Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

Genome Biology

Volumn 14, Issue 11, 2013, Pages

  Grob, Stefan ^a   Schmid, Marc W ^a   Luedtke, Nathan W ^b   Wicker, Thomas ^a   Grossniklaus, Ueli ^a  

^a Botanical Institute of the University of Basel   (Switzerland)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKININ; HISTONE H3; EUCHROMATIN; GENETIC MARKER; HETEROCHROMATIN; HISTONE;

ARABIDOPSIS; ARTICLE; CELL NUCLEUS; CENTROMERE; CHROMOSOME 4; CHROMOSOME ANALYSIS; CHROMOSOME CONDENSATION; CHROMOSOME STRUCTURE; CYTOGENETICS; DNA METHYLATION; DROSOPHILA; EPIGENETICS; EUCHROMATIN; FLUORESCENCE IN SITU HYBRIDIZATION; GENE MAPPING; GENOME SIZE; HETEROCHROMATIN; HIGH THROUGHPUT SEQUENCING; HISTONE MODIFICATION; NONHUMAN; NUCLEOLAR LOCALIZATION SIGNAL; PLANT CHROMOSOME; PLANT GENOME; PROTEIN INTERACTION; SEEDLING; TELOMERE; CHEMISTRY; DNA SEQUENCE; GENETIC MARKER; GENETICS; METABOLISM; PRINCIPAL COMPONENT ANALYSIS;

ARABIDOPSIS;

ARABIDOPSIS; CELL NUCLEUS; CENTROMERE; CHROMOSOMES, PLANT; DNA METHYLATION; EPIGENOMICS; EUCHROMATIN; GENETIC MARKERS; GENOME, PLANT; HETEROCHROMATIN; HISTONES; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 84887932087     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-11-r129     Document Type: Article

References (53)

1. Dittmer TA, Stacey NJ, Sugimoto-Shirasu K, Richards EJ. LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana. Plant Cell 2007, 19:2793-2803.
2. Arnott S, Hukins DW Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun 1972, 47:1504-1509.
3. Roudier FCO, Ahmed I, Rard CBE, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut LEN, s BDE, Drevensek SEP, Barneche FED, Rozier SDE, Brunaud VER, Aubourg SEB, Schnittger A, Bowler C, Martin-Magniette M-L, Robin SEP, Caboche M, Colot V Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 2011, 30:1928-1938.
4. Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143:212-224.
5. Pfluger J, Wagner D Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 2007, 10:645-652.
6. Rabl C: Über die Zelltheilung. Morphologisches Jahrbuch 1885, 10:214-330.
7. Heitz E Das Heterochromatin der Moose. 1 Jahrb Wiss Bot 1929, 69:762-818.
8. La Cour L Heterochromatin and the organization of nucleoli in plants. Heredity 1951, 5:37.
9. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D The dynamic architecture of Hox gene clusters. Science 2011, 334:222-225.
10. Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res 2010, 38:4325-4336.
11. McClintock B Chromosome morphology in Zea mays. Science 1929, 69:629.
12. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 2000, 100:367-376.
13. Laboratory TCSH, Washington University Genome Sequencing Center, Consortium PBAS: The complete sequence of a heterochromatic island from a higher eukaryote. Cell 2000, 100:377-386.
14. Fransz P, Armstrong S, Alonso-Blanco C, Fischer TC, Torres-Ruiz RA, Jones G Cytogenetics for the model system Arabidopsis thaliana. Plant J 1998, 13:867-876.
15. Dekker J, Rippe K, Dekker M, Kleckner N Capturing chromosome conformation. Science 2002, 295:1306-1311.
16. De Wit E, De Laat W A decade of 3C technologies: insights into nuclear organization. Genes Dev 2012, 26:11-24.
17. Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 2006, 38:1341-1347.
18. Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
19. Louwers M, Bader R, Haring M, Van Driel R, De Laat W, Stam M Tissue- and expression level-specific chromatin looping at maize b1 epialleles. Plant Cell 2009, 21:832-842.
20. Crevillen P, Sonmez C, Wu Z, Dean C A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization. EMBO J 2012, 32:140-148.
21. Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen S MORC family ATPases required for heterochromatin condensation and gene silencing. Science 2012, 336:1448-1451.
22. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 2012, 148:458-472.
23. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19:1639-1645.
24. Splinter E, de Wit E, van de Werken HJG, Klous P, De Laat W Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods 2012, 58:221-230.
25. Hou H, Zhou Z, Wang Y, Wang J, Kallgren SP, Kurchuk T, Miller EA, Chang F, Jia S Csi1 links centromeres to the nuclear envelope for centromere clustering. J Cell Biol 2012, 199:735-744.
26. de Nooijer S, Wellink J, Mulder B, Bisseling T Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res 2009, 37:3558-3568.
27. Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci U S A 2002, 99:14584-14589.
28. Fang Y, Spector DL Centromere positioning and dynamics in living Arabidopsis plants. Mol Biol Cell 2005, 16:5710-5718.
29. Gheldof N, Tabuchi TM, Dekker J The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc Natl Acad Sci U S A 2006, 103:12463-12468.
30. Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, De Laat W, van Lohuizen M, van Steensel B Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet 2011, 7:e1001343.
31. Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J 2012, 73:77-90.
32. Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 2013, 152:352-364.
33. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005, 102:15545-15550.
34. La Bastide DM, Huang E, Spiegel L, Gnoj L, Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, et al Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 2000, 408:823-826.
35. Maul GG, Deaven L Quantitative determination of nuclear pore complexes in cycling cells with differing DNA content. J Cell Biol 1977, 73:748-760.
36. Schubert V, Berr A, Meister A Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness. Chromosoma 2012, 121:369-387.
37. Jin QW, Fuchs J, Loidl J Centromere clustering is a major determinant of yeast interphase nuclear organization. J Cell Sci 2000, 113:1903-1912.
38. Duan Z, Andronescu M, Schutz K, Mcilwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS A three-dimensional model of the yeast genome. Nature 2010, 465:363-367.
39. Sanyal A, Baù D, Marti-Renom MA, Dekker J Chromatin globules: a common motif of higher order chromosome structure? Curr Opin Cell Biol 2011, 23:325-331
40. Armstrong SJ, Franklin FC, Jones GH Nucleolus-associated telomere clustering and pairing precede meiotic chromosome synapsis in Arabidopsis thaliana. J Cell Sci 2001, 114:4207-4217.
41. Watanabe K, Pecinka A, Meister A, Schubert I, Lam E DNA hypomethylation reduces homologous pairing of inserted tandem repeat arrays in somatic nuclei of Arabidopsis thaliana. Plant J 2005, 44:531-540.
42. Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo D-H, Shi J, Gao Z, Han F, Lee H, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK, Presting GG Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons. PLoS Genet 2009, 5:e1000743.
43. Nagaki K, Song J, Stupar RM, Parokonny AS, Yuan Q, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang J Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 2003, 163:759-770.
44. Henikoff S The centromere paradox: stable inheritance with rapidly evolving DNA. Science 2001, 293:1098-1102.
45. Berr A, Pecinka A, Meister A, Kreth G, Fuchs J, Blattner FR, Lysak MA, Schubert I Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata. Plant J 2006, 48:771-783.
46. Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 2003, 163:1221-1225.
47. Shibata F Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci 2004, 117:2963-2970.
48. Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001, 29:102-105.
49. Langmead B, Trapnell C, Pop M, Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
50. Schmid MW, Schmidt A, Klostermeier UC, Barann M, Rosenstiel P, Grossniklaus U A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLoS ONE 2012, 7:e29685.
51. Edgar R, Domrachev M, Lash AE Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-10.
52. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2011, 40:D1202-D1210.
53. Development Core Team R: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2008. http://www.R-project.org. ISBN 3-900051-07-0.