    Nucleus. 2012. V. 3(3). P. 300-311
    Abstract Free full text
40. Zlotina A., Galkina S., Krasikova A., Crooijmans R.P., Groenen M.A., Gaginskaya E., Deryusheva S.
    Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions.
    Chromosome Res. 2012. V. 20 (8). P. 1017-1032. DOI: 10.1007/s10577-012-9319-7
    Abstract Free full text
41. Krasikova A., Fukagawa T., Zlotina A.
    High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes.
    Chromosome Res. 2012. V. 20 (8). P. 995-1008. DOI: 10.1007/s10577-012-9321-0
    Abstract Free full text
42. Krasikova A., Khodyuchenko T., Maslova A., Vasilevskaya E.
    Three-dimensional organisation of RNA-processing machinery in avian growing oocyte nucleus.
    Chromosome Res. 2012. V. 20 (8). P. 979-994. DOI: 10.1007/s10577-012-9321-0
    Abstract Free full text
43. Khodyuchenko T., Gaginskaya E., Krasikova A.
    Non-canonical Cajal bodies form in the nucleus of late stage avian oocytes lacking functional nucleolus.
    Histochem Cell Biol. 2012. V 138(1), P. 57-73
    Abstract
44. Maslova A., Krasikova A.
    Spatial Arrangement of Macro-, Midi-, and Microchromosomes in Transcriptionally Active Nuclei of Growing Oocytes in Birds of Order Galliformes.
    Cell and Tissue Biology. 2011. V. 5. N. 3. P. 281-293.
    Abstract
45. Krasikova A., Vasilevskaya E., Gaginskaya E.
    Chicken Lampbrush Chromosomes: Transcription of Tandemly Repetitive DNA Sequences.
    Russian Journal of Genetics. 2010. V. 46(10). P. 1173-1177.
    Abstract
46. Daks A., Deryusheva S., Krasikova A., Zlotina A., Gaginskaya E., Galkina S.
    Lampbrush Chromosomes of the Japanese Quail (Coturnix coturnix japonica): A New Version of Cytogenetic Maps.
    Russian Journal of Genetics. 2010. V. 46(10). P. 1178-1181.
    Abstract
47. Krasikova A., Gaginskaya E.
    Organisation of centromere regions of chromosomes in the lampbrush phase.
    Tsitologiia. 2010. V. 52(7). P. 515-33.
    Abstract
48. Zlotina A., Galkina S., Krasikova A., Crooijmans R.P., Groenen M.A., Gaginskaya E., Deryusheva S.
    Precise centromere positioning on chicken chromosome 3.
    Cytogenet Genome Res. 2010. V. 129(4). P.310-313.
    Abstract
49. Krasikova A., Daks A., Zlotina A., Gaginskaya E.
    Polymorphic heterochromatic segments in Japanese quail microchromosomes.
    Cytogenetics and Genome Research. 2009. V. 126. P.148-155
    Abstract
50. Gaginskaya E., Kulikova T., Krasikova A.
    Avian Lampbrush Chromosomes: a Powerful Tool for Exploration of Genome Expression.
    Cytogenet Genome Res. 2009. V.124. P.251-267.
    Abstract
51. Deryusheva S., Krasikova A., Kulikova T., Gaginskaya E.
    Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes.
    Chromosoma. 2007. V. 116 P.519-530.
    Abstract
52. Krasikova A., Deryusheva S., Galkina S., Kurganova A., Evteev A., Gaginskaya E.
    On the positions of centromeres in chicken lampbrush chromosomes.
    Chromosome Res. 2006 V. 14 P.777-789.
    Abstract
53. Krasikova A., Barbero J.L., Gaginskaya E.
    Cohesion proteins are present in centromere protein bodies associated with avian lampbrush chromosomes.
    Chromosome Res. 2005. V.13. P.675-685.
    Abstract
54. Krasikova A., Kulikova T., Saifitdinova A., Derjusheva S., Gaginskaya E.
    Centromeric protein bodies on avian lampbrush chromosomes contain a protein detectable with an antibody against DNA topoisomerase II.
    Chromosoma. 2004. V. 116. P. 316 323.
    Abstract
55. Derjusheva S., Kurganova A., Krasikova A., Saifitdinova A., Habermann F.A., Gaginskaya E.
    Precize identification of chicken chromosomes in the lampbrush form using chromosome painting probes.
    Chromosome research. 2003. V. 11. P. 749 757.
    Abstract
56. Saifitdinova A., Derjusheva S., Krasikova A., Gaginskaya E.
    Lampbrush chromosomes of the chaffinch ( Fringilla coelebs L.).
    Chromosome research. 2003. V. 11. P. 99-113.
    Abstract