Abstract
The spatial organization of the genome within the interphase nucleus is important for mediating genome functions. The radial organization of chromosome territories has been studied traditionally using two-dimensional fluorescence in situ hybridization (FISH) using labeled whole chromosome probes. Information from 2D-FISH images is analyzed quantitatively and is depicted in the form of the spatial distribution of chromosomes territories. However, to the best of our knowledge no open-access tools are available to delineate the position of chromosome territories from 2D-FISH images. In this chapter we present a methodology termed Image Analysis of Chromosomes for computing their localization (IMACULAT). IMACULAT is an open-access, automated tool that partitions the cell nucleus into shells of equal area or volume and computes the spatial distribution of chromosome territories.
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References
Alberts B, Lewis J, Raff M et al (2007) Molecular biology of the cell, 5th edn. Garland Science, New York
Boyle S, Gilchrist S, Bridger JM et al (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10:211–219
Cremer C, Zorn C, Cremer T (1974) An ultraviolet laser microbeam for 257 nm. Microsc Acta 75:331–337
Croft JA, Bridger JM, Boyle S et al (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145:1119–1131
Zorn C, Cremer C, Cremer T et al (1979) Unscheduled DNA synthesis after partial UV irradiation of the cell nucleus. Distribution in interphase and metaphase. Exp Cell Res 124:111–119
Meaburn KJ, Misteli T (2007) Cell biology: chromosome territories. Nature 445:379–781
Parada L, Misteli T (2002) Chromosome positioning in the interphase nucleus. Trends Cell Biol 12:425–432
Foster HA, Bridger JM (2005) The genome and the nucleus: a marriage made by evolution. Chromosoma 114:212–229
Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2:292–301
Tanabe H, Muller S, Neusser M et al (2002) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A 99: 4424–4429
Foster HA, Griffin DK et al (2012) Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues. BMC Cell Biol 13:30
Strouboulis J, Wolffe AP (1996) Functional compartmentalization of the nucleus. J Cell Sci 109:1991–2000
van Driel R, Humbel B, de Jong L (1991) The nucleus: a black box being opened. J Cell Biochem 47:311–316
Fraser P, Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 447:413–417
Bickmore WA, van Steensel B (2013) Genome architecture: domain organization of interphase chromosomes. Cell 152:1270–1284
Brown JM, Leach J, Reittie JE et al (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172:177–187
Eils R, Dietzel S, Bertin E et al (1996) Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. J Cell Biol 135:1427–1440
Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119–1130
Ferrai C, Xie SQ, Luraghi P et al (2010) Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol 8:e1000270
Chubb JR, Boyle S, Perry P et al (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439–445
Kim SH, McQueen PG, Lichtman MK et al (2004) Spatial genome organization during T-cell differentiation. Cytogenet Genome Res 105:292–301
Hewitt SL, High FA, Reiner SL et al (2004) Nuclear repositioning marks the selective exclusion of lineage-inappropriate transcription factor loci during T helper cell differentiation. Eur J Immunol 34:3604–3613
Zink D, Amaral MD, Englmann A et al (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166:815–825
Gilbert N, Gilchrist S, Bickmore WA (2005) Chromatin organization in the mammalian nucleus. Int Rev Cytol 242:283–336
Casolari JM, Brown CR, Drubin DA et al (2005) Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 19:1188–1198
Kuroda M, Tanabe H, Yoshida K et al (2004) Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci 117:5897–5903
Panning MM, Gilbert DM (2005) Spatio-temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells. J Cell Biochem 95:74–82
Parada LA, McQueen PG, Misteli T (2004) Tissue-specific spatial organization of genomes. Genome Biol 5:R44
Mehta IS, Kulashreshtha M, Chakraborty S et al (2013) Chromosome territories reposition during DNA damage-repair response. Genome Biol 14:R135
Volpi EV, Bridger JM (2008) FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 45:385–386
Mehta I, Chakraborty S, Rao BJ (2013) IMACULAT – an open access package for the quantitative analysis of chromosome localization in the nucleus. PLoS One 8:e61386
Mehta IS, Amira M, Harvey AJ et al (2010) Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts. Genome Biol 11:R5
Bridger JM, Herrmann H, Munkel C et al (1998) Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin. J Cell Sci 111:1241–1253
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Chakraborty, S., Mehta, I., Kulashreshtha, M., Rao, B.J. (2015). Quantitative Analysis of Chromosome Localization in the Nucleus. In: Hancock, R. (eds) The Nucleus. Methods in Molecular Biology, vol 1228. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1680-1_17
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DOI: https://doi.org/10.1007/978-1-4939-1680-1_17
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