Одной из наиболее актуальных и динамически развивающихся областей биологии в последние годы стало направление сравнительного изучения геномов и хромосом. Это направление может получить дальнейшее развитие за счет создания в НГУ Лаборатории структурной, функциональной и сравнительной геномики на базе сотрудничества с лабораториями ИМКБ СО РАН. В Лаборатории будут проведены работы по следующим направлениям:

• структурно-функциональная организация хромосом
• кластерная организация генов
• молекулярная организация гетерохроматина животных и растений
• разработка системы для внесения направленных модификаций в геном
• организация и эволюция хромосом и геномов позвоночных
• палеогеномика
• структура добавочных хромосом
• хромосомные системы определения пола
• функциональный и эволюционный анализ геномной компоненты иммунной системы

В рамках проекта были выпущены следующие статьи:

2017

1. Ilyin AA, Ryazansky SS, Doronin SA, Olenkina OM, Mikhaleva EA, Yakushev EY, Abramov YA, Belyakin SN, Ivankin AV, Pindyurin AV, Gvozdev VA, Klenov MS, Shevelyov YY. Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells. Nucleic Acids Res 45(13): 7666-7680, 2017
   (IF = 10.162)

2. 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. Genes Dev 31: 603-616, 2017
   (IF = 9.413)

3. Giovannotti M, Trifonov VA, Paoletti A, Kichigin IG, O’Brien PCM, Kasai F, Giovagnoli G, Ng BL, Ruggeri P, Nisi Cerioni P, Splendiani A, Pereira JC, Olmo E, Rens W, Caputo Barucchi V, Ferguson-Smith MA. New insights into sex chromosome evolution in anole lizards (Reptilia, Dactyloidae). Chromosoma 126(2): 245–260, 2017
   (IF = 4.414)

4. Romanenko SA, Serdyukova NA, Perelman PL, Pavlova SV, Bulatova NS, Golenishchev FN, Stanyon R, Graphodatsky AS. Intrachromosomal rearrangements in rodents from the perspective of comparative region-specific painting. Genes 8(9): 215, 2017
   (IF = 3.600)

5. Proskuryakova AA, Kulemzina AI, Perelman PL, Makunin AI, Larkin DM, Farré M, Kukekova AV, Johnson JL, Lemskaya NA, Beklemisheva VR, Roelke-Parker ME, Bellizzi J, Ryder OA, O’Brien SJ, Graphodatsky AS. X chromosome evolution in Cetartiodactyla. Genes 8(9): 216, 2017
   (IF = 3.600)

6. 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. Curr Genomics, 18(2): 214-226, 2017
   (IF = 1.835)

7. Dymova MA, Zadorozhny AV, Mishukova OV, Khrapov EA, Druzhkova AS, Trifonov VA, Kichigin IG, Tishkin AA, Grushin SP, Filipenko ML. Mitochondrial DNA analysis of ancient sheep from Altai. Anim Genet 48(5): 615-618, 2017
   (IF=1.815)

8. Кулемзин СВ, Кузнецова ВВ, Мамонкин М, Таранин АВ, Горчаков АА. Основы дизайна химерных антигенных рецепторов. Acta Naturae 9(1): 6-15, 2017
   (IF = 1.667)

9. Trifonov VA, Makunin AI, Romanenko SA, Biltueva LS, Beklemisheva VR, Pobedintseva MA, Prokopov DYu, Andreyushkova DA, Graphodatsky AS. Whole genome duplications in vertebrate evolution. Mol Cytogenet 10(Suppl 1): 20(L17), 2017
   (IF = 1.455)

10. Biltueva LS, Prokopov DY, Makunin AI, Komissarov AS, Kudryavtseva AV, Lemskaya NA, Vorobieva NV, Serdyukova NA, Romanenko SA, Gladkikh OL, Graphodatsky AS, Trifonov VA. Genomic organization and physical mapping of tandemly arranged repetitive DNAs in sterlet (Acipenser ruthenus). Cytogenet Genome Res, 2017, doi: 10.1159/000479472
    (IF = 1.354)

11. Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Heteromorphism of “homomorphic” sex chromosomes in two Anole species (Squamata, Dactyloidae) revealed by synaptonemal complex analysis.  Cytogenet Genome Res  151: 89-95, 2017
    (IF = 1.354)

12. Poplavskaya NS, Romanenko SA, Serdyukova NA, Trifonov VA, Yang F, Nie W, Wang J, Bannikova AA, Surov AV, Lebedev VS. Karyotype evolution and phylogenetic relationships of Cricetulus sokolovi Orlov et Malygin 1988 (Cricetidae, Rodentia) inferred from chromosomal painting and molecular data. Cytogenet Genome Res 152: 65-72, 2017
    (IF = 1.354)

13. Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Immunocytological analysis  of  meiotic  recombination  in  two  anole  lizards  (Squamata,  Dactyloidae).  Comp Cytogen 11(1): 129–141, 2017
    (IF = 1.151)

14. Кулемзин СВ, Кузнецова ВВ, Мамонкин М, Таранин АВ, Горчаков АА. CAR T-клеточная терапия: баланс эффективности и безопасности. Молекулярная биология 51(2): 274–287, 2017
    (IF = 0.799)

15. Кулемзин СВ, Чикаев НА, Волкова ОЮ, Кузнецова ВВ, Таранин АВ, Горчаков АА. Модульная система лентивирусных векторов для работы с химерными антигенными рецепторами. Биоорганическая химия 43(2): 124-132, 2017
    (IF = 0.690)

16. Druzhkova AS, Makunin AI, Vorobieva NV, Vasiliev SK, Ovodov ND, Shunkov MV, Trifonov VA, Graphodatsky AS. Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia). Mitochondrial DNA Part B 2(1): 79-81, 2017

2016

1. Bian C,... Trifonov V,... Shi Q. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. (doi: 10.1038/srep24501) Sci Repts 6: 24501, 2016
   (IF = 5.228)

2. Trifonov VA, Romanenko SS, Beklemisheva VR, Biltueva LS, Makunin AI, Lemskaya NA, Kulemzina AI, Stanyon R, Graphodatsky AS. Evolutionary plasticity of acipenseriform genomes. Chromosoma 125: 661-668, 2016
   (IF = 4.303)

3. Makunin AI, Kichigin IG, Larkin DM, O’Brien PCM, Ferguson-Smith MA, Yang F, Proskuryakova AA, Vorobieva NV, Chernyaeva EN, O’Brien SJ, Graphodatsky AS, Trifonov VA. Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosomespecific DNA sequencing. BMC Genomics 17: 618, 2016
   (IF = 3.867)

4. Beklemisheva VR, Perelman PL, Lemskaya NA, Kulemzina AI, Proskuryakova AA, Burkanov VN, Graphodatsky AS. The ancestral carnivore karyotype as substantiated by comparative chromosome painting of three pinnipeds, the walrus, the steller sea lion and the Baikal seal (Pinnipedia, Carnivora). PLoS ONE 11(1): e0147647, 2016
   (IF = 3.057)

5. Gladkikh OL, Romanenko SA, Lemskaya NA, Serdyukova NA, O’Brien PCM, Kovalskaya JM, Smorkatcheva AV, Golenishchev FN, Perelman PL, Trifonov VA, Ferguson-Smith MA, Yang F, Graphodatsky AS. Rapid karyotype evolution in Lasiopodomys involved at least two autosome – sex chromosome translocations. PLoS ONE 11(12): e0167653, 2016
   (IF = 3.057)

6. 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. PLoS ONE 11(6): e0157147, 2016
   (IF = 3.057)

7. Kichigin IG, Giovannotti M, Makunin AI, Ng BL, Kabilov MR, Tupikin AE, Barucchi VC, Splendiani A, Ruggeri P, Rens W, O’Brien PCM, Ferguson-Smith MA, Graphodatsky AS, Trifonov VA. Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA. Mol Genet Genomics 291: 1955-1966, 2016
   (IF = 2.622)

8. Kuznetsova IS, Ostromyshenskii DI, Komissarov AS, Prusov AN, Waisertreiger IS, Gorbunova AV, Trifonov VA, Ferguson-Smith MA, Podgornaya OI. LINE-related component of mouse heterochromatin and complex chromocenters’ composition. Chromosome Res 24: 309-323, 2016
   (IF = 2.590)

9. Maksimov DA, Laktionov PP, Belyakin SN. Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster. Chromosome Res 24: 481-494, 2016
   (IF = 2.590)

10. Romanenko SA, Lemskaya NA, Trifonov VA, Serdyukova NA, O’Brien PCM, Bulatova NSh, Golenishchev FN, Ferguson-Smith MA, Yang F, Graphodatsky AS. Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus. Chromosome Res 24: 145-159, 2016
    (IF = 2.590)

11. Munzarova A, Popova J, Razuvaeva A, Shloma V, Gatti M, Omelyanchuk L. Accurate measurement of poleward microtubule flux in the spindle of Drosophila S2 cells. Cell Biol Int 40: 984-990, 2016
    (IF = 1.663)

12. Kulemzina AI, Proskuryakova AA, Beklemisheva VR, Lemskaya NA, Perelman PL, Graphodatsky AS. Comparative chromosome map and heterochromatin features of the gray whale karyotype (Cetacea). Cytogenet Genome Res 148: 25-34, 2016
    (IF = 1.638)

13. Жимулев ИФ, Болдырева ЛВ, Демакова ОВ, Похолкова ГВ, Хорошко ВА, Зыкова TЮ, Лавров СА, Беляева ЕС. Формирование дисков политенных хромосом из интронов генов у дрозофилы. Доклады Акад Наук 466(5): 607–610, 2016
    (IF = 0.394)

14. Strunov A, Boldyreva LV, Pavlova GA, Pindyurin AV, Gatti M, Kiseleva E. A simple and effective method for ultrastructural analysis of mitosis in Drosophila S2 cells. MethodsX 3: 551-559, 2016

2015

1. Hoskins RA,... Demakova OV, Andreyeva EN, Boldyreva LV,... Zhimulev IF,... Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 25: 445-458, 2015
   (IF = 14.630)

2. Dobrynin P,... Makunin A,... Perelman P,... O’Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biology 16: 277, 2015
   (IF = 10.810)

3. Koryakov DE, Zhimulev IF. DNA replication in nurse cell polytene chromosomes of Drosophila melanogaster otu mutants. Chromosoma 124: 95-106, 2015
   (IF = 4.602)

4. Romanets-Korbut O, Najakshin AM, Yurchenko M, Malysheva TA, Kovalevska L, Shlapatska LM, Zozulya YA, Taranin AV, Horvat B, Sidorenko SP. Expression of CD150 in tumors of the central nervous system: identification of a novel isoform. PLoS One 10(2): e0118302, 2015
   (IF = 3.234)

5. Trifonov VA, Paoletti A, Caputo Barucchi V, Kalinina T, O’Brien PCM, Ferguson-Smith MA, Giovannotti M. Comparative chromosome painting and NOR distribution suggest a complex hybrid origin of triploid Lepidodactylus lugubris (Gekkonidae). PLoS ONE 10(7): e0132380, 2015
   (IF = 3.234)

6. Romanenko SA, Perelman PP, Trifonov VA, Serdyukova NA, Li T, Fu B, O’Brien PCM, Ng BL, Nie W, Liehr T, Stanyon R, Graphodatsky AS, Yang F. A first generation comparative chromosome map between guinea pig (Cavia porcellus) and humans. PLoS ONE 10(5): e0127937, 2015
   (IF = 3.234)

7. 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. Nucleus 6: 249-253, 2015
   (IF = 3.033)

8. Guselnikov SV, Grayfer L, De Jesús Andino F, Rogozin IB, Robert J, Taranin AV. Retention of duplicated ITAM-containing transmembrane signaling subunits in the tetraploid amphibian species Xenopus laevis. Dev Comp Immunol 53: 158-168, 2015
   (IF = 2.815)

9. Avila F, Baily MP, Merriwether DA, Trifonov VA, Rubes J, Kutzler MA, Chowdhary R, Janečka J, Raudsepp T. A cytogenetic and comparative map of camelid chromosome 36 and the minute in alpacas. Chromosome Res 23: 237-251, 2015
   (IF = 2.478)

10. Pokorná MJ, Trifonov VA, Rens W, Ferguson-Smith MA, Kratochvíl L. Low rate of interchromosomal rearrangements during old radiation of gekkotan lizards (Squamata: Gekkota). Chromosome Res 23: 299-309, 2015
    (IF = 2.478)

11. Pindyurin AV, Gatti M. Chromosomes in the taiga. Chromosome Res 23: 641-647, 2015
    (IF = 2.478)

12. Romanenko SA, Lemskaya NA, Trifonov VA, Serdyukova NA, O’Brien PCM, Bulatova NSh, Golenishchev FN, Ferguson-Smith MA, Yang F, Graphodatsky AS. Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus. Chromosome Res, 2015, doi: 10.1007/s10577-015-9504-6
    (IF = 2.478)

13. Pindyurin AV, de Jong J, Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics 106: 171–177, 2015
    (IF = 2.284)

14. Johnson JL, Kosyza A, Kharlamova AV, Gulevich RG, Perelman PL, Fong HTW, Vladimirova AV, Oskina IN, Trut LN, Kukekova AV: Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT. Anim Genet 46: 190–199, 2015
    (IF = 2.207)

15. Romanenko SA, Biltueva LS, Serdyukova NA, Kulemzina AI, Beklemisheva VR, Gladkikh OL, Lemskaya NA, Interesova EA, Korentovich MA, Vorobieva NV, Graphodatsky AS, Trifonov VA. Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting. Mol Cytogenet 8: 90, 2015
    (IF = 2.140)

16. Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive analyses of white-handed gibbon chromosomes enables access to 92 evolutionary conserved breakpoints compared to the human genome. Cytogenet Genome Res 145: 42-49, 2015
    (IF = 1.561)

17. Lemskaya NA, Kartavtseva IV, Rubtsova NV, Golenishchev FN, Sheremetyeva IN, Graphodatsky AS. Chromosome polymorphism in Microtus (Alexandromys) mujanensis (Arvicolinae, Rodentia). Cytogenet Genome Res 146: 238-242, 2015
    (IF = 1.561)

18. Дружкова АС, Воробьева НВ, Трифонов ВА, Графодатский АС. Древняя ДНК: итоги и перспективы (к 30-летию начала исследований). Генетика 51: 627–643, 2015
    (IF = 0.446)

2014

1. Jarvis ED,... Perelman P,... Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331, 2014
   (IF = 31.477)

2. 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. Cell Reports 9: 841–849, 2014
   (IF = 7.207)

3. 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. PLoS ONE 9(7): e101631, 2014
   (IF = 3.534)

4. 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. Chromosoma 124: 209-220, 2015
   (IF = 3.260)

5. Makunin AI, Dementyeva PV, Graphodatsky AS, Volobujev VT, Kukekova AV, Trifonov VA. Genes on B chromosomes of vertebrates. Mol Cytogenet 7: 99, 2014
   (IF = 2.662)

6. Kulemzina AI, Perelman PL, Grafodatskaya DA, Nguyen TT, Thompson M, Roelke-Parker ME, Graphodatsky AS. Comparative chromosome painting of pronghorn (Antilocapra americana) and saola (Pseudoryx nghetinhensis) karyotypes with human and dromedary camel probes. BMC Genetics 15: 68, 2014
   (IF = 2.356)

7. Biltueva L, Kulemzina A, Vorobieva N, Perelman P, Kochneva M, Zhidenova A, Graphodatsky A. A new case of an inherited reciprocal translocation in cattle: rcp(13;26)(q24;q11). Cytogenet Genome Res 144: 208-211, 2014
   (IF = 1.561)

8. Avila F, Baily MP, Perelman P, Das PJ, Pontius J, Chowdhary R, Owens E, Johnson WE, Merriwether DA, Raudsepp T. A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos). Cytogenet Genome Res 144: 193-204, 2014
   (IF = 1.561)

9. Volkova O, Guselnikov S, Mechetina L, Chikaev N, Baranov K, Kulemzin S, Reshetnikova E, Najakshin A, Taranin A. Development and characterization of domain-specific monoclonal antibodies produced against human SLAMF9. Monoclon Antib Immunodiagn Immunother 33: 209-214, 2014
   (ex-Hybridoma) (IF = 0.244)