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: 
      Name Position Academic
Degree
Contacts
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   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)  
thomson_logo.gif scopus_logo.jpg Goncharov Fedor research assistant   fedoratmcb [dot] nsc [dot] ru
      Ivanov Roman research assistant   ivanovroatmcb [dot] nsc [dot] ru
      Shulutkova Alena research assistant   shulutkova [dot] alenaatmcb [dot] nsc [dot] ru
      Sysoeva Maria research assistant    
      Dovgan Victoria research assistant   dovganatmcb [dot] nsc [dot] ru
      Graphodatskaya Victoria lab technician   vikaatmcb [dot] nsc [dot] ru
      Shmakova Margarita lab technician   margarita_shmakovaatmcb [dot] nsc [dot] ru
      Dolbak Evgenia lab technician   eugenyatmcb [dot] nsc [dot] ru
  scopus_logo.jpg Moshkin Yuri part-time research fellow PhD (Biology)  
thomson_logo.gif scopus_logo.jpgscopus_logo.jpg Andreyenkova Natalia part-time junior research fellow PhD (Biology) anataatmcb [dot] nsc [dot] ru
      Skvortsova Tatiana part-time research assistant    
      Tatarinov Mikhail part-time engineer    

Former research workers:

Belyaeva Elena, DSc
Nerusheva (Kokoza) Elena, PhD
Semeshin Valery, DSc

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. 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

  2. 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

  3. 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.0195207PLoS ONE 13(4): e0195207, 2018

  4. 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.0192634PLoS ONE 13(4): e0192634, 2018

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

  6. 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/s00412-017-0647-4Chromosoma 127(1): 85-102, 2018

  7. 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-zEpigenetics Chromatin 10: 56, 2017
  8. 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-zArthritis Res Ther 19: 85, 2017

  9. 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.295717.116Genes Dev 31: 603-616, 2017

  10. 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.6b05992ACS Nano 11(2): 1328-1339, 2017 

  11. 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:  10.2174/1389202917666160512164913Curr Genomics, 18(2): 214-226, 2017

  12. 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. Cancer Treatment and Research Communications, 2016, doi: 10.1016/j.ctarc.2016.08.006

  13. 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

  14. 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/BCJ20160563Biochem J 473: 4129-4143, 2016
  15. 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

  16. 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.0157147PLoS ONE 11(6): e0157147, 2016

  17. 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/s12885-016-2240-2BMC Cancer 16: 201, 2016

  18. 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/gkv978Nucleic Acids Res 44: 1036-1051, 2016

  19. 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

  20. 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/s10577-014-9447-3Chromosome Res 23: 409-410, 2015

  21. 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: 10.1080/19491034.2015.1074366Nucleus 6: 249-253, 2015

  22. 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.185579.114Genome Res 25: 445-458, 2015

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

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

  25. 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/s00412-014-0491-8Chromosoma 124: 209-220, 2015

  26. Palchikova IG, Ivankina EA, Semeshin VF, Omelyanchuk LV, Zhimulev IF, Smirnov ES. DNA Feulgen cytophotometry and chromatin diminution. In: International Multidisciplinary Microscopy Congress: Proceedings of InterM, Antalya, Turkey, October 10-13, 2013 (eds. Polychroniadis EK, Oral AY, Ozer M). Springer-Verlag Berlin Heidelberg, pp 233-239, 2014 (doi: 10.1007/978-3-319-04639-6_33)

  27. Nordman JT, Kozhevnikova EN, Verrijzer CP, Pindyurin AV, Andreyeva EN, Shloma VV, Zhimulev IF, Orr-Weaver TL. DNA copy-number control through inhibition of replication fork progression. (doi: 10.1016/j.celrep.2014.10.005Cell Reports 9: 841–849, 2014

  28. Makunin IV, Kolesnikova TD, Andreyenkova NG. Under-replicated regions in D. melanogaster are enriched with fast evolving genes and highly conserved noncoding sequences. (doi: 10.1093/gbe/evu156Genome Biol Evol 6: 2050-2060, 2014

  29. Zhimulev IF, Zykova TYu, Goncharov FP, Khoroshko VA, Demakova OV, Semeshin VF, Pokholkova GV, Boldyreva LV, Demidova DS, Babenko VN, Demakov SA, Belyaeva ES. Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster. (doi: 10.1371/journal.pone.0101631PLoS ONE 9(7): e101631, 2014

  30. Basquin D, Spierer A, Begeot F, Koryakov DE, Todeschini A-L, Ronsseray S, Vieira C, Spierer P, Delattre M. The Drosophila Su(var)3–7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing. (doi: 10.1371/journal.pone.0096802PLoS ONE 9(5): e96802, 2014

  31. Maksimov DA, Koryakov DE, Belyakin SN. Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster. (doi: 10.1007/s00412-013-0445-6Chromosoma 123: 253-264, 2014

  32. Andreyenkova NG, Kolesnikova TD, Makunin IV, Pokholkova GV, Boldyreva LV, Zykova TYu, Zhimulev IF, Belyaeva ES. Late replication domains are evolutionary conserved in the Drosophila genome. (doi: 10.1371/journal.pone.0083319PLoS ONE 8(12): e83319, 2013

  33. Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF. Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. (doi: 10.1007/s00412-012-0390-9Chromosoma 122: 55-66, 2013

  34. Kershengolts BM, Zhimulev IF, Goncharov NP, Zhang RV, Filippova GV, Shein AA, Prokopiev IA. Preservation of the gene pool of plants under permafrost conditions: State, advantages, and prospects. Rus J Genetics: Applied Research 3: 35-39, 2013

Selected talks: 
  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

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

  9. 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

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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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