Department of Structure and Function of Chromosomes

Laboratory of Molecular Cytogenetics

Zhimulev Igor
Head of the Department
Head of the Laboratory

Curriculum vitae

Staff: 
thomson_logo.gif scopus_logo.jpg Zhimulev Igor head DSc (Biology) zhimulevatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg   Pokholkova Galina leading research fellow DSc (Biology) galinaatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Kolesnikova Tatiana leading research fellow DSc (Biology) kolesnikovaatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Koryakov Dmitry leading research fellow PhD (Biology) koryakovatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Vatolina Tatiana leading research fellow PhD (Biology) vatolinaatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg   Antonenko Oksana research fellow PhD (Biology) ovantatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Khoroshko Varvara junior research fellow PhD (Biology) vicernaatmcb [dot] nsc [dot] ru
  scopus_logo.jpg   Maltseva Maria research assistant    
      Boryakova Kseniya research assistant    
      Graphodatskaya Victoria lab technician   vikaatmcb [dot] nsc [dot] ru
      Dolbak Evgenia lab technician   eugenyatmcb [dot] nsc [dot] ru
      Marusov Danila research assistant    
      Turtapkina Vera research assistant    
thomson_logo.gif scopus_logo.jpg   Levitsky Victor part-time leading research fellow PhD (Biology)  
thomson_logo.gif scopus_logo.jpg   Tsukanov Anton part-time senior research fellow PhD (Biology)  
  scopus_logo.jpg   Dovgan Victoria part-time research assistant   dovganatmcb [dot] nsc [dot] ru

Former research workers:

Azarov Victoria Maria
Belyaeva Elena, DSc
Gataullin Nikita
Ivanov Roman
Goncharov Fedor
Kolodyazhnaya Aleksandra
Makunin Igor, PhD		 Moshkin Yuri, PhD
Nerusheva (Kokoza) Elena, PhD
Semeshin Valery, DSc
Shmakova Margarita
Shulutkova Alena
Skvortsova Tatiana
Veselova Olga

BDGP_logo.jpg

The staff of the Laboratory are among the contributors of Release 6 reference sequence of the Drosophila melanogaster genome
Recent publications: 

  1. Kolesnikova TD, Veselova OV, Pokholkova GV, Schubert V, Klenov MS. Localization of rDNA-associated retrotransposons refines the heterochromatin map of the X chromosome in Drosophila melanogaster. Cytogenet Genome Res, 2025, doi: 10.1159/000546918

  2. Osadchiy I, Umnova A, Pokholkova GV, Golovnin A, Gvozdev VA, Zhimulev IF, Georgiev P, Maksimenko O. Drosophila architectural proteins M1BP and Opbp cooperatively form the active promoter of a ribosomal protein gene. (doi: 10.1186/s13072-025-00584-8) Epigenetics Chromatin 18: 20, 2025

  3. Evdokimova AA, Kolesnikova TD, Mazina MYu, Krasnov AN, Erokhin M, Chetverina D, Vorobyeva NE. Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation. (doi: 10.1093/nar/gkaf284) Nucleic Acids Res 53(7): gkaf284, 2025

  4. Veryaskina YA, Titov SE, Kovynev IB, Fyodorova SS, Berezina OV, Zhurakovskij IP, Antonenko OV, Demakov SA, Demenkov PS, Ruzankin PS, Tarasenko AS, Pospelova TI, Zhimulev IF. MicroRNAs in diffuse large B-cell lymphoma (DLBCL): biomarkers with prognostic potential. (doi: 10.3390/cancers17081300) Cancers 17(8): 1300, 2025

  5. Levitsky VG, Raditsa VV, Tsukanov AV, Mukhin AM, Zhimulev IF, Merkulova TI. Asymmetry of motif conservation within their homotypic pairs distinguishes DNA-binding domains of target transcription factors in ChIP-seq data. (doi: 10.3390/ijms26010386) Int J Mol Sci 26(1): 386, 2025

  6. Veryaskina YA, Titov SE, Skvortsova NV, Kovynev IB, Antonenko OV, Demakov SA, Demenkov PS, Pospelova TI, Ivanov MK, Zhimulev IF. Multiple myeloma: Genetic and epigenetic biomarkers with clinical potential. (doi: 10.3390/ijms252413404) Int J Mol Sci 25(24): 13404, 2024

  7. Arifulin EA, Sorokin DV, Anoshina NA, Kuznetsova MA, Valyaeva AA, Potashnikova DM, Omelchenko DO, Schubert V, Kolesnikova TD, Sheval EV. Global nuclear reorganization during heterochromatin replication in the giant-genome plant Nigella damascena L. (doi: 10.1111/tpj.17063) Plant J 120(4): 1508-1521, 2024

  8. Titov SE, Kozorezova ES, Lukyanov SA, Sergiyko SV, Demenkov PS, Veryaskina YA, Vorobyev SL, Sleptsov IV, Chernikov RA, Timofeeva NI, Barashkova SV, Lushnikova EL, Uspenskaya AA, Zolotoukho AV, Romanova OV, Zhimulev IF.  Could SLC26A7 be a promising marker for preoperative diagnosis of high-grade papillary thyroid carcinoma? (doi: 10.3390/diagnostics14232652) Diagnostics 14(23): 2652, 2024

  9. Veryaskina YA, Titov SE, Kovynev IB, Pospelova TI, Fyodorova SS, Shebunyaeva YY, Demakov SA, Demenkov PS, Zhimulev IF. MicroRNA: A signature for the clinical progression of chronic lymphocytic leukemia. (doi: 10.3390/lymphatics2030013) Lymphatics 2(3): 157-167, 2024

  10. Andreyenkova NG, Hong S-Y, Lin H-S, Iwami Y, Kirillin RA, Literak I, Zhimulev IF, Karyakin IV. Genetic relationships of populations of the Black Kite Milvus migrans (Accipitriformes: Accipitridae) in the east of its range in Asia and Australia. (doi: 10.11646/zootaxa.5523.1.5) Zootaxa 5523(1): 83-99, 2024

  11. Ye WD, Tan LC, Veryaskina YA, Han PZ, Yu PC, Shi X, Liu WL, Kai ZT, Lin RJ, Huang LS, Semenov A, Zhimulev IF, Ji QH, Qu N, Titov SE, Wang YL. Synchronous papillary and follicular thyroid carcinomas: the first retrospective cohort study and literature review. (doi: 10.21037/tcr-23-1526) Transl Cancer Res 13(4): 1924-1935, 2024

  12. Zhimulev I, Vatolina T, Levitsky V, Tsukanov A. Developmental and housekeeping genes: Two types of genetic organization in the Drosophila genome. (doi: 10.3390/ijms25074068) Int J Mol Sci 25(7): 4068, 2024

  13. Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. (doi: 10.1002/bies.202300163) BioEssays 46(2): 2300163, 2024

  14. Kolesnikova TD, Nokhova AR, Shatskikh AS, Klenov MS, Zhimulev IF. Otu and Rif1 double mutant enables analysis of satellite DNA in polytene chromosomes of ovarian germ cells in Drosophila melanogaster. (doi: 10.1134/S160767292360046X) Dokl Biochem Biophys 513 (Suppl 1): S87-S91, 2023

  15. Romanov SE, Shloma VV, Maksimov DA, Koryakov DE. SetDB1 and Su(var)3-9 are essential for late stages of larval development of Drosophila melanogaster. (doi: 10.1007/s10577-023-09743-7) Chromosome Res 31: 35, 2023

  16. Golovnin A, Melnikova L, Babosha V, Pokholkova GV, Slovohotov I, Umnova A, Maksimenko O, Zhimulev IF, Georgiev P. The N-terminal part of Drosophila CP190 is a platform for interaction with multiple architectural proteins. (doi: 10.3390/ijms242115917) Int J Mol Sci 24(21): 15917, 2023

  17. Zhimulev IF, Vatolina TY, Levitsky VG, Kolesnikova TD, Tsukanov AV. Development of N.K. Koltsov’s idea about genetic organization of interbands in Drosophila melanogaster polytene chromosomes. (doi: 10.1134/S1062360423020066) Russ J Dev Biol 54: 156-159, 2023

  18. Zykova TY, Maltseva MV, Demakov SA, Pokholkova GV, Veryaskina YuA, Lavrik OI, Kolesnikova TD, Zhimulev IF. Conservative protein RCC1 is a new component of black bands of Drosophila melanogaster polytene phromosomes. (doi: 10.1134/S1062360423020078) Russ J Dev Biol 54: 160-163, 2023

  19. Veryaskina YA, Titov SE, Kovynev IB, Pospelova TI, Fyodorova SS, Shebunyaeva YY, Sumenkova DV, Zhimulev IF. MicroRNA expression profile in bone marrow and lymph nodes in B-cell lymphomas. (doi: 10.3390/ijms242015082) Int J Mol Sci 24(20): 15082, 2023

  20. Stupak EV, Veryasikina YA, Titov SE, Askandaryan AS, Hiana JC, Zhimulyov IF, Stupak VV. MicroRNAs in the diagnosis of malignancy of supratentorial brain gliomas and prognosis of disease progression. (doi: 10.7759/cureus.35906) Cureus 15(3): e35906, 2023

  21. Romanov SE, Shloma VV, Koryakov DE, Belyakin SN, Laktionov PP. Insulator protein CP190 regulates expression оf spermatocyte differentiation genes in Drosophila melanogaster male germline. (doi: 10.1134/S0026893323010120) Mol Biol 57(1): 113-126, 2023

  22. Kolesnikova TD, Pokholkova GV, Dovgan VV, Zhimulev IF, Schubert V. Super-resolution microscopy reveals stochastic initiation of replication in Drosophila polytene chromosomes. (doi: 10.1007/s10577-021-09679-w) Chromosome Res 30(4): 361-383, 2022

  23. Kolesnikova TD, Klenov MS, Nokhova AR, Lavrov SA, Pokholkova GV, Schubert V, Maltseva SV, Cook KR, Dixon MJ, Zhimulev IF. A spontaneous inversion of the X chromosome heterochromatin provides a tool for studying the structure and activity of the nucleolus in Drosophila melanogaster. (doi: 10.3390/cells11233872) Cells 11(23): 3872, 2022

  24. Veryaskina YA, Titov SE, Zhimulev IF. Reference genes for qPCR-based miRNA expression profiling in 14 human tissues. (doi: 10.1159/000524283) Med Princ Pract 31: 322-332, 2022

  25. Veryaskina YuA, Titov SE, Ivanov MK, Ruzankin PS, Tarasenko AS, Shevchenko SP, Kovynev IB, Stupak EV, Pospelova TI, Zhimulev IF. Selection of reference genes for quantitative analysis of microRNA expression in three different types of cancer. (doi: 10.1371/journal.pone.0254304) PLoS ONE 17(2): e0254304, 2022

  26. Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. (doi: 10.1093/genetics/iyab147) Genetics 219(3): iyab147, 2021

  27. Andreyenkova NG, Karyakin IV, Starikov IJ, Sauer-Gürth H, Literák I, Andreyenkov OV, Shnayder EP, Bekmansurov RH, Alexeyenko MN, Wink M, Zhimulev IF. Phylogeography and demographic history of the black kite Milvus migrans, a widespread raptor in Eurasia, Australia and Africa.  (doi: 10.1111/jav.02822) J Avian Biol 52(10): e02822, 2021 

  28. Zykova T, Maltseva M, Goncharov F, Boldyreva L, Pokholkova G, Kolesnikova T, Zhimulev I. The organization of pericentromeric heterochromatin in polytene chromosome 3 of the Drosophila melanogaster line with the Rif11; SuURES Su(var)3-906 mutations suppressing underreplication. (doi: 10.3390/cells10112809) Cells 10(11): 2809, 2021

  29. Veryaskina YA, Titov SE, Kovynev IB, Fedorova SS, Pospelova TI, Zhimulev IF. MicroRNAs in the myelodysplastic syndrome. (doi: 10.32607/actanaturae.11209) Acta Naturae 13(2): 4-15, 2021

  30. de Jong TV, Guryev V, Moshkin YM. Estimates of gene ensemble noise highlight critical pathways and predict disease severity in H1N1, COVID-19 and mortality in sepsis patients. (doi: 10.1038/s41598-021-90192-9) Sci Rep 11: 10793, 2021

  31. Sabirov M, Kyrchanova O, Pokholkova GV, Bonchuk A, Klimenko N, Belova E, Zhimulev IF, Maksimenko O, Georgiev P. Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster. (doi: 10.1186/s13072-021-00391-x) Epigenetics Chromatin 14: 16, 2021

  32. Kalashnikova DA, Maksimov DA, Romanov SE, Laktionov PP, Koryakov DE. SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster. (doi: 10.1242/jcs.253096) J Cell Sci 134(2): jcs253096, 2021

  33. Kovynev IB, Titov SE, Ruzankin PS, Agakishiev MM, Veryaskina YA, Nedel’ko VM, Pospelova TI, Zhimulev IF. Profiling 25 bone marrow microRNAs in acute leukemias and secondary nonleukemic hematopoietic conditions. (doi: 10.3390/biomedicines8120607) Biomedicines 8(12): 607, 2020

  34. Levitsky VG, Zykova TYu, Moshkin YuM, Zhimulev IF. Nucleosome positioning around transcription start site correlates with gene expression only for active chromatin state in Drosophila interphase chromosomes. (doi: 10.3390/ijms21239282) Int J Mol Sci 21(23): 9282, 2020

  35. Veryaskina YuA, Titov SE, Kovynev IB, Pospelova TI, Zhimulev IF. The miRNA profile in non-Hodgkin’s lymphoma patients with secondary myelodysplasia. (doi: 10.3390/cells9102318) Cells 9(10): 2318, 2020

  36. Veryaskina YuA, Titov SE, Kovynev IB, Pospelova TI, Zhimulev IF. Prognostic markers of myelodysplastic syndromes. (doi: 10.3390/medicina56080376) Medicina 56(8): 376, 2020

  37. Kolesnikova TD, Kolodyazhnaya AV, Pokholkova GV, Schubert V, Dovgan VV, Romanenko SA, Prokopov DYu, Zhimulev IF. Effects of mutations in the Drosophila melanogaster Rif1 gene on the replication and underreplication of pericentromeric heterochromatin in salivary gland polytene chromosomes. (doi: 10.3390/cells9061501) Cells 9(6): 1501, 2020 

  38. Veryaskina YuA, Titov SE, Kometova VV, Rodionov VV, Zhimulev IF. Intratumoral heterogeneity of expression of 16 miRNA in luminal cancer of the mammary gland. (doi: 10.3390/ncrna6020016) Non-Coding RNA 6(2): 16, 2020

  39. Khoroshko VA, Pokholkova GV, Levitsky VG, Zykova TY, Antonenko OV, Belyaeva ES, Zhimulev IF. Genes containing long introns occupy series of bands and interbands in Drosophila melanogaster polytene chromosomes. (doi: 10.3390/genes11040417) Genes 11(4): 417, 2020

  40. Demakova OV, Demakov SA, Boldyreva LV, Zykova TYu, Levitsky VG, Semeshin VF, Pokholkova GV, Sidorenko DS, Goncharov FP, Belyaeva ES, Zhimulev IF. Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. (doi: 10.1007/s00412-019-00728-2) Chromosoma 129(1): 25-44, 2020

Publications for previous years

Selected talks: 

  1. Kolesnikova T. Otu and Rif1 double mutant enables analysis of satellite DNA and piRNA clusters  in polytene chromosomes of ovarian germ cells in Drosophila melanogaster. 15th International Conference on Drosophila Heterochromatin, 9-15 June 2024, Gubbio, Italy

  2. Zhimulev I. Developmental and housekeeping genes: two types of genetic organization in the Drosophila genome. 15th International Conference on Drosophila Heterochromatin, 9-15 June 2024, Gubbio, Italy

  3. Kolesnikova T. The organization of replication in Drosophila polytene chromosomes. 14th International conference on Drosophila heterochromatin, 9-15 June 2019, Spoleto, Italy

  4. Kolesnikova T. Ultrastructural investigation of early replication in Drosophila polytene chromosomes. 26th Wilhelm Bernhard Workshop, 20-23 May 2019, Dijon, France

  5. Zhimulev IF. Polytene chromosomes – a portrait of functional organization of the Drosophila genome. International Conference “Chromosome – 2018”, 20-24 August 2018, Novosibirsk, Russia

  6. Kolesnikova TD. Spatial-temporal organization of replication in polytene chromosomes of Drosophila. International Conference “Chromosome – 2018”, 20-24 August 2018, Novosibirsk, Russia

  7. Koryakov DE. Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster. International Conference “Chromosome – 2018”, 20-24 August 2018, Novosibirsk, Russia

  8. Kolesnikova T. Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. 25th Wilhelm Bernhard Workshop on the Cell Nucleus, June 19-22, 2017, Nizhny Novgorod, Russia

  9. Kolesnikova T. Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. 13th International conference on Drosophila heterochromatin, June 4-10, 2017, Cagliari, Italy

  10. Khoroshko V. Gene location in intercalary chromatin bands in polytene chromosomes of Drosophila melanogaster. 13th International conference on Drosophila heterochromatin, June 4-10, 2017, Cagliari, Italy

  11. Kolesnikova TD. Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. International mini-conference "Chromosomes and Mitosis – 2016", November 25, 2016, Novosibirsk, Russia

  12. Kolesnikova T. Chromatin states and replication patterns in polytene chromosomes of Drosophila melanogaster. Twelfth International Conference on Drosophila Heterochromatin, May 24-30, 2015, Palermo, Italy

  13. Kolesnikova TD. Chromatin states and replication patterns in polytene chromosomes of Drosophila melanogaster. BIT's 5th Annual World Congress of Molecular & Cell Biology-2015, April 25-28, 2015, Nanjing, China

  14. Zhimulev IF. Molecular and genetic organization of banding pattern in Drosophila melanogaster chromosomes. 11th International Conference on Drosophila Heterochromatin, 23-29 June, 2013, Lecce, Italy

  15. Zhimulev IF. Chromosomal organization of Drosophila melanogaster genome. 52nd Annual Drosophila Research Conference, 30 March-3 April 2011, San Diego, USA

  16. Zhimulev IF. Chromosomal organization of genome: intercalary heterochromatin as a marker for determination
    of bands and interbands in polytene chromosomes of Drosophila melanogaster. 10th International Conference
    on Drosophila Heterochromatin, 12-18 June 2011, Gubbio, Italy

  17. Kolesnikova TD. SUUR protein physically interacts with replication machinery in Drosophila melanogaster.
    10th International Conference on Drosophila Heterochromatin, 12-18 June 2011, Gubbio, Italy

  18. Kolesnikova TD. The SUUR protein does not affect the replication fork rate in the Drosophila melanogaster salivary gland polytene chromosomes. 9th International Conference on Drosophila Heterochromatin, 23-30 May 2009, Gubbio, Italy

  19. Zhimulev IF. Ultrastructural analysis of “swellings” arising in heterochromatin regions of D. melanogaster polytene chromosomes under condition of ectopic expression of the SuUR gene. 9th International Conference on Drosophila Heterochromatin, 23-30 May 2009, Gubbio, Italy

  20. Zhimulev IF. Interaction between SUUR and HP1 determines late replication timing of intercalary heterochromatin in Drosophila. The 16th International Workshop on the molecular and developmental biology of Drosophila,22-28 June 2008, Kolymbari, Greece

  21. Zhimulev IF. Molecular-cytogenetic organization of the intercalary heterochromatin 75C1-2 band of D. melanogaster. 8th International Conference on Drosophila Heterochromatin, 3-9 June 2007, Gubbio, Italy

  22. Kolesnikova TD. High resolution analysis of heterochromatin organization using SuUR Su(var)3-9 double mutants in Drosophila melanogaster. 8th International Conference on Drosophila Heterochromatin, 3-9 June 2007, Gubbio, Italy

  23. Koryakov DE. The SUUR protein takes part in histone methylation and binding of SU(VAR)3-9 in polytene chromosomes of Drosophila melanogaster. 20th European Drosophila Research Conference, 12-14 September 2007, Vienna, Austria

Collaboration: 

  • The University of California, Berkeley, CA, USA

  • Netherlands Cancer Institute, Amsterdam, Netherlands

  • Martin-Luther-Universität Halle-Wittenberg, Halle, Germany

  • Università di Roma “Sapienza”, Italy

  • Universidad Autónoma de Madrid, Spain

  • Harvard University, Boston, MA, USA

  • Department of Molecular Biology, Umeå University, Umeå, Sweden

  • University of Veterinary and Pharmaceutical Science, Brno, Czech Republic

  • Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany

Research Groups

Department of Structure and Function of Chromosomes
Department of Regulation of Genetic Processes