Department of the 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   Demakova Olga leading research fellow PhD (Biology) demakovaatmcb [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 Kolesnikova Tatiana leading research fellow PhD (Biology) kolesnikovaatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Zykova 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   vicernaatmcb [dot] nsc [dot] ru
thomson_logo.gif scopus_logo.jpg Makunin Igor research assistant PhD (Biology)  
      Maltseva Maria research assistant    
      Dovgan Victoria research assistant   dovganatmcb [dot] nsc [dot] ru
      Veselova Olga research assistant    
      Graphodatskaya Victoria lab technician   vikaatmcb [dot] nsc [dot] ru
      Shmakova Margarita lab technician    
      Dolbak Evgenia lab technician   eugenyatmcb [dot] nsc [dot] ru
  scopus_logo.jpg Moshkin Yuri part-time research fellow PhD  
thomson_logo.gif scopus_logo.jpg Andreyenkova Natalia part-time junior research fellow PhD (Biology) anataatmcb [dot] nsc [dot] ru
      Tatarinov Mikhail part-time engineer    

Former research workers:

Belyaeva Elena, DSc
Ivanov Roman
Goncharov Fedor
Kolodyazhnaya Aleksandra
Nerusheva (Kokoza) Elena, PhD
Semeshin Valery, DSc
Shulutkova Alena
Skvortsova Tatiana

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. 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

  2. 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

  3. 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

  4. 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

  5. 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

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

  7. 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 

  8. 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

  9. 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

  10. 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

  11. Literák I, Skyrpan M, Andreyenkova NG. A mixed pair of black and red kites in ukraine, including DNA analysis of hybrid offspring. (doi: 10.2478/s11756-019-00268-1) Biologia 75: 115-120, 2020

  12. Volkova EI, Andreyenkova NG, Andreyenkov OV, Sidorenko DS, Zhimulev IF, Demakov SA.  Structural and functional dissection of the 5’ region of the Notch gene in Drosophila melanogaster. (doi: 10.3390/genes10121037) Genes 10(12): 1037, 2019

  13. Titov SE, Ivanov MK, Demenkov PS, Katanyan GA, Kozorezova ES, Malek AV, Veryaskina YuA, Zhimulev IF. Combined quantitation of HMGA2 mRNA, microRNAs, and mitochondrial-DNA content enables the identification and typing of thyroid tumors in fine-needle aspiration smears. (doi: 10.1186/s12885-019-6154-7) BMC Cancer 19: 1010, 2019

  14. Maksimov DA, Koryakov DE. Binding of SU(VAR)3-9 partially depends on SETDB1 in the chromosomes of Drosophila melanogaster. (doi: 10.3390/cells8091030) Cells 8(9): 1030, 2019

  15. Kolesnikov NN, Veryaskina YuA, Titov SE, Rodionov VV, Gening TP, Abakumova TV, Kometova VV, Torosyan MKh, Zhimulev IF. Expression of micrornas in molecular genetic breast cancer subtypes. (doi: 10.1016/j.ctarc.2016.08.006) Cancer Treat Res Commun 20: 100026, 2019

  16. Zykova TYu, Levitsky VG, Zhimulev IF. Architecture of promoters of house-keeping genes in polytene chromosome interbands of Drosophila melanogaster. (doi: 10.1134/S1607672919020029) Dokl Biochem Biophys 485(1): 95-100, 2019

  17. Sidorenko DS, Sidorenko IA, Zykova TY, Goncharov FP, Larsson J, Zhimulev IF. Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster. (doi: 10.1007/s00412-019-00703-x) Chromosoma 128(2): 97-117, 2019

  18. de Jong TV, Moshkin YuM, Guryev V. Gene expression variability: the other dimension in transcriptome analysis. (doi: 10.1152/physiolgenomics.00128.2018) Physiol Genomics 51(5): 145–158, 2019

  19. Khoroshko VA, Pokholkova GV, Zykova TYu, Osadchiy IS, Zhimulev IF. Gene dunce localization in the polytene chromosome of Drosophila melanogaster long span batch of adjacent chromosomal structures. (doi: 10.1134/S1607672919010137) Doklady Biochem Biophys 484(1): 55-58, 2019

  20. Maslennikova SO, Gerlinskaya LA, Kontsevaya GV, Anisimova MV, Nedospasov SA,  Feofanova NA, Moshkin MP, Moshkin YM. TNFα is responsible for the canonical offspring number-size trade-off. (doi: 10.1038/s41598-019-38844-9) Sci Reports 9(1): 4568, 2019

  21. Andreyenkova NG, Starikov IJ, Wink M, Karyakin IV, Andreyenkov OV, Zhimulev IF. The problems of genetic support of dividing the black kite (Milvus migrans) into subspecies. (doi: 10.18699/VJ19.486) Vavilov J Genetics Breeding 23(2): 226-231, 2019

  22. Andreyenkov OV, Volkova EI, Andreyenkova NG, Demakov SA. The study of the regulatory region of the Drosophila melanogaster Notch gene by new methods of directed genome editing. (doi: 10.18699/VJ19.482) Vavilov J Genetics Breeding 23(2): 199-202, 2019

  23. Sidorenko DS, Zykova TYu, Khoroshko VA, Pokholkova GV, Demakov SA, Larsson J, Belyaeva ES, Zhimulev IF. Polytene chromosomes reflect functional organization of the Drosophila genome. (doi: 10.18699/VJ19.474) Vavilov J Genetics Breeding 23(2): 148-153, 2019

  24. Kolesnikova TD, Antonenko OV, Makunin IV. Replication timing in Drosophila and its peculiarities in polytene chromosomes. (doi: 10.18699/VJ19.473) Vavilov J Genetics Breeding 23(2): 140-147, 2019

  25. Zykova TYu, Popova OO, Khoroshko VA, Levitsky VG, Lavrov SA, Zhimulev IF. Genetic organization of open chromatin domains situated in polytene chromosome interbands in Drosophila. (doi: 10.1134/S1607672918060078) Doklady Biochem Biophys 483(1): 297–301, 2018

  26. Andreyenkova NG, Andreyenkov OV, Karyakin IV, Zhimulev IF. New haplotypes of the mitochondrial gene CytB in the nesting population of the siberian black kite Milvus migrans lineatus Gray, 1831 in the territory of the Republic of Tyva. (doi: 10.1134/S1607672918050034) Doklady Biochem Biophys 482(1): 242–244, 2018

  27. Khoroshko VA, Zykova TY, Popova OO, Zhimulev IF. Border structure of intercalary heterochromatin bands of Drosophila melanogaster polytene chromosomes. (doi: 10.1134/S1607672918020163) Dokl Biochem Biophys 479(1): 114-117, 2018

  28. Kolesnikova TD. Banding pattern of polytene chromosomes as a representation of universal principles of chromatin organization into topological domains. (doi: 10.1134/S0006297918040053) Biochemistry (Mosc) 83(4): 338-349, 2018

  29. Kolesnikova TD, Goncharov FP, Zhimulev IF. Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. (doi: 10.1371/journal.pone.0195207) PLoS ONE 13(4): e0195207, 2018

  30. Pokholkova GV, Demakov SA, Andreenkov OV, Andreenkova NG, Volkova EI, Belyaeva ES, Zhimulev IF. Tethering of CHROMATOR and dCTCF proteins results in decompaction of condensed bands in the Drosophila melanogaster polytene chromosomes but does not affect their transcription and replication timing. (doi: 10.1371/journal.pone.0192634) PLoS ONE 13(4): e0192634, 2018

  31. Zykova TYu, Levitsky VG, Belyaeva ES, Zhimulev IF. Polytene chromosomes – a portrait of functional organization of the Drosophila genome. (doi: 10.2174/1389202918666171016123830) Curr Genomics 19(3): 179-191, 2018

  32. Maksimov DA, Laktionov PP, Posukh OV, Belyakin SN, Koryakov DE. Genome-wide analysis of SU(VAR)3-9 distribution in chromosomes of Drosophila melanogaster. (doi: 10.1007/s00412-017-0647-4) Chromosoma 127(1): 85-102, 2018

  33. Posukh OV, Maksimov DA, Laktionov PP, Koryakov DE, Belyakin SN. Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile. (doi: 10.1186/s13072-017-0163-z) Epigenetics Chromatin 10: 56, 2017

  34. Rykova E, Sizikov A, Roggenbuck D, Antonenko O, Bryzgalov L, Morozkin E, Skvortsova K, Vlassov V, Laktionov P, Kozlov V. Circulating DNA in rheumatoid arthritis: pathological changes and association with clinically used serological markers. (doi: 10.1186/s13075-017-1295-z) Arthritis Res Ther 19: 85, 2017

  35. Andreyeva EN, Bernardo TJ, Kolesnikova TD, Lu X, Yarinich LA, Bartholdy BA, Guo X, Posukh OV, Healton S, Willcockson MA, Pindyurin AV, Zhimulev IF, Skoultchi AI, Fyodorov DV. Regulatory functions and chromatin loading dynamics of linker histone H1 during endoreplication in Drosophila. (doi: 10.1101/gad.295717.116) Genes Dev 31: 603-616, 2017

  36. Romashchenko AV, Kan T-W, Petrovski DV, Gerlinskaya LA, Moshkin MP, Moshkin YuM. Nanoparticles associate with intrinsically disordered RNA-binding proteins. (doi: 10.1021/acsnano.6b05992) ACS Nano 11(2): 1328-1339, 2017 

  37. Boldyreva LV, Goncharov FP, Demakova OV, Zykova TYu, Levitsky VG, Kolesnikov NN, Pindyurin AV, Semeshin VF, Zhimulev IF. Protein and genetic composition of four chromatin types in Drosophila melanogaster cell lines. (doi:  10.2174/1389202917666160512164913) Curr Genomics, 18(2): 214-226, 2017

  38. Stupak EV, Veryaskina YuA, Titov SE, Achmerova LG, Stupak VV, Ivanov MK, Zhimulev IF, Kolesnikov NN. MicroRNA profiling in the malignant progression of gliomas. AIP Conf Proc 1760, 020065, doi: 10.1063/1.4960284, 2016

  39. Horvath M, Mihajlovic Z, Slaninova V, Perez-Gomez R, Moshkin Y, Krejci A. The silent information regulator 1 (Sirt1) is a positive regulator of the Notch pathway in Drosophila. (doi: 10.1042/BCJ20160563) Biochem J 473: 4129-4143, 2016

  40. Kolesnikova  TD, Goncharov FP, Zhimulev IF. Fine mapping of late-replicating bands partitions the Drosophila genome into two contrasting types of domains whose properties are dependent on their size. Cytogenet Genome Res 148: 90, 2016

  41. Khoroshko VA, Levitsky VG, Zykova TY, Antonenko OV, Belyaeva ES, Zhimulev IF. Chromatin heterogeneity and distribution of regulatory elements in the late-replicating intercalary heterochromatin domains of Drosophila melanogaster chromosomes. (doi: 10.1371/journal.pone.0157147) PLoS ONE 11(6): e0157147, 2016

  42. Titov SE, Ivanov MK, Karpinskaya EV, Tsivlikova EV, Shevchenko SP, Veryaskina YA, Akhmerova LG, Poloz TL, Klimova OA, Gulyaeva LF, Zhimulev IF, Kolesnikov NN. miRNA profiling, detection of BRAF V600E mutation and RET-PTC1 translocation in patients from Novosibirsk oblast (Russia) with different types of thyroid tumors. (doi: 10.1186/s12885-016-2240-2) BMC Cancer 16: 201, 2016

  43. Chereji RV, Kan T-W, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YuM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. (doi: 10.1093/nar/gkv978) Nucleic Acids Res 44: 1036-1051, 2016

  44. Zykova T, Demidova D, Levitsky V, Khoroshko V, Belyaeva E, Kokoza E, Zhimulev I. Molecular and genetic structure of polytene chromosome banding pattern in Drosophila melanogaster. Athens: ATINER'S Conference Paper Series, No: BIO2015-1700: 4-15, 2015

  45. Zhimulev IF, Zykova TYu, Goncharov FP, Khoroshko VA, Demakova OV, Semeshin VF, Pokholkova GV, Boldyreva LV, Demidova DS, Levitsky VG, Demakov SA, Belyaeva ES. Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster. (doi: 10.1007/s10577-014-9447-3) Chromosome Res 23: 409-410, 2015

  46. Posukh OV, Maksimov DA, Skvortsova KN, Koryakov DE, Belyakin SN. The effects of SUUR protein suggest its role in repressive chromatin renewal during replication in Drosophila. (doi: 10.1080/19491034.2015.1074366) Nucleus 6: 249-253, 2015

  47. Hoskins RA,... Demakova OV, Andreyeva EN, Boldyreva LV,... Zhimulev IF,... Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. (doi: 10.1101/gr.185579.114) Genome Res 25: 445-458, 2015

  48. Okotrub KA, Surovtsev NV, Semeshin VF, Omelyanchuk LV. Raman spectroscopy for DNA quantification in cell nucleus. (doi: 10.1002/cyto.a.22585) Cytometry A 87: 68-73, 2015

  49. Koryakov DE, Zhimulev IF. DNA replication in nurse cell polytene chromosomes of Drosophila melanogaster otu mutants. (doi: 10.1007/s00412-014-0487-4) Chromosoma 124: 95-106, 2015

  50. Pokholkova GV, Koryakov DE, Pindyurin AV, Kozhevnikova EN, Belyakin SN, Andreyenkov OV, Belyaeva ES, Zhimulev IF. Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes. (doi: 10.1007/s00412-014-0491-8) Chromosoma 124: 209-220, 2015

Selected talks: 

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

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

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

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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

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

  14. 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

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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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 the Structure and Function of Chromosomes
Department of the Diversity and Evolution of Genomes
Department of the Regulation of Genetic Processes