Skip to main content
SpringerLink
Log in

High Resolution Fiber-Fluorescence In Situ Hybridization

  • Protocol
  • First Online:
Cancer Cytogenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1541))

Abstract

High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips. These released DNA/chromatin fibers are suitable for an array of cytogenetic/cytogenomic analyses.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Heng H, Chen WY (1985) The study of the chromatin and the structure for Bufo gargarizans by the light microscope. J Sichuan Union Univ Nat Sci 2:105–109

    Google Scholar 

  2. Heng HH, Shi XM (1997) From free chromatin analysis to high resolution fiber FISH. Cell Res 7:119–124

    Article  CAS  PubMed  Google Scholar 

  3. Heng HH, Tsui LC (1998) High resolution free chromatin/DNA fiber fluorescent in situ hybridization. J Chromatogr A 806:219–229

    Article  CAS  PubMed  Google Scholar 

  4. Heng HH, Spyropoulos B, Moens P (1997) Fish technology in chromosome and genome research. BioEssays 10:75–84

    Article  Google Scholar 

  5. Heng HH, Liu G, Stevens JB et al (2013) Karyotype heterogeneity and unclassified chromosomal abnormalities. Cytogenet Genome Res 139:144–157

    Article  CAS  PubMed  Google Scholar 

  6. Heng HH, Squire J, Tsui LC (1991) Chromatin mapping - a strategy for physical characterization of the human genome by hybridization in situ. Proc 8th Int Cong Hum Gen Am J Hum Genet 49:368

    Google Scholar 

  7. 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 89:9509–9513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wiegant J, Kalle W, Mullenders L et al (1992) High resolution in situ hybridization using DNA halo preparation. Hum Mol Genet 1:587–592

    Article  CAS  PubMed  Google Scholar 

  9. Parra I, Windle B (1993) High resolution visual mapping of stretched DNA by fluorescent hybridization. Nat Genet 5:17–21

    Article  CAS  PubMed  Google Scholar 

  10. Houseal TW, Dackowski WR, Landes GM et al (1994) High resolution mapping of overlappingcosmids by fluorescence in situ hybridization. Cytometry 15:193–198

    Article  CAS  PubMed  Google Scholar 

  11. Fidlerova H, Senger G, Kost M et al (1994) Two simple procedures for releasing chromatin from routinely fixed cells for fluorescence in situ hybridization. Cytogenet Cell Genet 65:203–205

    Article  CAS  PubMed  Google Scholar 

  12. Haaf T, Ward DC (1994) High resolution ordering of YAC contigs using extended chromatin and chromosomes. Hum Mol Genet 3:629–633

    Article  CAS  PubMed  Google Scholar 

  13. Heiskanen M, Karhu R, Hellsten E et al (1994) High resolution mapping using fluorescence in situ hybridization to extended DNA fibers prepared from agarose embedded cells. Bio Techniques 17:928–933

    CAS  Google Scholar 

  14. Bensimon A, Simon A, Chiffaudel A et al (1994) Alignment and sensitive detection of DNA by a moving interface. Science 265:2096–2098

    Article  CAS  PubMed  Google Scholar 

  15. Heng HH (2002) High resolution FISH mapping using chromatin and DNA fiber. In: Beatty B, Mai S, Squire J (eds) FISH: a practical approach. Oxford University Press, Oxford, pp 77–92

    Google Scholar 

  16. Heng HH, Windle B, Tsui LC (2005) High –resolution FISH analysis. In: Dracopoli NC, Haines JL, Korf BR (eds) Current protocols in human genetics. John Wiley & Sons, New York, Volume 23 (Suppl 44) 4.5.1–4.5.23

    Google Scholar 

  17. Fransz PF, Alonso-Blanco CM, Liharska TB et al (1996) High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J 9:421–430

    Article  CAS  PubMed  Google Scholar 

  18. Jackson SA, Wang ML, Goodman HM et al (1998) Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41:566–572

    Article  CAS  PubMed  Google Scholar 

  19. Tsuchiya D, Taga M (2001) Application of fibre-FISH (fluorescence in situ hybridization) to filamentous fungi: visualization of the rRNA gene cluster of the ascomycete Cochliobolus heterostrophus. Microbiology 147:1183–1187

    Article  CAS  PubMed  Google Scholar 

  20. Pauciullo A, Fleck K, Lühken G et al (2013) Dual-color high-resolution fiber-FISH analysis on lethal white syndrome carriers in sheep. Cytogenet Genome Res 140:46–54

    Article  CAS  PubMed  Google Scholar 

  21. Wang K, Zhang W, Jiang Y et al (2013) Systematic application of DNA fiber-FISH technique in cotton. PLoS One 8, e75674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Iafrate AJ, Feuk L, Rivera MN et al (2004) Detection of large-scale variation in the human genome. Nat Genet 36:949–951

    Article  CAS  PubMed  Google Scholar 

  23. Horelli-Kuitunen N, Aaltonen J, Yaspo ML et al (1999) Mapping ESTs by fiber-FISH. Genome Res 9:62–71

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Lestou VS, Strehl S, Lion T et al (1996) High-resolution FISH of the entire integrated Epstein-Barr virus genome on extended human DNA. Cytogenet Cell Genet 74:211–217

    Article  CAS  PubMed  Google Scholar 

  25. Gervasini C, Bentivegna A, Venturin M et al (2002) Tandem duplication of the NF1 gene detected by high-resolution FISH in the 17q11.2 region. Hum Genet 111:465–467

    Article  Google Scholar 

  26. Vesa J, Hellsten E, Verkruyse LA et al (1995) Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis. Nature 376:584–587

    Article  CAS  PubMed  Google Scholar 

  27. Trower MK, Orton SM, Purvis IJ et al (1996) Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus). Proc Natl Acad Sci U S A 93:1366–1369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Gusso Goll L, Matiello RR, Artoni RF et al (2015) High-resolution physical chromosome mapping of multigene families in Lagria villosa (Tenebrionidae): occurrence of interspersed ribosomal genes in coleoptera. Cytogenet Genome Res 146:64–70

    Article  PubMed  Google Scholar 

  29. Rottger S, Yen PH, Schempp W (2002) A fiber-FISH contig spanning the non-recombining region of the human Y chromosome. Chromosome Res 10:621–635

    Article  PubMed  Google Scholar 

  30. Heng HH, Chamberlain JW, Shi XM et al (1996) Regulation of meiotic chromatin loop size by chromosomal position. Proc Natl Acad Sci U S A 93:2795–2800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Heng HH, Krawetz SK, Lu W et al (2001) Re-defining the chromatin loop domain. Cytogent Cell Genet 93:155–161

    Article  CAS  Google Scholar 

  32. Heng HH, Goetze S, Ye CJ et al (2004) Chromatin loops are selectively anchored using scaffold/matrix attachment regions. J Cell Sci 117:999–1008

    Article  CAS  PubMed  Google Scholar 

  33. Haaf T (1996) High-resolution analysis of DNA replication in released chromatin fibers containing 5-bromodeoxyuridine. Biotechniques 21:1050–1054

    CAS  PubMed  Google Scholar 

  34. Florijn RJ, Bonden LA, Vrolijk H et al (1995) High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes. Hum Mol Genet 4:831–836

    Article  CAS  PubMed  Google Scholar 

  35. Riemersma SA, Jordanova ES, Schop RF et al (2000) Extensive genetic alterations of the HLA region, including homozygous deletions of HLA class II genes in B-cell lymphomas arising in immune-privileged sites. Blood 96:3569–3577

    CAS  PubMed  Google Scholar 

  36. Inoue K, Osaka H, Imaizumi K et al (1999) Proteolipid protein gene duplications causing Pelizaeus-Merzbacher Disease: molecular mechanism and phenotypic manifestations. Ann Neurol 45:624–632

    Article  CAS  PubMed  Google Scholar 

  37. Jiang F, Lin F, Price R et al (2002) Rapid detection of IgH/BCL2 rearrangement in follicular lymphoma by interphase fluorescence in situ hybridization with bacterial artificial chromosome probes. J Mol Diagn 4:144–149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Poulsen TS, Silahtaroglu AN, Gisselo CG et al (2001) Detection of illegitimate rearrangement within the immunoglobulin locus on 14q32.3 in B-cell malignancies using end-sequenced probes. Genes Chromosomes Cancer 32:265–274

    Article  CAS  PubMed  Google Scholar 

  39. Heng HH (2009) The genome-centric concept: resynthesis of evolutionary theory. Bioessays 31:512–525

    Article  PubMed  Google Scholar 

  40. Heng HH, Liu G, Stevens JB et al (2011) Decoding the genome beyond sequencing: the new phase of genomic research. Genomics 98:242–252

    Article  CAS  PubMed  Google Scholar 

  41. Heng HH (2016) Debating cancer: the paradox of cancer research. World Scientific, Hackensack, NJ

    Google Scholar 

  42. Stevens JB, Abdallah BY, Horne SD et al (2013) Genetic and epigenetic heterogeneity in cancer. eLs – Wiley Online Library. doi:10.1002/9780470015902.a0023592

    Google Scholar 

  43. Liu G, Stevens JB, Horne SD et al (2014) Genome chaos: survival strategy during crisis. Cell Cycle 13:528–537

    Article  CAS  PubMed  Google Scholar 

  44. Heng HH, Regan SM, Liu G et al (2016) Why it is crucial to analyze non clonal chromosome aberrations or NCCAs? Mol Cytogenet 9:e15

    Article  Google Scholar 

  45. Heng HH, Bremer SW, Stevens JB et al (2013) Chromosomal instability (CIN): what it is and why it is crucial to cancer evolution. Cancer Metastasis Rev 32:325–340

    Article  PubMed  Google Scholar 

  46. Labit H, Goldar A, Guilbaud G et al (2008) A simple and optimized method of producing silanized surfaces for FISH and replication mapping on combed DNA fibers. BioTechniques 45:649–658

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA

    Christine J. Ye

  2. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 3226 Scott Hall, 540 E, Detroit, MI, 48201, USA

    Henry H. Heng

  3. Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA

    Henry H. Heng

  4. Karmanos Cancer Institute, Detroit, MI, 48201, USA

    Henry H. Heng

Authors
  1. Christine J. Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Henry H. Heng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Henry H. Heng .

Editor information

Editors and Affiliations

  1. Haematology Division Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong Prince of Wales Hospital, Shatin, Hong Kong, China

    Thomas S.K. Wan

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Ye, C.J., Heng, H.H. (2017). High Resolution Fiber-Fluorescence In Situ Hybridization. In: Wan, T. (eds) Cancer Cytogenetics. Methods in Molecular Biology, vol 1541. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6703-2_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6703-2_14

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6701-8

  • Online ISBN: 978-1-4939-6703-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation