3С-МЕТОДЫ В ИССЛЕДОВАНИЯХ ПРОСТРАНСТВЕННОЙ ОРГАНИЗАЦИИ ГЕНОМА
Аннотация
Пространственная трехмерная организация генома эукариот играет важную роль в функционировании ядерного материала. До недавнего времени единственной возможностью исследования пространственной организации генома в ядре клеток было использование методов световой и электронной микроскопии. Появление метода захвата конформации хромосом (chromosome conformation capture, 3С) позволило изучать хромосомные контакты, используя только молекулярно-биологические подходы. На сегодняшний день на основе 3С разработано целое семейство методов реконструкции пространственной организации генома.
Об авторах
Н. Р. БатуллинРоссия
В. С. Фишман
Россия
Ю. Л. Орлов
Россия
А. Г. Мензоров
Россия
Д. А. Афонников
Россия
О. Л. Серов
Россия
Список литературы
1. Akhtar A., Gasser S.M. The nuclear envelope and transcriptional control // Nat. Rev. Genet. 2007. V. 8. P. 507–517.
2. Andrulis E.D., Neiman A.M., Zappulla D.C. et al. Perinuclear localization of chromatin facilitates transcriptional silencing // Nature. 1998. V. 394. P. 592–595.
3. Beams H.W., Tahmisian T.T., Devine R. et al. Ultrastructure of the nuclear membrane of a gregarine parasitic in grasshoppers // Exp. Cell Res. 1957. V. 13. P. 200–204.
4. Belton J.M., McCord R.P., Gibcus J.H. et al. Hi-C: A comprehensive technique to capture the conformation of genomes // Methods. 2012. V. 58. P. 268–76.
5. Bian Q., Belmont A.S. Revisiting higher-order and large-scale chromatin organization // Curr. Opin. Cell Biol. 2012. V. 24. P. 359–366.
6. Cremer C., Cremer T., Gray J.W. Induction of chromosome damage by ultraviolet light and caffeine: correlation of cytogenetic evaluation and fl ow karyotype // Cytometry. 1982. V. 2. P. 287–290.
7. de Wit E., de Laat W. A decade of 3C technologies: insights into nuclear organization // Genes Dev. 2012. V. 26. P. 11–24.
8. Dekker J., Rippe K., Dekker M. et al. Capturing chromosome conformation // Science. 2002. V. 295. P. 1306–1311.
9. Dixon J.R., Selvaraj S., Yue F. et al. Topological domains in mammalian genomes identifi ed by analysis of chromatin interactions // Nature. 2012. V. 485. P. 376–380.
10. Dostie J., Richmond T.A., Arnaout R.A. et al. Chromosome сonformation сapture сarbon сopy (5C): a massively parallel solution for mapping interactions between genomic elements // Genome Res. 2006. V. 16. P. 1299–1309.
11. Fujita N., Wade P.A. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes // Methods. 2004. V. 33. P. 81–85.
12. Fullwood M.J., Wei C.L., Liu E.T. et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses // Genome Res. 2009. V. 19. P. 521–532.
13. Gilbert N., Boyle S., Fiegler H. et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fi bers // Cell. 2004. V. 118. P. 555–566.
14. Grosberg A., Nechaev S., Shakhnovich E. The role of topological constraints in the kinetics of collapse of macromolecules // J. Physique. 1988. V. 49. P. 2095–2100.
15. Grosberg A., Rabin Y., Havlin S. et al. Crumpled globule model of the 3-dimensional structure of DNA // Europhys. Lett. 1993. V. 23. P. 373-378.
16. Guelen L., Pagie L., Brasset E. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions // Nature. 2008. V. 453. P. 948–951.
17. Horike S., Cai S., Miyano M. et al. Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome // Nat. Genet. 2005. V. 37. P. 31–40.
18. Jackson V. Formaldehyde cross-linking for studying nucleosomal dynamics // Methods. 1999. V. 17. P. 125–139.
19. Kalhor R., Tjong H., Jayathilaka N. et al. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling // Nat. Biotechnol. 2012. V. 30. P. 90–98.
20. Kosak S.T., Skok J.A., Medina K.L. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development // Science. 2002. V. 296. P. 158–162.
21. Lieberman-Aiden E., van Berkum N.L., Williams L. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome // Science. 2009. V. 326. P. 289–293.
22. Mateos-Langerak J., Bohn M., de Leeuw W. et al. Spatially confi ned folding of chromatin in the interphase nucleus // Proc. Natl Acad. Sci. USA. 2009. V. 106. P. 3812–3817.
23. Misteli T. Beyond the sequence: cellular organization of genome function // Cell. 2007. V. 128. P. 787–800.
24. Morey C., Da Silva N.R., Perry P. et al. Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation // Development. 2007. V. 134. P. 900-919.
25. Munkel C., Langowski J. Chromosome structure predicted by a polymer model // Phys. Rev. E. 1998. V. 57. P. 5888–5896.
26. Orlando V., Strutt H., Paro R. Analysis of chromatin structure by in vivo formaldehyde cross-linking // Methods. 1997. V. 11. P. 205–214.
27. Peric-Hupkes D., Meuleman W., Pagie L. et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation // Mol. Cell. 2010. V. 38. P. 603–613.
28. Pickersgill H., Kalverda B., de Wit E. et al. Characterization of the Drosophila melanogaster genome at the nuclear lamina // Nat. Genet. 2006. V. 38. P. 1005–1014.
29. Ryba T., Hiratani I., Lu J. et al. Evolutionarily conserved replication timing profi les predict long-range chromatin interactions and distinguish closely related cell types // Genome Res. 2010. V. 20. P. 761–770.
30. Shaw P.J. Mapping chromatin conformation // F1000 Biol. Rep. 2010. V. 2.
31. Shopland L.S., Lynch C.R., Peterson K.A. et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence // J. Cell Biol. 2006. V. 174. P. 27–38.
32. Simonis M., Klous P., Splinter E. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) // Nat. Genet. 2006. V. 38. P. 1348–1354.
33. Solovei I., Kreysing M., Lanctôt C. et al. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution // Cell. 2009. V. 137. P. 356–368.
34. Splinter E., Heath H., Kooren J. et al. CTCF mediates long-range chromatin looping and local histone modifi cation in the betaglobin locus // Genes Dev. 2006. V. 20. P. 2349–2354.
35. Taddei A., Hediger F., Neumann F. R. et al. The function of nuclear architecture: a genetic approach // Annu. Rev. Genet. 2004. V. 38. P. 305–345.
36. Wang K.C., Yang Y.W., Liu B. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression // Nature. 2011. V. 472. P. 120–124.
37. Würtele H., Chartrand P. Genome-wide scanning of HoxB1- associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology // Chromosome Res. 2006. V. 14. P. 477–495.
38. Zhao Z., Tavoosidana G., Sjцlinder M. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions // Nat. Genet. 2006. V. 38. P. 1341–1347.