Structural analysis of interphase X-chromatin based on statistical shape theory

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1783, Issue 11, 2008, Pages 2089-2099

  Yang, Siwei ^a   Illner, Doris ^b   Teller, Kathrin ^b   Solovei, Irina ^b   van Driel, Roel ^c   Joffe, Boris ^b   Cremer, Thomas ^b,d   Eils, Roland ^a   Rohr, Karl ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d Munich Center for Integrated Protein Science   (Germany)

Author keywords

3D chromatin structure; 3D multicolor FISH microscopy; Cell nuclei; Genomic region; Geometrical morphometrics; Non rigid image registration; Shape distribution; Shape normalization; Statistical shape theory

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMATIN STRUCTURE; CONTROLLED STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; HUMAN CELL; INTERPHASE; MORPHOMETRICS; NUCLEAR SHAPE; PRIORITY JOURNAL; STRUCTURE ANALYSIS; X CHROMATIN; X CHROMOSOME;

CHROMOSOMES, HUMAN, X; FEMALE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INTERPHASE; MODELS, GENETIC; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION;

EID: 53449088104     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2008.08.007     Document Type: Article

References (48)

1. Fraser P., and Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 447 (2007) 413-417
2. Lanctôt C., Cheutin T., Cremer M., Cavalli G., and Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8 2 (2007) 104-115
3. Sexton T., Schober H., Fraser P., and Gasser S. Gene regulation through nuclear organization. Nat. Struct. Mol. Biol. 14 (2007) 1049-1055
4. Soutoglou E., and Misteli T. Mobility and immobility of chromatin in transcription and genome stability. Curr. Opin. Genet. Dev. 17 (2007) 435-442
5. Chuang C., Carpenter A., Fuchsova B., Johnson T., de Lanerole P., and Belmont A.S. Long-range directional movement of an interphase chromosome site. Curr. Biol. 16 (2006) 825-831
6. Chuang C., and Belmont A. Moving chromatin within the interphase nucleus-controlled transitions?. Semin. Cell Dev. Biol. 18 (2007) 698-706
7. Dundr M., Ospina J., Sung M., John S., Upender M., Ried T., Hager G., and Matera A. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J. Cell Biol. 179 (2007) 1095-1103
8. Kosak S., and Groudine M. Form follows function: the genomic organization of cellular differentiation. Genes Dev. 18 (2004) 1371-1384
9. Ragoczy T., Bender M., Telling A., Byron R., and Groudine M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev. 20 (2006) 1447-1457
10. Lyon M. Gene action in the x-chromosome of the mouse (Mus musculus l.). Nature 190 (1961) 372-373
11. Sproul D., Gilbert N., and Bickmore W. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet. 6 (2005) 775-781
12. Sachs R., Engh G., Trask B., Yokota H., and Hearst J. A random-walk/giant-loop model for interphase chromosomes. PNAS 92 (1995) 2710-2714
13. Yokota H., van den Engh G., Jearst J., Sachs R., and Trask B. Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human g0/g1 interphase nucleus. J. Cell Biol. 130 (1995) 1239-1249
14. Ostashevsky J. A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. Mol. Biol. Cell 9 (1998) 3031-3040
15. Skalníková M., Kozubek S., Lukášova E., Bártová E., Jirsová P., Cafourková A., Koutná I., and Kozubek M. Spatial arrangement of genes, centromeres and chromosomes in human blood cell nuclei and its changes during the cell cycle, differentiation and after irradiation. Chromosom. Res. 8 (2000) 487-499
16. Shopland L.S., Lynch C.R., Peterson K.A., Thornton K., Kepper N., von Hase J., Stein S., Vincent S., Molloy K.R., Kreth G., Cremer C., Bult C.J., and Brien T.P.O. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biol. 174 1 (2006) 27-38
17. Zink D., Amaral M.D., Englmann A., Lang S., Clarke L.A., Rudolph C., Alt F., Luther K., Braz C., Sadoni N., Rosenecker J., and Schindelhauer D. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J. Cell Biol. 166 6 (2004) 815-825
18. Bohn M., Heermann D.W., and van Driel R. Random loop model for long polymers. Phys. Rev. E 76 (2007) 051805
19. Münkel C., Eils R., Dietzel S., Zink D., Mehring C., Wedemann G., Cremer T., and Langowski J. Compartmentalization of interphase chromosomes observed in simulation and experiment. J. Mol. Biol. 285 (1999) 1053-1065
20. Lawrence J.B., Singer R.H., and McNeil J.A. Interphase and metaphase resolution of different distances within the human dystrophin gene. Science 249 (1990) 928-932
21. Gilbert N., Boyle S., Fiegler H., Woodfine K., Carter N.P., and Bickmore W.A. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118 (2004) 555-566
22. Parreira L., Telhada M., Ramos C., Hernandez R., Neves H., and Carmo-Fonseca M. The spatial distribution of human immunoglobulin genes within the nucleus: evidence for gene topography independent of cell type and transcriptional activity. Hum. Genet. 100 (1997) 588-594
23. Cremer M., von Hase J., Volm T., Brero A., Kreth G., Walter J., Fischer C., Solovei I., Cremer C., and Cremer T. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosom. Res. 9 7 (2001) 541-567
24. Zlatanova J., Leuba S., and van Holde K. Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys. J. 74 (1998) 2554-2566
25. Kozubek S., Lukásová E., Jirsová P., Koutná I., Kozubek M., Ganová A., Bártová E., Falk M., and Paseková R. 3D structure of the human genome: order in randomness. Chromosoma 111 (2002) 321-331
26. Ronneberger O., Baddeley D., Scheipl F., Verveer P., Burkhardt H., Cremer C., Fahrmeir L., Cremer T., and Joffe B. Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls. Chromosom. Res. 16 (2008) 523-562
27. Götze S., Mateos-Langerak J., Gierman H.J., de Leeuw W., Giromus O., Indemans M.H.G., Koster J., Ondrej V., Versteeg R., and van Driel R. The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol. Cell. Biol. 27 12 (2007) 4475-4487
28. Adams D.C., Rohlf F.J., and Slice D.E. Geometric morphometrics: ten years of progress following the 'revolution'. Monit. Zool. Ital. 71 (2004) 5-16
29. Yang S., Götze S., Mateos-Langerak J., van Driel R., Eils R., and Rohr K. Variability analysis of the large-scale structure of interphase chromatin fiber based on statistical shape theory. Advances in Mass-Data, Analysis of Images and Signals in Medicine, Biotechnology and Chemistry (MDA) (2007) 37-46
30. Solovei I., Walter J., Cremer M., Habermann F., Schermelleh L., and Cremer T. FISH: a practical approach. Ch. 7 FISH on three-dimensionally preserved nuclei (2002), Oxford University Press, Oxford 119-157
31. M. Cremer, S. Müller, D. Köhler, A. Brero, I. Solovei, Cell preparation and multicolor FISH in 3D preserved cultured mammalian cells, CSH Protocols, doi:10.1101/pdb.prot4723 (2007).
32. Walter J., Joffe B., Bolzer A., Albiez H., Benedetti P., Müller S., Speicher M., Cremer T., Cremer M., and Solovei I. Towards many colors in FISH on 3D-preserved interphase nuclei. Cytogenet. Genome Res. 114 (2006) 367-378
33. Mardia K.V., and Jupp P.E. Directional Statistics (2000), John Wiley and Sons, Chichester
34. Chikuse Y., and Jupp P.E. A test of uniformity on shape spaces. J. Multivar. Anal. 88 (2004) 163-176
35. Horn B. Closed-form solution of absolute orientation using unit quaternions. J. Opt. Soc. Am. A 4 (1987) 629-642
36. Dryden I., and Mardia K. Statistical Shape Analysis (1998), John Wiley and Sons, Chichester
37. Fisher N.I., Lewis T., and Embleton B. Statistical analysis of spherical data (1987), The Press Syndicate of the University of Cambridge, Cambridge
38. Jupp P.E., and Mardia K.V. A general correlation coefficient for directional data and related regression problems. Biometrika 67 1 (1980) 163-173
39. Yang S., Köhler D., Teller K., Cremer T., Baccon P.L., Heard E., Eils R., and Rohr K. Non-rigid registration of 3D multichannel microscopy images of cell nuclei. In: Larsen R., Nielsen M., and Sporring J. (Eds). Proceedings of the 9th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06), Lecture Notes in Computer Science 4190 (2006), Springer-Verlag Berlin Heidelberg, Copenhagen, Denmark 907-914
40. Rohlf F.J., and Marcus I.F. A revolution in morphometrics. Trends Ecol. Evol. 8 (1993) 129-132
41. S. T. Kosak, D. Scalzo, S. V. Alworth, F. Li, S. Palmer, T. Enver, J. S. Lee, M. Groudine, Coordinate gene regulation during hematopoiesis is related to genomic organization, PLoS Biology 5 (11), e309 doi:10.1371/journal.pbio.0050309.
42. Küpper K., Kölbl A., Biener D., Dittrich S., von Hase J., Thormeyer T., Fiegler H., Carter N., Speicher M., Cremer T., and Cremer M. Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116 (2007) 285-306
43. Ferreira J., Paolella G., Ramos C., and Lamond A.I. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J. Cell Biol. 139 7 (1997) 1597-1610
44. Sadoni N., Langer S., Fauth C., Bernardi G., Cremer T., Turner B.M., and Zink D. Nuclear organization of mammalian genomes. polar chromosome territories build up functionally distinct higher order compartments. J. Cell Biol. 146 (1999) 1211-1226
45. Federico C., Cantarella C.D., Di Mare P., Tosi S., and Saccone S. The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density. Chromosoma 117 4 (2008) 399-410
46. Murmann A.E., Gao J., Encinosa M., Gautier M., Peter M.E., Eils R., Lichter P., and Rowley J.D. Local gene density predicts the spatial position of genetic loci in the interphase nucleus. Exp. Cell Res. 311 (2005) 14-26
47. Ibanez L., Schroeder W., Ng L., and Cates J. The ITK Software Guide (2005), Kitware, New York
48. Schroeder W., Matin K., and Lorensen B. The Visualization Toolkit, An Object-Oriented Approach to 3D Graphics. third ed. (2003), Kitware, New York