3D fluorescent in situ hybridization using arabidopsis leaf cryosections and isolated nuclei

Plant Methods

Volumn 5, Issue 1, 2009, Pages

  Tirichine, Lela ^a,f   Andrey, Philippe ^b,c,d,e   Biot, Eric ^a   Maurin, Yves ^a,b,c,d   Gaudin, Valérie ^a  

^a LABORATOIRE DE BIOLOGIE CELLULAIRE   (France)

^b INRA   (France)

^c UNIVERSITÉ PARIS SACLAY   (France)

^d IFR 144 Neuro Sud Paris   (France)

^e SORBONNE UNIVERSITÉ   (France)

^f CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAMMALIA;

EID: 69449101914     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-5-11     Document Type: Article

References (33)

1. Chromosome territories ? a functional nuclear landscape. T Cremer M Cremer S Dietzel S Muller I Solovei S Fakan, Curr Opin Cell Biol 2006 18 3 307 316 10.1016/j.ceb.2006.04.007 16687245
2. Chromosome organization: new facts, new models. MR Branco A Pombo, Trends Cell Biol 2007 17 3 127 134 10.1016/j.tcb.2006.12.006 17197184 (Pubitemid 46343873)
3. Chromosome territories have a highly nonspherical morphology and nonrandom positioning. A Khalil JL Grant LB Caddle E Atzema KD Mills A Arneodo, Chromosome Res 2007 15 7 899 916 10.1007/s10577-007-1172-8 17926137 (Pubitemid 350160095)
4. Simultaneous localization of MLL, AF4 and ENL genes in interphase nuclei by 3D-FISH: MLL translocation revisited. M Gué JS Sun T Boudier, BMC Cancer 2006 6 20 10.1186/1471-2407-6-20 16433901 (Pubitemid 43336729)
5. The architecture of chicken chromosome territories changes during differentiation. S Stadler V Schnapp R Mayer S Stein C Cremer C Bonifer T Cremer S Dietzel, BMC Cell Biol 2004 5 1 44 10.1186/1471-2121-5-44 15555075 (Pubitemid 39615365)
6. Tissue-specific spatial organization of genomes. LA Parada PG McQueen T Misteli, Genome Biol 2004 5 7 R44 10.1186/gb-2004-5-7-r44 15239829
7. Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes. C Weierich A Brero S Stein J von Hase C Cremer T Cremer I Solovei, Chromosome Res 2003 11 5 485 502 10.1023/A:1025016828544 12971724 (Pubitemid 37041208)
8. Cytogenetics as a tool to study gene regulation. F Tessadori R van Driel P Fransz, Trends Plant Sci 2004 9 3 147 153 10.1016/j.tplants.2004.01.008 15003238 (Pubitemid 38300261)
9. Cytogenetic analyses of Arabidopsis. M Lysak P Fransz I Schubert, Methods Mol Biol: Arabidopsis protocols Humana press Inc Totowa, NJ, Salinas J, Sanchez-Serrano JJ, 2 2006 323 173 186
10. Interphase chromosome arrangement in Arabidopsis thaliana is similar in differentiated and meristematic tissues and shows a transient mirror symmetry after nuclear division. A Berr I Schubert, Genetics 2007 176 2 853 863 10.1534/genetics.107.073270 17409060 (Pubitemid 46961090)
11. Tandem repetitive transgenes and fluorescent chromatin tags alter local interphase chromosome arrangement in Arabidopsis thaliana. A Pecinka N Kato A Meister AV Probst I Schubert E Lam, J Cell Sci 2005 118 16 3751 3758 10.1242/jcs.02498 16076901 (Pubitemid 41309421)
12. Fluorescence in situ hybridization on vibratome sections of plant tissues. P Prieto G Moore P Shaw, Nat Protoc 2007 2 7 1831 1838 10.1038/nprot.2007.265 17641652
13. Chromatin organization and cell fate switch respond to positional information in Arabidopsis. S Costa P Shaw, Nature 2006 439 7075 493 496 10.1038/nature04269 16362059 (Pubitemid 43152842)
14. In situ Methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research. AP Santos E Wegel GC Allen WF Thompson E Stoger P Shaw R Abranches, Plant Methods 2006 2 18 10.1186/1746-4811-2-18 17081287
15. Influence of cell fixation on chromatin topography. S Kozubek E Lukasova J Amrichova M Kozubek A Liskova J Slotova, Anal Biochem 2000 282 1 29 38 10.1006/abio.2000.4538 10860496 (Pubitemid 30409421)
16. Analysis by atomic force microscopy of morphological changes in barley chromosomes during FISH treatment. M Shichiri D Fukushi S Sugiyama T Yoshino T Ohtani, Chromosome Res 2003 11 1 65 71 10.1023/A:1022062100358 12675307 (Pubitemid 36315359)
17. Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. F Tessadori MC Chupeau Y Chupeau M Knip S Germann R van Driel P Fransz V Gaudin, J Cell Sci 2007 120 7 1200 1208 10.1242/jcs.000026 17376962 (Pubitemid 46711838)
18. Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes. A Pecinka V Schubert A Meister G Kreth M Klatte MA Lysak J Fuchs I Schubert, Chromosoma 2004 113 5 258 269 10.1007/s00412-004-0316-2 15480725 (Pubitemid 39462368)
19. Recent progress in chromosome painting of Arabidopsis and related species. MA Lysak A Pecinka I Schubert, Chromosome Res 2003 11 3 195 204 10.1023/A:1022879608152 12769287 (Pubitemid 36549521)
20. Free-D: an integrated environment for three-dimensional reconstruction from serial sections. P Andrey Y Maurin, J Neurosci Methods 2005 145 1? 2 233 244 10.1016/j.jneumeth.2005.01.006 15922039 (Pubitemid 40732447)
21. Picture thresholding using an interactive selection method. T Ridler S Calvard, IEEE Transactions on Systems, Man and Cybernetics 1978 8 630 632 10.1109/TSMC.1978.4310039
22. Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, Methods, pitfalls. O Ronneberger D Baddeley F Scheipl PJ Verveer H Burkhardt C Cremer L Fahrmeir T Cremer B Joffe, Chromosome Res 2008 16 3 523 562 10.1007/s10577-008-1236-4 18461488 (Pubitemid 351644867)
23. P Soille, Morphological image analysis: Principles and applications Berlin: Springer Verlag 2 2003
24. Marching cubes: a high resolution (3D) surface construction algorithm. W Lorensen H Cline, AMC Computer Graphics 1987 21 4 163 169 10.1145/37402.37422
25. A Language and Environment for Statistical Computing. R Development Core Team R, R Foundation for Statistical Computing Vienna, Austria 2007 http://www.R-project.org
26. Preservation of large-scale chromatin structure in FISH experiments. C Hepperger S Otten J von Hase S Dietzel, Chromosoma 2007 116 2 117 133 10.1007/s00412-006-0084-2 17119992 (Pubitemid 46404508)
27. Dynamic elastic behavior of alpha-satellite DNA domains visualized in situ in living human cells. RD Shelby KM Hahn KF Sullivan, J Cell Biol 1996 135 3 545 557 10.1083/jcb.135.3.545 8909532 (Pubitemid 26372914)
28. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). I Solovei A Cavallo L Schermelleh F Jaunin C Scasselati D Cmarko C Cremer S Fakan T Cremer, Exp Cell Res 2002 276 1 10 23 10.1006/excr.2002.5513 11978004 (Pubitemid 34948347)
29. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. A Bolzer G Kreth I Solovei D Koehler K Saracoglu C Fauth S Muller R Eils C Cremer MR Speicher T Cremer, PLoS Biol 2005 3 5 e157 10.1371/journal.pbio.0030157 15839726 (Pubitemid 40958405)
30. Quantitative assessment of the alteration of chromatin during the course of FISH procedures. Fluorescent in situ hybridization. F Mongelard C Vourc'h M Robert-Nicoud Y Usson, Cytometry 1999 36 2 96 101 10.1002/(SICI)1097- 0320(19990601)36:2<96::AID-CYTO23.0.CO;2-X 10554156
31. Optimization of nuclear transcript detection by FISH and combination with fluorescence immunocytochemical detection of transcription factors. C Jolly F Mongelard M Robert-Nicoud C Vourc'h, J Histochem Cytochem 1997 45 12 1585 1592 9389761
32. The random primer labeling technique applied to in situ hybridization on tissue sections. M Thomas-Cavallin O Ait-Ahmed, J Histochem Cytochem 1988 36 10 1335 1340 3138309
33. Rapid fluorescence in situ hybridization with repetitive DNA probes: quantification by digital image analysis. D Celeda K Aldinger FM Haar M Hausmann M Durm H Ludwig C Cremer, Cytometry 1994 17 1 13 25 10.1002/cyto.990170103 8001456