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Technological Solutions in Human Interphase Cytogenetics

Chapter

Abstract

Numerous interphase molecular cytogenetic approaches are useful for the analysis of chromosomes in normal and abnormal human cells. Interphase fluorescence in situ hybridization techniques offer unique possibilities to visualize individual chromosomes or chromosomal regions in single nondividing cells isolated from any given tissue. Despite technological difficulties encountered during studying human interphase chromosomes in health and disease, molecular cytogenetics or cytogenomics (“chromosomics”) does provide solutions for high-resolution single-cell analysis of genome organization, structure, and behavior at all stages of the cell cycle. However, usually relatively little attention is paid to interphase molecular cytogenetics in current biomedical literature. Looking through the voluminous amount of original research papers and reviews dedicated to human interphase chromosomes, one can conclude that the technological aspects of studying human interphase chromosomes applied to basic and clinical research are rarely addressed. In an attempt to fill this gap, the present chapter provides a description of technological solutions in human interphase cytogenetics.

Keywords

Preimplantation Genetic Diagnosis Interphase Nucleus Interphase Chromosome Molecular Cytogenetic Technique Asynchronous Replication 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors are supported by DLR/BMBF (RUS 2011–2013) and RFFI grant program 12-04-00215-а (Russian Federation, 2012–2014). We gratefully acknowledge the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, Baltimore, MD, USA for providing the brain tissue samples for I-FISH experiments (partially shown in Figs. 11.1, 11.3, 11.4, 11.5, 11.6, and 11.8).

References

  1. Amiel A, Avivi L, Gaber E, Fejgin MD (1998) Asynchronous replication of allelic loci in Down syndrome. Eur J Hum Genet 6(4):359–364PubMedCrossRefGoogle Scholar
  2. Amiel A, Korenstein A, Gaber E, Avivi L (1999) Asynchronous replication of alleles in genomes carrying an extra autosome. Eur J Hum Genet 7(2):223–230PubMedCrossRefGoogle Scholar
  3. Aubert G, Hills M, Lansdorp PM (2012) Telomere length measurement-caveats and a critical assessment of the available technologies and tools. Mutat Res 730(1–2):59–67PubMedGoogle Scholar
  4. Baumgartner A, Weier JF, Weier H-UG (2006) Chromosome-specific DNA repeat probes. J Histochem Cytochem 54:1363–1370PubMedCrossRefGoogle Scholar
  5. Bejjani BA, Shaffer LG (2008) Clinical utility of contemporary molecular cytogenetics. Annu Rev Genomics Hum Genet 9:71–86PubMedCrossRefGoogle Scholar
  6. Bridger JM, Volpi EV (eds) (2010) Fluorescence in situ hybridization (FISH): protocols and applications. Humana Press, New YorkGoogle Scholar
  7. Carter NP (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39:S16–S21PubMedCrossRefGoogle Scholar
  8. Cremer T, Landegent J, Brückner A, Scholl HP, Schardin M, Hager HD et al (1986) Detection of chromosome aberrations in the human interphase nucleus by visualization of specific target DNAs with radioactive and non-radioactive in situ hybridization techniques: diagnosis of trisomy 18 with probe L1.84. Hum Genet 74(4):346–352PubMedCrossRefGoogle Scholar
  9. Dundas SR, Boyle S, Bellamy CO, Hawkins W, Garden OJ, Ross JA, Bickmore W (2001) Dual Y-chromosome painting and immunofluorescence staining of archival human liver transplant biopsies. J Histochem Cytochem 49:1321–1322PubMedCrossRefGoogle Scholar
  10. Durm M, Haar F-M, Hausmann M, Ludwig H, Cremer C (1997) Optimized Fast-FISH with α-satellite probes: acceleration by microwave activation. Braz J Med Biol Res 30(1):15–22PubMedCrossRefGoogle Scholar
  11. Ensminger AW, Chess A (2004) Coordinated replication timing of monoallelically expressed genes along human autosomes. Hum Mol Genet 13:651–658PubMedCrossRefGoogle Scholar
  12. Fung J, Weier H-UG, Pedersen RA (2001) Detection of structural and numerical chromosome abnormalities in interphase cells using spectral imaging. J Histochem Cytochem 49:797–798PubMedCrossRefGoogle Scholar
  13. Gersen SL, Keagle MB (2005) The principles of clinical cytogenetics, 2nd edn. Humana Press, Totowa, NJCrossRefGoogle Scholar
  14. Goetze S, Mateos-Langerak J, van Driel R (2007) Three-dimensional genome organization in interphase and its relation to genome function. Semin Cell Dev Biol 18(5):707–714PubMedCrossRefGoogle Scholar
  15. Halder A, Jain M, Kabra M, Gupta N (2008) Mosaic 22q11.2 microdeletion syndrome: diagnosis and clinical manifestations of two cases. Mol Cytogenet 1:18PubMedCrossRefGoogle Scholar
  16. Heng HH, Squire J, Tsui LC (1992) High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci U S A 89(20):9509–9513PubMedCrossRefGoogle Scholar
  17. Iourov IY (2009) Microscopy and imaging systems. In: Liehr T (ed) Fluorescence in situ hybridization (FISH)—application guide. Springer Verlag, Berlin, pp 75–84CrossRefGoogle Scholar
  18. Iourov IY (2012) To see an interphase chromosome or: how a disease can be associated with specific nuclear genome organization. BioDiscovery 4:5. doi: 10.7750/BioDiscovery.2012.4.5 Google Scholar
  19. Iourov IY, Soloviev IV, Vorsanova SG, Monakhov VV, Yurov YB (2005) An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics. J Histochem Cytochem 53:401–408PubMedCrossRefGoogle Scholar
  20. Iourov IY, Vorsanova SG, Yurov YB (2006a) Chromosomal variations in mammalian neuronal cells: known facts and attractive hypotheses. Int Rev Cytol 249:143–191PubMedCrossRefGoogle Scholar
  21. Iourov IY, Vorsanova SG, Pellestor F, Yurov YB (2006b) Brain tissue preparations for chromosomal PRINS labeling. Methods Mol Biol 334:123–132PubMedGoogle Scholar
  22. Iourov IY, Vorsanova SG, Yurov YB (2006c) Intercellular genomic (chromosomal) variations resulting in somatic mosaicism: mechanisms and consequences. Curr Genomics 7:435–446CrossRefGoogle Scholar
  23. Iourov IY, Liehr T, Vorsanova SG, Yurov YB (2007) Interphase chromosome-specific multicolor banding (ICS-MCB): a new tool for analysis of interphase chromosomes in their integrity. Biomol Eng 24:415–417PubMedCrossRefGoogle Scholar
  24. Iourov IY, Vorsanova SG, Yurov YB (2008a) Recent patents on molecular cytogenetics. Recent Pat DNA Gene Seq 2:6–15PubMedCrossRefGoogle Scholar
  25. Iourov IY, Vorsanova SG, Yurov YB (2008b) Molecular cytogenetics and cytogenomics of brain diseases. Curr Genomics 9:452–465PubMedCrossRefGoogle Scholar
  26. Iourov IY, Vorsanova SG, Yurov YB (2008c) Fluorescence intensity profiles of in situ hybridization signals depict genome architecture within human interphase nuclei. Tsitol Genet 42(5):3–8PubMedGoogle Scholar
  27. Iourov IY, Vorsanova SG, Liehr T, Yurov YB (2009a) Aneuploidy in the normal, Alzheimer’s disease and ataxia-telangiectasia brain: differential expression and pathological meaning. Neurobiol Dis 34:212–220PubMedCrossRefGoogle Scholar
  28. Iourov IY, Vorsanova SG, Liehr T, Kolotii AD, Yurov YB (2009b) Increased chromosome instability dramatically disrupts neural genome integrity and mediates cerebellar degeneration in the ataxia-telangiectasia brain. Hum Mol Genet 18:2656–2669PubMedCrossRefGoogle Scholar
  29. Iourov IY, Vorsanova SG, Soloviev IV, Yurov YB (2009c) Interphase FISH: detection of intercellular genomic variations and somatic chromosomal mosaicism. In: Liehr T (ed) Fluorescence in situ hybridization (FISH)—application guide. Springer, Berlin, pp 301–311CrossRefGoogle Scholar
  30. Iourov IY, Vorsanova SG, Yurov YB (2010) Somatic genome variations in health and disease. Curr Genomics 11(6):387–396PubMedCrossRefGoogle Scholar
  31. Iourov IY, Vorsanova SG, Yurov YB (2012) Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics 13(6):477–488PubMedCrossRefGoogle Scholar
  32. Klewes L, Höbsch C, Katzir N, Rourke D, Garini Y, Mai S (2011) Novel automated three-dimensional genome scanning based on the nuclear architecture of telomeres. Cytometry A 79(2):159–166PubMedGoogle Scholar
  33. Krueger C, Osborne CS (2006) Raising the curtains on interchromosomal interactions. Trends Genet 22:637–639PubMedCrossRefGoogle Scholar
  34. Lee C, Wevrick R, Fisher RB, Ferguson-Smith MA, Lin CC (1997) Human centromeric DNAs. Hum Genet 100:291–304PubMedCrossRefGoogle Scholar
  35. Leitch AR (2000) Higher levels of organization in the interphase nucleus of cycling and differentiated cells. Microbiol Mol Biol Rev 64(1):138–152PubMedCrossRefGoogle Scholar
  36. Levsky JM, Singer RH (2003) Fluorescence in situ hybridization: past, present and future. J Cell Sci 116(pt 14):2833–2838PubMedCrossRefGoogle Scholar
  37. Liehr T (2009) Fluorescence in situ hybridization (FISH)—application guide. Springer, BerlinCrossRefGoogle Scholar
  38. Liehr T, Claussen U (2002) Multicolor-FISH approaches for the characterization of human chromosomes in clinical genetics and tumor cytogenetics. Curr Genomics 3:231–235CrossRefGoogle Scholar
  39. Liehr T, Pfeiffer RA, Trautmann U, Gebhart E (1998) Centromeric alphoid DNA heteromorphisms of chromosome 22 as revealed by FISH-technique. Clin Genet 53:231–232PubMedCrossRefGoogle Scholar
  40. Liehr T, Heller A, Starke H, Rubtsov N, Trifonov V, Mrasek K, Weise A, Kuechler A, Claussen U (2002) Microdissection based high resolution multicolor banding for all 24 human chromosomes. Int J Mol Med 9:335–339PubMedGoogle Scholar
  41. Liehr T, Starke H, Weise A, Lehrer H, Claussen U (2004) Multicolor FISH probe sets and their applications. Histol Histopathol 19:229–237PubMedGoogle Scholar
  42. Litmanovitch T, Altaras MM, Dotan A, Avivi L (1998) Asynchronous replication of homologous alpha-satellite DNA loci in man is associated with nondisjunction. Cytogenet Cell Genet 81(1):26–35PubMedCrossRefGoogle Scholar
  43. Lu CM, Kwan J, Baumgartner A, Weier JF, Wang M, Escudero T, Munne S, Zitzelsberger HF, Weier H-UG (2009) DNA probe pooling for rapid delineation of chromosomal breakpoints. J Histochem Cytochem 57:587–597PubMedCrossRefGoogle Scholar
  44. Manvelyan M, Hunstig F, Mrasek K, Bhatt S, Pellestor F, Weise A, Liehr T (2008) Position of chromosomes 18, 19, 21 and 22 in 3D-preserved interphase nuclei of human and gorilla and white hand gibbon. Mol Cytogenet 1:9PubMedCrossRefGoogle Scholar
  45. Marcais B, Vorsanova SG, Roizes G, Yurov YB (1999) Analysis of alphoid DNA variation and kinetochore size in human chromosome 21: evidence against pathological significance of alphoid satellite DNA diminutions. Tsitol Genet 33(1):25–31Google Scholar
  46. Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T (2009) Disease-specific gene repositioning in breast cancer. J Cell Biol 187:801–812PubMedCrossRefGoogle Scholar
  47. Mitelman F, Johanson B, Martens F (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233–245PubMedCrossRefGoogle Scholar
  48. Nicholson JM, Duesberg P (2009) On the karyotypic origin and evolution of cancer cells. Cancer Genet Cytogenet 194:96–110PubMedCrossRefGoogle Scholar
  49. Nietzel A, Rocchi M, Starke H, Heller A, Fiedler W, Wlodarska I et al (2001) A new multicolor-FISH approach for the characterization of marker chromosomes: centromere-specific multicolor-FISH (cenM-FISH). Hum Genet 108:199–204PubMedCrossRefGoogle Scholar
  50. Raap A, Florijn RJ, Blonden LA, Wiegant J, Vaandrager J-W, Vrolijk H et al (1996) Fiber FISH as a DNA mapping tool. Methods 9(1):67–73PubMedCrossRefGoogle Scholar
  51. Rouquette J, Cremer C, Cremer T, Fakan S (2010) Functional nuclear architecture studied by microscopy: present and future. Int Rev Cell Mol Biol 282:1–90PubMedCrossRefGoogle Scholar
  52. Schrock E, du Manoir S, Veldman T, Schoell B, Weinberg J, Ferguson-Smith MA et al (1996) Multicolor spectral karyotyping of human chromosomes. Science 273:494–497PubMedCrossRefGoogle Scholar
  53. Selig S, Okumura K, Ward DC, Cedar H (1992) Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J 11(3):1217–1225PubMedGoogle Scholar
  54. Sen S, Hopwood V (2010) Molecular cytogenetic evidence for multistep tumorigenesis: implications for risk assessment and early detection. Cancer Biomark 9(1–6):113–132PubMedGoogle Scholar
  55. Soloviev IV, Yuri B, Yurov YB, Vorsanova SG, Malet P (1994) Microwave activation of fluorescence in situ hybridization: a novel method for rapid chromosome detection and analysis. Focus 16(4):115–116Google Scholar
  56. Soloviev IV, Yurov YB, Vorsanova SG, Fayet F, Roizes G, Malet P (1995) Prenatal diagnosis of trisomy 21 using interphase fluorescence in situ hybridization of postreplicated cells with site-specific cosmid and cosmid contig probes. Prenat Diagn 15:237–248PubMedCrossRefGoogle Scholar
  57. Soloviev IV, Yurov YB, Vorsanova SG, Malet P, Zerova TE, Buzhievskaya TI (1998a) Double color in situ hybridization of alpha-satellite chromosome 13, 21 specific cosmid clones for a rapid screening of their specificity. Tsitol Genet 32:60–64PubMedGoogle Scholar
  58. Soloviev IV, Yurov YB, Vorsanova SG, Marcais B, Rogaev EI, Kapanadze BI et al (1998b) Fluorescent in situ hybridization analysis of α-satellite DNA in cosmid libraries specific for human chromosomes 13, 21 and 22. Russ J Genet 34:1247–1255Google Scholar
  59. Speicher MR, Ballard GS, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12:368–375PubMedCrossRefGoogle Scholar
  60. Steinhaeuser U, Starke H, Nietzel A, Lindenau J, Ullmann P, Claussen U et al (2002) Suspension (S)-FISH, a new technique for interphase nuclei. J Histochem Cytochem 50:1697–1698PubMedCrossRefGoogle Scholar
  61. Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T (2010) 4D chromatin dynamics in cycling cells: Theodor Boveri’s hypotheses revisited. Nucleus 1(3):284–297PubMedCrossRefGoogle Scholar
  62. Stumm M, Wegner R-D, Bloechle M, Eckel H (2006) Interphase M-FISH applications using commercial probes in prenatal and PGD diagnostics. Cytogenet Genome Res 114:296–301PubMedCrossRefGoogle Scholar
  63. Vanneste E, Bittman L, Van der Aa N, Voet T, Vermeesch JR (2012) New array approaches to explore single cells genomes. Front Genet 3:44PubMedCrossRefGoogle Scholar
  64. Verma RS, Luke S (1992) Variation in alphoid DNA sequences escape detection of aneuploidy in interphase FISH technique. Genomics 14:113–116PubMedCrossRefGoogle Scholar
  65. Virgili A, Brazma D, Reid AG, Howard-Reeves J, Valgañón M, Chanalaris A et al (2008) FISH mapping of Philadelphia negative BCR/ABL1 positive CML. Mol Cytogenet 1:14PubMedCrossRefGoogle Scholar
  66. Vorsanova SG, Yurov YB, Alexandrov IA, Demidova IA, Mitkevich SP, Tirskaya AF (1986) 18p- syndrome: an unusual case and diagnosis by in situ hybridization with chromosome 18-specific alphoid DNA sequence. Hum Genet 72:185–187PubMedCrossRefGoogle Scholar
  67. Vorsanova SG, Yurov YB, Deryagin GV, Soloviev IV, Bytenskaya GA (1991) Diagnosis of aneuploidy by in situ hybridization: analysis of interphase nuclei. Bull Exp Biol Med 112:413–415CrossRefGoogle Scholar
  68. Vorsanova SG, Yurov YB, Kolotii AD, Soloviev IV (2001a) FISH analysis of replication and transcription of chromosome X loci: new approach for genetic analysis of Rett syndrome. Brain Dev 23:S191–S195PubMedCrossRefGoogle Scholar
  69. Vorsanova SG, Yurov YB, Ulas VY, Demidova IA, Kolotii AD, Gorbatchevskaia NL, Beresheva AK, Soloviev IV (2001b) Cytogenetic and molecular-cytogenetic studies of Rett syndrome (RTT): a retrospective analysis of a Russian cohort of RTT patients (the investigation of 57 girls and three boys). Brain Dev 23:S196–S201PubMedCrossRefGoogle Scholar
  70. Vorsanova SG, Yurov YB, Brusquant D, Carles E, Roizes G (2002) Two new cases of the christchurch (Ch1) chromosome 21: evidence for clinical consequences of de novo deletion 21p-. Tsitol Genet 36(1):46–49PubMedGoogle Scholar
  71. Vorsanova SG, Iourov IY, Beresheva AK, Demidova IA, Monakhov VV, Kravets VS et al (2005a) Non-disjunction of chromosome 21, alphoid DNA variation, and sociogenetic features of Down syndrome. Tsitol Genet 39(6):30–36PubMedGoogle Scholar
  72. Vorsanova SG, Kolotii AD, Iourov IY, Monakhov VV, Kirillova EA, Soloviev IV, Yurov YB (2005b) Evidence for high frequency of chromosomal mosaicism in spontaneous abortions revealed by interphase FISH analysis. J Histochem Cytochem 53:375–380PubMedCrossRefGoogle Scholar
  73. Vorsanova SG, Iourov IY, Voinova-Ulas VY, Weise A, Monakhov VV, Kolotii AD et al (2008) Partial monosomy 7q34-qter and 21pter-q22.13 due to cryptic unbalanced translocation t(7;21) but not monosomy of the whole chromosome 21: a case report plus review of the literature. Mol Cytogenet 1:13PubMedCrossRefGoogle Scholar
  74. Vorsanova SG, Yurov YB, Iourov IY (2010a) Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 3:1PubMedCrossRefGoogle Scholar
  75. Vorsanova SG, Yurov YB, Soloviev IV, Iourov IY (2010b) Molecular cytogenetic diagnosis and somatic genome variations. Curr Genomics 11:440–446PubMedCrossRefGoogle Scholar
  76. Walter J, Joffe B, Bolzer A, Albiez H, Benedetti PA, Muller S et al (2006) Towards many colors in FISH on 3D-preserved interphase nuclei. Cytogenet Genome Res 114:367–378PubMedCrossRefGoogle Scholar
  77. Weier H-UG (2001) DNA Fiber mapping techniques for the assembly of high-resolution physical maps. J Histochem Cytochem 49(8):939–948PubMedCrossRefGoogle Scholar
  78. Weise A, Liehr T, Claussen U, Halbhuber K-J (2005) Increased efficiency of fluorescence in situ hybridization (FISH) using the microwave. J Histochem Cytochem 53(10):1301–1303PubMedCrossRefGoogle Scholar
  79. Weise A, Gross M, Hinreiner S, Witthuhn V, Mkrtchyan H, Liehr T (2010) POD-FISH: a new technique for parental origin determination based on copy number variation polymorphism. Methods Mol Biol 659:291–298PubMedCrossRefGoogle Scholar
  80. Weise A, Mrasek K, Klein E, Mulatinho M, Llerena JC Jr, Hardekopf D et al (2012) Microdeletion and microduplication syndromes. J Histochem Cytochem 60(5):346–358PubMedCrossRefGoogle Scholar
  81. Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JM, Dauwerse JG et al (1992) High-resolution in situ hybridization using DNA halo preparations. Hum Mol Genet 1(8):587–591PubMedCrossRefGoogle Scholar
  82. Yang F, Shao C, Vedanarayanan V, Ehrlich M (2004) Cytogenetic and immuno-FISH analysis of the 4q subtelomeric region, which is associated with facioscapulohumeral muscular dystrophy. Chromosoma (Berl) 112:350–359CrossRefGoogle Scholar
  83. Yeshaya J, Shalgi R, Shohat M, Avivi L (1999) FISH-detected delay in replication timing of mutated FMR1 alleles on both active and inactive X-chromosomes. Hum Genet 105(1–2):86–97PubMedCrossRefGoogle Scholar
  84. Yeshaya J, Amir I, Rimon A, Freedman J, Shohat M, Avivi L (2009) Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA. Mol Cytogenet 2:11PubMedCrossRefGoogle Scholar
  85. Yurov YB, Soloviev IV, Vorsanova SG, Marcais B, Roizes G, Lewis R (1996) High resolution fluorescence in situ hybridization using cyanine and fluorescein dyes: ultra-rapid chromosome detection by directly fluorescently labeled alphoid DNA probes. Hum Genet 97:390–398PubMedCrossRefGoogle Scholar
  86. Yurov YB, Vorsanova SG, Iourov IY, Demidova IA, Beresheva AK, Kravetz VS et al (2007) Unexplained autism is frequently associated with low-level mosaic aneuploidy. J Med Genet 44(8):521–525PubMedCrossRefGoogle Scholar
  87. Yurov YB, Vorsanova SG, Iourov IY (2009) GIN ‘n’ CIN hypothesis of brain aging: deciphering the role of somatic genetic instabilities and neural aneuploidy during ontogeny. Mol Cytogenet 2:23PubMedCrossRefGoogle Scholar

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© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Mental Health Research Center, Russian Academy of Medical SciencesMoscowRussia
  2. 2.Institute of Pediatrics and Children Surgery, Ministry of Health of Russian FederationMoscowRussia
  3. 3.Moscow City University of Psychology and EducationMoscowRussia

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