Кандидатные SNP-маркеры социального доминирования, способные влиять на сродство ТАТА-связывающего белка к промоторам генов человека
https://doi.org/10.18699/VJ16.196
- Р Р‡.МессенРТвЂВВВВВВВВжер
- РћРТвЂВВВВВВВВнокласснРСвЂВВВВВВВВРєРСвЂВВВВВВВВ
- LiveJournal
- Telegram
- ВКонтакте
- РЎРєРѕРїРСвЂВВВВВВВВровать ссылку
Полный текст:
Аннотация
Предложена эвристическая гипотеза, согласно которой, если избыток какого-либо белка в ряде органов животных был экспериментально установлен как физиологический маркер повышенной агрессивности и если некоторый полиморфизм (SNP) человека вызывает суперэкспрессию гена, гомологичного гену этого белка у животных, то этот полиморфизм может быть кандидатным SNP-маркером предрасположенности к социальному доминированию, тогда как случаю дефицитной экспрессии может соответствовать социальное подчинение и наоборот. В рамках этой гипотезы проанализировали 21 ген человека: ADORA2A, BDNF, CC2D1A, CC2D1B, ESR2, FEV, FOS, GH1, GLTSCR2, GRIN1, HTR1B, HTR1A, HTR2A, HTR2C, LGI4, LEP, MAOA, SLC17A7, SLC6A3, SNCA, TH, – которые представляют функции белков, известных как физиологические маркеры агрессивного поведения животных: гормоны и их рецепторы, ферменты биосинтеза и рецепторы нейромедиаторов, транскрипционные и нейротропные факторы. Эти белки могут играть важную роль при установлении иерархических отношений у социальных видов животных. С использованием созданного нами ранее Web-сервиса SNP_TATA_Comparator (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl) мы проанализировали 381 SNP в районе [–70;–20] перед стартами белок-кодирующих транскриптов (район связывания ТАТА-связывающего белка, ТВР) из базы данных dbSNP (выпуск № 147). Было найдено 45 и 47 кандидатных SNP-маркеров доминирования и подчинения соответственно (например, rs373600960 и rs747572588). В рамках предложенной эвристической гипотезы и выпуска № 147 базы данных dbSNP мы получили статистически достоверные (α < 10–5) свидетельства о действии естественного отбора как против дефицитной экспрессии генов, способных влиять на предрасположенность к доминированию, так и в пользу того, что подчинение и доминирование могут характеризовать норму реакции агрессивности (отличие незначимо: α > 0.35). Предложенная гипотеза, выявленные на ее основе кандидатные SNP-маркеры и закономерности их влияния естественного отбора на геном человека обсуждаются в контексте литературных данных: могут ли они иметь какое-либо отношение к социальному доминированию у людей. Сделано заключение – эти результаты нуждаются в экспериментальной проверке.
Об авторах
И. В. ЧадаеваРоссия
Новосибирск, Россия
Д. А. Рассказов
Россия
Новосибирск, Россия
Е. Б. Шарыпова
Россия
Новосибирск, Россия
Л. К. Савинкова
Россия
Новосибирск, Россия
П. М. Пономаренко
Соединённые Штаты Америки
США
М. П. Пономаренко
Россия
Новосибирск, Россия
Список литературы
1. Genomes Project Consortium. Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., Kang H.M., Marth G.T., McVean G.A. An integrated map of genetic variation from 1.092 human genomes. Nature. 2012;491(7422):56- 65. https://doi.org/10.1038/nature11632.
2. Abbas A., Lechevrel M., Sichel F. Identification of new single nucleotid polymorphisms (SNP) in alcohol dehydrogenase class IV ADH7 gene within a French population. Arch. Toxicol. 2006;80(4):201-205. https://doi.org/10.1007/s00204-005-0031-7.
3. Amberger J.S., Bocchini C.A., Schiettecatte F., Scott A.F., Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucl. Acids Res. 2015;43:D789-D798. https://doi.org/10.1093/nar/gku1205.
4. Arkova O.V., Kuznetsov N.A., Fedorova O.S., Kolchanov N.A., Savinkova L.K. Real-time interaction between ТВР and the TATA box of the human triosephosphate isomerase gene promoter in the norm and pathology. Acta Naturae. 2014;6(2):36-40.
5. Arkova O.V., Ponomarenko M.P., Rasskazov D.A., Drachkova I.A., Arshinova T.V., Ponomarenko P.M., Savinkova L.K., Kolchanov N.A. Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters. BMC Genomics. 2015;16(Suppl. 13):S5. https://doi.org/10.1186/1471-2164-16-S13-S5.
6. Belyaev D.K. The Wilhelmine E. Key 1978 invitational lecture. Destabilizing selection as a factor in domestication. J. Hered. 1979;70(5): 301-308.
7. Bondar N.P., Boyarskikh U.A., Kovalenko I.L., Filipenko M.L., Kudryavtseva N.N. Molecular implications of repeated aggression: Th, Dat1, Snca and Bdnf gene expression in the VTA of victorious male mice. PLoS ONE. 2009;4(1):e4190. https://doi.org/10.1371/journal.pone.0004190.
8. Cao J., Joyner L., Mickens J.A., Leyrer S.M., Patisaul H.B. Sex-specific ESR2 mRNA expression in the rat hypothalamus and amygdala is altered by neonatal bisphenol A exposure. Reproduction. 2014;147(4):537-554. https://doi.org/10.1530/REP-13-0501.
9. Chadaeva I.V., Ponomarenko M.P., Rasskazov D.A., Sharypova E.B., Kashina E.V., Matveeva M.Yu., Arshinova T.V., Ponomarenko P.M., Arkova O.V., Bondar N.P., Savinkova L.K., Kolchanov N.A. Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters. BMC Genomics. 17(Suppl.14):53. https://doi.org/10.1186/s12864-16-3353-3.
10. Colonna V., Ayub Q., Chen Y., Pagani L., Luisi P., Pybus M., Garrison E., Xue Y., Tyler-Smith C. 1000 Genomes Project Consortium. Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., Kang H.M., Marth G.T., McVean G.A. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole- genome sequences. Genome Biol. 2014;15(6):R88. https://doi.org/10.1186/gb-2014-15-6-r88.
11. Delgadillo R.F., Whittington J.E., Parkhurst L.K., Parkhurst L.J. The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism. Biochemistry. 2009; 48(8):1801-1809. https://doi.org/10.1021/bi8018724.
12. Deplancke B., Alpern D., Gardeux V. The genetics of transcription factor DNA binding variation. Cell. 2016;166(3):538-554. https://doi.org/10.1016/j.cell.2016.07.012.
13. Drachkova I., Savinkova L., Arshinova T., Ponomarenko M., Peltek S., Kolchanov N. The mechanism by which TATA-box polymorphisms associated with human hereditary diseases influence interactions with the TATA-binding protein. Hum. Mutat. 2014;35(5):601-608. https://doi.org/10.1002/humu.22535.
14. Dusek A., Bartos L., Svecova L. The effect of a mother’s rank on her offspring’s pre-weaning rank in farmed red deer. Appl. Anim. Behav. Sci. 2007;103(1-2):146-155. https://doi.org/10.1016/j.applanim.2006.03.020.
15. Ehrman L., Parsons P.A. Behavior genetics and evolution. N.Y.: Mc-Graw-Hill, 1981.
16. Eldakar O.T., Gallup A.C. The group-level consequences of sexual conflict in multigroup populations. PLoS ONE. 2011;6(10):e26451. https://doi.org/10.1371/journal.pone.0026451.
17. Ellingrod V.L., Perry P.J., Ringold J.C., Lund B.C., Bever-Stille K., Fleming F., Holman T.L., Miller D. Weight gain associated with the -759C/T polymorphism of the 5HT2C receptor and olanzapine. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2005;134B(1):76-78. https://doi.org/10.1002/ajmg.b.20169.
18. Engh A.L., Esch K., Smale L., Holekamp K.E. Mechanisms of maternal rank “inheritance” in the spotted hyaena, Crocuta cr. Anim. Behav. 2000;60(3):323-332. https://doi.org/10.1006/anbe.2000.1502.
19. Haeussler M., Raney B.J., Hinrichs A.S., Clawson H., Zweig A.S., Karolchik D., Casper J., Speir M.L., Haussler D., Kent W.J. Navigating protected genomics data with UCSC genome browser in a box. Bioinformatics. 2015;31(5):764-766. https://doi.org/10.1093/bioinformatics/btu712.
20. Haldane J.B.S. The cost of natural selection. J. Genet. 1957;55:511-524.
21. Heyne H.O., Lautenschlager S., Nelson R., Besnier F., Rotival M., Cagan A., Kozhemyakina R., Plyusnina I.Z., Trut L., Carlborg O., Petretto E., Kruglyak L., Paabo S., Schoneberg T., Albert F.W. Genetic influences on brain gene expression in rats selected for tameness and aggression. Genetics. 2014;198(3):1277-1290. https://doi.org/10.1534/genetics. 114.168948.
22. Hinde R.A. Animal Behaviour. New York: McGraw-Hill, 1970.
23. Ilchibaeva T.V., Kondaurova E.M., Tsybko A.S., Kozhemyakina R.V., Popova N.K., Naumenko V.S. Brain-derived neurotrophic factor (BDNF) and its precursor (proBDNF) in genetically defined fear-induced aggression. Behav. Brain Res. 2015;290:45-50. https://doi.org/10.1016/j.bbr.2015.04.041.
24. Jegou S., El Yacoubi M., Mounien L., Ledent C., Parmentier M., Costentin J., Vaugeois J.M., Vaudry H. Adenosine A2A receptor gene disruption provokes marked changes in melanocortin content and pro-opiomelanocortin gene expression. J. Neuroendocrinol. 2003;15(12):1171-1177.
25. Ji N.Y., Findling R.L. Pharmacotherapy for mental health problems in people with intellectual disability. Curr. Opin. Psychiat. 2016;29: 103-125. https://doi.org/10.1097/YCO.0000000000000233.
26. Kasowski M., Grubert F., Heffelfinger C., Hariharan M., Asabere A., Waszak S.M., Habegger L., Rozowsky J., Shi M., Urban A.E., Hong M.Y., Karczewski K.J., Huber W., Weissman S.M., Gerstein M.B., Korbel J.O., Snyder M. Variation in transcription factor binding among humans. Science. 2010;328(5975):232-235. https://doi.org/10.1126/science.1183621.
27. Kimura M. Evolutionary rate at the molecular level. Nature. 1968; 217(5129):624-626. https://doi.org/10.1038/217624a0.
28. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980;16:111-120.
29. Kleshchev M.A., Gutorova N., Osadchuk L.V. The genetic characteristics of age dynamics of agonistic behavior in male laboratory mice in a social hierarchy. Ekologicheskaya genetika = Ecological genetics. 2013;11(4):64-72. (in Russian)
30. Kondaurova E.M., Ilchibaeva T.V., Tsybko A.S., Kozhemyakina R.V., Popova N.K., Naumenko V.S. 5-HT1A receptor gene silencers Freud-1 and Freud-2 are differently expressed in the brain of rats with genetically determined high level of fear-induced aggression or its absence. Behav. Brain Res. 2016;310:20-25. https://doi.org/10.1016/j.bbr.2016.04.050.
31. Kudryavtseva N.N., Bondar N.P., Boyarskikh U.A., Filipenko M.L. Snca and Bdnf gene expression in the VTA and raphe nuclei of midbrain in chronically victorious and defeated male mice. PLoS ONE. 2010;5(11):e14089. https://doi.org/10.1371/journal.pone.0014089.
32. Kulikov A.V., Bazhenova E.Y., Kulikova E.A., Fursenko D.V., Trapezova L.I., Terenina E.E., Mormede P., Popova N.K., Trapezov O.V. Interplay between aggression, brain monoamines and fur color mutation in the American mink. Genes Brain Behav. 2016. https://doi.org/10.1111/gbb.12313.
33. Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., Maglott D.R. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucl. Acids Res. 2014;42(Database issue):D980-5. https://doi.org/10.1093/nar/gkt1113.
34. Lin D., Boyle M.P., Dollar P., Lee H., Lein E.S., Perona P., Anderson D.J. Functional identification of an aggression locus in the mouse hypothalamus. Nature. 2011;470(7333):221-226. https://doi.org/10.1038/nature09736.
35. Lorenz K. On Aggression. Hove (UK): Psychology Press, 2002.
36. Martianov I., Viville S., Davidson I. RNA polymerase II transcription in murine cells lacking the TATA binding protein. Science. 2002;298(5595):1036-1039. https://doi.org/10.1126/science.1076327.
37. Michopoulos V., Higgins M., Toufexis D., Wilson M.E. Social subordination produces distinct stress-related phenotypes in female rhesus monkeys. Psychoneuroendocrinology. 2012;37(7):1071-1085. https://doi.org/10.1016/j.psyneuen.2011.12.004.
38. Mogno I., Vallania F., Mitra R.D., Cohen B.A. TATA is a modular component of synthetic promoters. Genome Res. 2010;20(10):1391- 1397. https://doi.org/10.1101/gr.106732.110.
39. Moore A.J. Genetic influences on social dominance: cow wars. Heredity. 2013;110(1):1-2. https://doi.org/10.1038/hdy.2012.85.
40. Naumenko E.V., Osadchuk A.V., Serova L.I., Shishkina G.T. Genetikofiziologicheskie mekhanizmy regulyatsii funktsiy semennikov [Genetic and Physiological Mechanisms of the Regulation of Testicular Functions]. Novosibirsk, Nauka Publ., 1983. (in Russian)
41. Osadchuk L.B., Bragin A.V., Osadchuk A.V. Interstrain differences in social and time patterns of agonistic behavior in male laboratory mice. Zhurnal vysshey nervnoy deyatel’nosti im. I.P. Pavlova = I.P. Pavlov Journal of Higher Nervous Activity. 2009;59(4):473-481. (in Russian)
42. Osadchuk L.B., Salomacheva I.N., Bragin A.V., Osadchuk A.V. The reproductive correlates of social hierarchy in laboratory male mice. Zhurnal vysshey nervnoy deyatel’nosti im. I.P. Pavlova = I.P. Pavlov Journal of Higher Nervous Activity. 2007;57(5):604-612. (in Russian)
43. Podkolodnyy N.L., Afonnikov D.A., Vaskin Yu.Yu., Bryzgalov L.O., Ivanisenko V.A., Demenkov P.S., Ponomarenko M.P., Rasskazov D.A., Gunbin K.V., Protsyuk I.V., Shutov I.Yu., Leontyev P.N., Fursov M.Yu., Bondar N.P., Antontseva E.V., Merkulova T.I., Kolchanov N.A. Program complex SNP-MED for analysis of singlenucleotide polymorphism (SNP) effects on the function of genes associated with socially significant diseases. Russ. J. Genet. Appl. Res. 2014;4(3):159-167. https://doi.org/10.1134/S2079059714030034.
44. Ponomarenko M., Arkova O., Rasskazov D., Ponomarenko P., Savinkova L., Kolchanov N. Candidate SNP markers of gender-biased autoimmune complications of monogenic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters. Front. Immunol. 2016;7:130. https://doi.org/10.3389/fimmu.2016.00130.
45. Ponomarenko M., Mironova V., Gunbin K., Savinkova L. Hogness Box. Eds. S. Maloy, K. Hughes. Brenner’s Encyclopedia of Genetics. San Diego: Acad. Press, Elsevier Inc. 2013;3:491-494. https://doi.org/10.1016/B978-0-12-374984-0.00720-8.
46. Ponomarenko M., Rasskazov D., Arkova O., Ponomarenko P., Suslov V., Savinkova L., Kolchanov N. How to use SNP_TATA_Comparator to find a significant change in gene expression caused by the regulatory SNP of this gene’s promoter via a change in affinity of the TATA-binding protein for this promoter. Biomed. Res. Int. 2015;2015:35983004625. https://doi.org/10.1155/2015/359835.
47. Ponomarenko P.M., Ponomarenko M.P., Drachkova I.A., Lysova M.V., Arshinova T.V., Savinkova L.K., Kolchanov N.A. Prediction of the affinity of the TATA-binding protein to TATA boxes with single nucleotide polymorphisms. Mol. Biol. (Mosk.). 2009;43(3):472-479. https://doi.org/10.1134/S0026893309030157.
48. Ponomarenko P., Rasskazov D., Suslov V., Sharypova E., Savinkova L., Podkolodnaya O., Podkolodny N., Tverdokhleb N., Chadaeva I., Ponomarenko M., Kolchanov N. Candidate SNP markers of chronopathologies are predicted by a significant change in the affinity of TATA- binding protein for human gene promoters. BioMed Res. Int. 2016;2016:8642703. https://doi.org/10.1155/2016/8642703.
49. Ponomarenko P.M., Savinkova L.K., Drachkova I.A., Lysova M.V., Arshinova T.V., Ponomarenko M.P., Kolchanov N.A. A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism. Dokl. Biochem. Biophys. 2008;419:88-92. https://doi.org/10.1134/S1607672908020117.
50. Ponomarenko P.M., Suslov V.V., Savinkova L.K., Ponomarenko M.P., Kolchanov N.A. A precise equilibrium equation for four steps of binding between TBP and TATA-box allows for the prediction of phenotypical expression upon mutation. Biophysics. 2010;55(3):358-369. https://doi.org/10.1134/S0006350910030036.
51. Popova N.K. From genes to aggressive behavior: the role of serotonergic system. Bioessays. 2006;28(5):495-503. https://doi.org/10.1002/bies.20412.
52. Popova N.K., Naumenko V.S., Kozhemyakina R.V., Plyusnina I.Z. Functional characteristics of serotonin 5-HT2A and 5-HT2C receptors in the brain and the expression of the 5-HT2A and 5-HT2C receptor genes in aggressive and non-aggressive rats. Neurosci. Behav. Physiol. 2010;40(4):357-361. https://doi.org/10.1007/s11055-010-9264-x.
53. Prud’Homme J., Chapais B. Aggressive interventions and matrilineal dominance relations in semifree-ranging Barbary macaques (Macaca sylvanus). Primates. 1993;34(3):271-283. https://doi.org/10.1007/BF02382621.
54. Reif A., Jacob C.P., Rujescu D., Herterich S., Lang S., Gutknecht L., Baehne C.G., Strobel A., Freitag C.M., Giegling I., Romanos M., Hartmann A., Rosler M., Renner T.J., Fallgatter A.J., Retz W., Ehlis A.C., Lesch K.P. Influence of functional variant of neuronal nitric oxide synthase on impulsive behaviors in humans. Arch. Gen. Psychiat. 2009;66(1):41-50. https://doi.org/10.1001/archgenpsychiatry.2008.510.
55. Rosenfeld C.S. Bisphenol A and phthalate endocrine disruption of parental and social behaviors. Front. Neurosci. 2015;9:57. https://doi.org/10.3389/fnins.2015.00057.
56. Rowell T.E. The concept of social dominance. Behav. Biol. 1974;11: 131-154.
57. Savinkova L., Drachkova I., Arshinova T., Ponomarenko P., Ponomarenko M., Kolchanov N. An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA- binding protein. PLoS ONE. 2013;8(2):e54626. https://doi.org/10.1371/journal.pone.0054626.
58. Savonenko A., Filipkowski R.K., Werka T., Zielinski K., Kaczmarek L. Defensive conditioning- related functional heterogeneity among nuclei of the rat amygdala revealed by c-Fos mapping. Neuroscience. 1999;94(3):723-733.
59. Serova L.I., Kozlova O.N., Naumenko E.V. The significance of the genotype and individual behavioral characteristics for the manifestation of the dominant phenotype in mouse micropopulations. Zhurnal vysshey nervnoy deyatel’nosti im. I.P. Pavlova = I.P. Pavlov Journal of Higher Nervous Activity. 1991;41(1):79-84. (in Russian)
60. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucl. Acids Res. 2001;29(1):308-311. https://doi.org/10.1093/nar/29.1.308.
61. Suslov V.V., Ponomarenko P.M., Ponomarenko M.P., Drachkova I.A., Arshinova T.V., Savinkova L.K., Kolchanov N.A. TATA box polymorphisms in genes of commercial and laboratory animals and plants associated with selectively valuable traits. Russ. J. Genet. 2010;46(4):394-403. https://doi.org/10.1134/S1022795410040022.
62. Van der Kooij M.A., Sandi C. The genetics of social hierarchies. Cur. Opin. Behav. Sci. 2015;2:52-57. https://doi.org/10.1016/j.cobeha.2014.09.001.
63. Zapata I., Serpell J.A., Alvarez C.E. Genetic mapping of canine fear and aggression. BMC Genomics. 2016;17:572. https://doi.org/10.1186/s12864-016-2936-3.
64. Zerbino D.R., Wilder S.P., Johnson N., Juettemann T., Flicek P.R. The Ensembl regulatory build. Genome Biol. 2015;16:56. https://doi.org/10.1186/s13059-015-0621-5.