Skip to main content
SpringerLink
Log in

Microscopic Analysis of Chromatin Localization and Dynamics in C. elegans

  • Protocol
  • First Online:
Book cover Imaging Gene Expression

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1042))

Abstract

During development, the genome undergoes drastic reorganization within the nuclear space. To determine tridimensional genome folding, genome-wide techniques (damID/Hi-C) can be applied using cell populations, but these have to be calibrated using microscopy and single-cell analysis of gene positioning. Moreover, the dynamic behavior of chromatin has to be assessed on living samples. Combining fast stereotypic development with easy genetics and microscopy, the nematode C. elegans has become a model of choice in recent years to study changes in nuclear organization during cell fate acquisition. Here we present two complementary techniques to evaluate nuclear positioning of genes either by fluorescence in situ hybridization in fixed samples or in living worm embryos using the GFP-lacI/lacO chromatin-tagging system.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Taddei A, Schober H, Gasser SM (2010) The budding yeast nucleus. Cold Spring Harb Perspect Biol 2(8):000612, doi:cshperspect.a000612 [pii] 10.1101/cshperspect.a000612

    Article  Google Scholar 

  2. Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM (2010) The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev 24(8):766–782, doi:24/8/766 [pii] 10.1101/gad.559610

    Article  PubMed  CAS  Google Scholar 

  3. Yuzyuk T, Fakhouri TH, Kiefer J, Mango SE (2009) The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos. Dev Cell 16(5):699–710, doi:S1534-5807(09)00127-0 [pii] 10.1016/j.devcel.2009.03.008

    Article  PubMed  CAS  Google Scholar 

  4. Towbin BD, Meister P, Pike BL, Gasser SM (2010) Repetitive transgenes in C. elegans accumulate heterochromatic marks and are sequestered at the nuclear envelope in a copy-number- and lamin-dependent manner. Cold Spring Harb Symp Quant Biol 75:555–565. doi:10.1101/sqb.2010.75.041

    Article  PubMed  CAS  Google Scholar 

  5. Yuen KW, Nabeshima K, Oegema K, Desai A (2011) Rapid de novo centromere formation occurs independently of heterochromatin protein 1 in C. elegans embryos. Curr Biol 21(21):1800–1807. doi:10.1016/j.cub.2011.09.016

    Article  PubMed  CAS  Google Scholar 

  6. Towbin BD, Gonzalez-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM (2012) Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 150(5):934–947. doi:10.1016/j.cell.2012.06.051

    Article  PubMed  CAS  Google Scholar 

  7. Frokjaer-Jensen C, Davis MW, Hopkins CE, Newman BJ, Thummel JM, Olesen SP, Grunnet M, Jorgensen EM (2008) Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet 40(11):1375–1383, doi:ng.248 [pii] 10.1038/ng.248

    Article  PubMed  CAS  Google Scholar 

  8. Frokjaer-Jensen C, Davis MW, Ailion M, Jorgensen EM (2012) Improved Mos1-mediated transgenesis in C. elegans. Nat Methods 9(2):117–118. doi:10.1038/nmeth.1865

    Article  PubMed  CAS  Google Scholar 

  9. Zeiser E, Frokjaer-Jensen C, Jorgensen E, Ahringer J (2011) MosSCI and gateway compatible plasmid toolkit for constitutive and inducible expression of transgenes in the C. elegans germline. PLoS One 6(5):e20082

    Article  PubMed  CAS  Google Scholar 

  10. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1(2):E45. doi:10.1371/journal.pbio.0000045

    Article  PubMed  Google Scholar 

  11. Carmi I, Kopczynski JB, Meyer BJ (1998) The nuclear hormone receptor SEX-1 is an X-chromosome signal that determines nematode sex. Nature 396(6707):168–173

    Article  PubMed  CAS  Google Scholar 

  12. Kaltenbach LS, Updike DL, Mango SE (2005) Contribution of the amino and carboxyl termini for PHA-4/FoxA function in Caenorhabditis elegans. Dev Dyn 234(2):346–354. doi:10.1002/dvdy.20550

    Article  PubMed  CAS  Google Scholar 

  13. Gonzalez-Serricchio AS, Sternberg PW (2006) Visualization of C. elegans transgenic arrays by GFP. BMC Genet 7:36

    Article  PubMed  Google Scholar 

  14. Robert VJ, Sijen T, van Wolfswinkel J, Plasterk RH (2005) Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes Dev 19(7):782–787

    Article  PubMed  CAS  Google Scholar 

  15. Rohner S, Gasser SM, Meister P (2008) Modules for cloning-free chromatin tagging in Saccharomyces cerevisiae. Yeast 25(3):235–239

    Article  PubMed  CAS  Google Scholar 

  16. Meister P, Gehlen L, Varela E, Kalck V, Gasser SM (2010) Visualizing yeast chromosomes and nuclear architecture. Methods Enzymol 470:537–569. doi:10.1016/S0076-6879(10)70021-5

    Google Scholar 

  17. Wood AJ, Lo TW, Zeitler B, Pickle CS, Ralston EJ, Lee AH, Amora R, Miller JC, Leung E, Meng X, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Meyer BJ (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333(6040):307. doi:10.1126/science.1207773

    Article  PubMed  CAS  Google Scholar 

  18. Robert V, Bessereau JL (2007) Targeted engineering of the Caenorhabditis elegans genome following Mos1-triggered chromosomal breaks. EMBO J 26(1):170–183

    Article  PubMed  CAS  Google Scholar 

  19. Woock AE, Cecile JP (2011) Inhibiting C. elegans movement with ethanol for live microscopy imaging. Worm Breeder’s Gazette 19(1):5

    Google Scholar 

Download references

Acknowledgements

We thank Darina Korčeková for expert help in developing 3D DNA FISH protocols, the Meister laboratory, Susan Gasser, and the Gasser laboratory for continuous support and helpful discussions. This work was funded in part by programs of the Charles University in Prague (UNCE 204022 and Prvouk/1LF/1) as well as by the Czech Science Foundation (grants P302/11/1262 and P302/12/G157), the Swiss National Foundation (SNF assistant professor grant PP00P3_133744), and the Fondation Suisse pour le Recherche sur les Maladies Musculaires.

Author information

Authors and Affiliations

  1. First Faculty of Medicine, Institute of Cellular Biology and Pathology, Charles University in Prague, Prague, Czech Republic

    Christian Lanctôt

  2. Institute of Cell Biology, University of Bern, Bern, Switzerland

    Peter Meister

Authors
  1. Christian Lanctôt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter Meister
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Bar-Ilan University Inst. of Nanotech & Advanced Materials, Ramat Gan, Israel

    Yaron Shav-Tal

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Lanctôt, C., Meister, P. (2013). Microscopic Analysis of Chromatin Localization and Dynamics in C. elegans . In: Shav-Tal, Y. (eds) Imaging Gene Expression. Methods in Molecular Biology, vol 1042. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-526-2_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-526-2_11

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-525-5

  • Online ISBN: 978-1-62703-526-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation