Analysis of β-globin chromatin micro-environment using a novel 3C variant, 4Cv

PLoS ONE

Volumn 5, Issue 9, 2010, Pages

  Pink, Ryan C ^a   Eskiw, Christopher H ^a,b   Caley, Daniel P ^a   Carter, David R F ^a  

^a OXFORD BROOKES UNIVERSITY   (United Kingdom)

^b BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN;

ANIMAL TISSUE; ARTICLE; CHROMATIN; CHROMOSOME STRUCTURE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE LOCUS; GENETIC VARIABILITY; MOUSE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; TRANSCRIPTION INITIATION;

ANIMALS; BETA-GLOBINS; BRAIN; CHROMATIN; CHROMOSOMES, MAMMALIAN; GENETIC TECHNIQUES; LIVER; MICE; MICE, INBRED C57BL; PROTEIN BINDING; TRANSCRIPTIONAL ACTIVATION;

MUS;

EID: 77958556789     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013045     Document Type: Article

References (55)

1. Misteli T, Soutoglou E (2009) The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol 10: 243-254.
2. de Wit E, van Steensel B (2009) Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma 118: 25-36.
3. Carter D, Eskiw C, Cook P (2008) Transcription factories. Biochem Soc Trans 36: 585-589.
4. Xu M, Cook P (2008) The role of specialized transcription factories in chromosome pairing. Biochim Biophys Acta 1783: 2155-2160.
5. Branco M, Pombo A (2007) Chromosome organization: new facts, new models. Trends Cell Biol 17: 127-134.
6. Saitoh Y, Laemmli U (1993) From the chromosomal loops and the scaffold to the classic bands of metaphase chromosomes. Cold Spring Harb Symp Quant Biol 58: 755-765.
7. Cook P (1995) A chromomeric model for nuclear and chromosome structure. J Cell Sci 108(Pt 9): 2927-2935.
8. Kumar P, Bischof O, Purbey P, Notani D, Urlaub H, et al. (2007) Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol 9: 45-56.
9. Marenduzzo D, Faro-Trindade I, Cook P (2007) What are the molecular ties that maintain genomic loops? Trends Genet 23: 126-133.
10. Chakalova L, Carter D, Fraser P (2004) RNA fluorescence in situ hybridization tagging and recovery of associated proteins to analyze in vivo chromatin interactions. Methods Enzymol 375: 479-493.
11. Carter D, Chakalova L, Osborne C, Dai Y, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32: 623-626.
12. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295: 1306-1311.
13. Tolhuis B, Palstra R, Splinter E, Grosveld F, de Laat W (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 10: 1453-1465.
14. Osborne C, Chakalova L, Brown K, Carter D, Horton A, et al. (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065-1071.
15. Osborne C, Chakalova L, Mitchell J, Horton A, Wood A, et al. (2007) Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 5: e192.
16. Blanton J, Gaszner M, Schedl P (2003) Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev 17: 664-675.
17. Murrell A, Heeson S, Reik W (2004) Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parentspecific chromatin loops. Nat Genet 36: 889-893.
18. Spilianakis C, Flavell R (2004) Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol 5: 1017-1027.
19. Bartlett J, Blagojevic J, Carter D, Eskiw C, Fromaget M, et al. (2006) Specialized transcription factories. Biochem Soc Symp: 67-75.
20. Sexton T, Umlauf D, Kurukuti S, Fraser P (2007) The role of transcription factories in large-scale structure and dynamics of interphase chromatin. Semin Cell Dev Biol 18: 691-697.
21. Marenduzzo D, Finan K, Cook P (2006) The depletion attraction: an underappreciated force driving cellular organization. J Cell Biol 175: 681-686.
22. Mitchell J, Fraser P (2008) Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 22: 20-25.
23. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348-1354.
24. Würtele H, Chartrand P (2006) Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res 14: 477-495.
25. Ling J, Li T, Hu J, Vu T, Chen H, et al. (2006) CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312: 269-272.
26. Lomvardas S, Barnea G, Pisapia D, Mendelsohn M, Kirkland J, et al. (2006) Interchromosomal interactions and olfactory receptor choice. Cell 126: 403-413.
27. Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38: 1341-1347.
28. Dostie J, Richmond T, Arnaout R, Selzer R, Lee W, et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299-1309.
29. Schoenfelder S, Sexton T, Chakalova L, Cope N, Horton A, et al. (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42: 53-61.
30. Lichter P, Cremer T, Borden J, Manuelidis L, Ward D (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80: 224-234.
31. Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, et al. (2006) Chromosome territories-a functional nuclear landscape. Curr Opin Cell Biol 18: 307-316.
32. Zirbel R, Mathieu U, Kurz A, Cremer T, Lichter P (1993) Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1: 93-106.
33. Chambeyron S, Da Silva N, Lawson K, Bickmore W (2005) Nuclear reorganisation of the Hoxb complex during mouse embryonic development. Development 132: 2215-2223.
34. Volpi E, Chevret E, Jones T, Vatcheva R, Williamson J, et al. (2000) Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113(Pt 9): 1565-1576.
35. Williams R, Broad S, Sheer D, Ragoussis J (2002) Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 272: 163-175.
36. Brown J, Leach J, Reittie J, Atzberger A, Lee-Prudhoe J, et al. (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172: 177-187.
37. Brown J, Green J, das Neves R, Wallace H, Smith A, et al. (2008) Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182: 1083-1097.
38. Kurz A, Lampel S, Nickolenko J, Bradl J, Benner A, et al. (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135: 1195-1205.
39. Mahy N, Perry P, Bickmore W (2002) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159: 753-763.
40. Brown K, Amoils S, Horn J, Buckle V, Higgs D, et al. (2001) Expression of alpha- and beta-globin genes occurs within different nuclear domains in haemopoietic cells. Nat Cell Biol 3: 602-606.
41. Ragoczy T, Telling A, Sawado T, Groudine M, Kosak S (2003) A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res 11: 513-525.
42. Ragoczy T, Bender M, Telling A, Byron R, Groudine M (2006) The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 20: 1447-1457.
43. Gribnau J, Diderich K, Pruzina S, Calzolari R, Fraser P (2000) Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. Mol Cell 5: 377-386.
44. Weintraub H, Groudine M (1976) Chromosomal subunits in active genes have an altered conformation. Science 193: 848-856.
45. Kornberg R, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98: 285-294.
46. Eskiw C, Rapp A, Carter D, Cook P (2008) RNA polymerase II activity is located on the surface of, 87 nm protein-rich factories. Manuscript submitted for publication.
47. Marshall W, Straight A, Marko J, Swedlow J, Dernburg A, et al. (1997) Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7: 930-939.
48. Chakalova L, Carter D, Debrand E, Goyenechea B, Horton A, et al. (2005) Developmental regulation of the beta-globin gene locus. Prog Mol Subcell Biol 38: 183-206.
49. Fullwood M, Liu M, Pan Y, Liu J, Xu H, et al. (2009) An oestrogen-receptoralpha- bound human chromatin interactome. Nature 462: 58-64.
50. Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
51. Branco M, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4: e138.
52. Verschure P, van Der Kraan I, Manders E, van Driel R (1999) Spatial relationship between transcription sites and chromosome territories. J Cell Biol 147: 13-24.
53. Spilianakis C, Lalioti M, Town T, Lee G, Flavell R (2005) Interchromosomal associations between alternatively expressed loci. Nature 435: 637-645.
54. Croft J, Bridger J, Boyle S, Perry P, Teague P, et al. (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145: 1119-1131.
55. Palstra R, Simonis M, Klous P, Brasset E, Eijkelkamp B, et al. (2008) Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS ONE 3: e1661.