Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Innovation
  • Published:

High-throughput fluorescence microscopy for systems biology

Nature Reviews Molecular Cell Biology volume 7, pages 690–696 (2006)Cite this article

Abstract

In this post-genomic era, we need to define gene function on a genome-wide scale for model organisms and humans. The fundamental unit of biological processes is the cell. Among the most powerful tools to assay such processes in the physiological context of intact living cells are fluorescence microscopy and related imaging techniques. To enable these techniques to be applied to functional genomics experiments, fluorescence microscopy is making the transition to a quantitative and high-throughput technology.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The steps in a high-throughput fluorescence-microscopy experiment.
Figure 2: Image analysis of high-throughput image data from fixed cells.
Figure 3: Image analysis of high-throughput image data from live cells.

Similar content being viewed by others

References

  1. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931?945 (2004).

  2. Lippincott-Schwartz, J. & Patterson, G. H. Development and use of fluorescent protein markers in living cells. Science 300, 87?91 (2003).

    Article  CAS  Google Scholar 

  3. Chudakov, D. M., Lukyanov, S. & Lukyanov, K. A. Fluorescent proteins as a toolkit for in vivo imaging. Trends Biotechnol. 23, 605?613 (2005).

    Article  CAS  Google Scholar 

  4. Tsien, R. Y. Building and breeding molecules to spy on cells and tumors. FEBS Lett. 579, 927?932 (2005).

    Article  CAS  Google Scholar 

  5. Mayer, T. U. et al. Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science 286, 971?974 (1999).

    Article  CAS  Google Scholar 

  6. Perlman, Z. E. et al. Multidimensional drug profiling by automated microscopy. Science 306, 1194?1198 (2004).

    Article  CAS  Google Scholar 

  7. Wheeler, D. B., Carpenter, A. E. & Sabatini, D. M. Cell microarrays and RNA interference chip away at gene function. Nature Genet. 37 (Suppl. 1), S25?S30 (2005).

    Article  CAS  Google Scholar 

  8. Starkuviene, V. et al. High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. Genome Res. 14, 1948?1956 (2004).

    Article  CAS  Google Scholar 

  9. Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 463, 78?86 (2005).

    Article  Google Scholar 

  10. Sonnichsen, B. et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462?469 (2005).

    Article  CAS  Google Scholar 

  11. Mitchison, T. J. Small-molecule screening and profiling by using automated microscopy. Chembiochem 6, 33?39 (2005).

    Article  CAS  Google Scholar 

  12. Abraham, V. C., Taylor, D. L. & Haskins, J. R. High content screening applied to large-scale cell biology. Trends Biotechnol. 22, 15?22 (2004).

    Article  CAS  Google Scholar 

  13. Patterson, G. H. & Lippincott-Schwartz, J. Selective photolabeling of proteins using photoactivatable GFP. Methods 32, 445?450 (2004).

    Article  CAS  Google Scholar 

  14. Meyer, T. & Teruel, M. N. Fluorescence imaging of signaling networks. Trends Cell Biol. 13, 101?106 (2003).

    Article  CAS  Google Scholar 

  15. Bastiaens, P. I. & Pepperkok, R. Observing proteins in their natural habitat: the living cell. Trends Biochem. Sci. 25, 631?637 (2000).

    Article  CAS  Google Scholar 

  16. Miyawaki, A., Nagai, T. & Mizuno, H. Engineering fluorescent proteins. Adv. Biochem. Eng Biotechnol. 95, 1?15 (2005).

    CAS  PubMed  Google Scholar 

  17. Wouters, F. S., Verveer, P. J. & Bastiaens, P. I. Imaging biochemistry inside cells. Trends Cell Biol. 11, 203?211 (2001).

    Article  CAS  Google Scholar 

  18. Phizicky, E., Bastiaens, P. I., Zhu, H., Snyder, M. & Fields, S. Protein analysis on a proteomic scale. Nature 422, 208?215 (2003).

    Article  CAS  Google Scholar 

  19. Miyawaki, A. Innovations in the imaging of brain functions using fluorescent proteins. Neuron 48, 189?199 (2005).

    Article  CAS  Google Scholar 

  20. Rabut, G. & Ellenberg, J. Automatic real-time three-dimensional cell tracking by fluorescence microscopy. J. Microsc. 216, 131?137 (2004).

    Article  CAS  Google Scholar 

  21. Liebel, U. et al. A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett. 554, 394?398 (2003).

    Article  CAS  Google Scholar 

  22. Herman, B., Krishnan, R. V. & Centonze, V. E. Microscopic analysis of fluorescence resonance energy transfer (FRET). Methods Mol. Biol. 261, 351?370 (2004).

    CAS  PubMed  Google Scholar 

  23. Rabut, G. & Ellenberg, J. in Live Cell Imaging: A Laboratory Manual (eds Goldman, R. D. & Spector, D. L.) 101?127 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2005).

    Google Scholar 

  24. Sprague, B. L. & McNally, J. G. FRAP analysis of binding: proper and fitting. Trends Cell Biol. 15, 84?91 (2005).

    Article  CAS  Google Scholar 

  25. Lippincott-Schwartz, J., Altan-Bonnet, N. & Patterson, G. H. Photobleaching and photoactivation: following protein dynamics in living cells. Nature Cell Biol. 5(Suppl.), S7?S14 (2003).

    Google Scholar 

  26. Kohl, T. & Schwille, P. Fluorescence correlation spectroscopy with autofluorescent proteins. Adv. Biochem. Eng. Biotechnol. 95, 107?142 (2005).

    CAS  PubMed  Google Scholar 

  27. Pramanik, A. Ligand?receptor interactions in live cells by fluorescence correlation spectroscopy. Curr. Pharm. Biotechnol. 5, 205?212 (2004).

    Article  CAS  Google Scholar 

  28. Conrad, C. et al. Automatic identification of subcellular phenotypes on human cell arrays. Genome Res. 14, 1130?1136 (2004).

    Article  CAS  Google Scholar 

  29. Hu, Y. & Murphy, R. F. Automated interpretation of subcellular patterns from immunofluorescence microscopy. J. Immunol. Methods 290, 93?105 (2004).

    Article  CAS  Google Scholar 

  30. Huang, K. & Murphy, R. F. Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinformatics 5, 78 (2004).

  31. Neumann, B. et al. High-throughput RNAi screening by time-lapse imaging of live human cells. Nature Methods 3, 385?390 (2006).

    Article  CAS  Google Scholar 

  32. Simpson, J. C., Neubrand, V. E., Wiemann, S. & Pepperkok, R. Illuminating the human genome. Histochem. Cell Biol. 115, 23?29 (2001).

    Article  CAS  Google Scholar 

  33. Wiemann, S. et al. cDNAs for functional genomics and proteomics: the German Consortium. C. R. Biol. 326, 1003?1009 (2003).

    Article  CAS  Google Scholar 

  34. Wu, J. Q. & Pollard, T. D. Counting cytokinesis proteins globally and locally in fission yeast. Science 310, 310?314 (2005).

    Article  CAS  Google Scholar 

  35. Bork, P. & Serrano, L. Towards cellular systems in 4D. Cell 121, 507?509 (2005).

    Article  CAS  Google Scholar 

  36. Blake, R. A. Cellular screening assays using fluorescence microscopy. Curr. Opin. Pharmacol. 1, 533?539 (2001).

    Article  CAS  Google Scholar 

  37. Yarrow, J. C., Feng, Y., Perlman, Z. E., Kirchhausen, T. & Mitchison, T. J. Phenotypic screening of small molecule libraries by high throughput cell imaging. Comb. Chem. High Throughput Screen. 6, 279?286 (2003).

    Article  CAS  Google Scholar 

  38. Keller, P., Toomre, D., Diaz, E., White, J. & Simons, K. Multicolour imaging of post-Golgi sorting and trafficking in live cells. Nature Cell Biol. 3, 140?149 (2001).

    Article  CAS  Google Scholar 

  39. Ziauddin, J. & Sabatini, D. M. Microarrays of cells expressing defined cDNAs. Nature 411, 107?110 (2001).

    Article  CAS  Google Scholar 

  40. Pawley, J. B. (ed.) Handbook of Biological Confocal microscopy 2nd edn (Plenum Press, New York, 1995).

    Book  Google Scholar 

  41. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283?1298 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Held for help in preparing the figures, and would like to acknowledge funding within the MitoCheck consortium by the European Commission (J.E.) as well as by the Federal Ministry of Education and Research in the framework of the National Genome Research Network (J.E. and R.P.).

Author information

Authors and Affiliations

  1. Cell Biology/Biophysics Unit,

    Rainer Pepperkok & Jan Ellenberg

  2. Gene Expression and Cell Biology/Biophysics Units, in the European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany

    Rainer Pepperkok & Jan Ellenberg

Authors
  1. Rainer Pepperkok
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jan Ellenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

FURTHER INFORMATION

Jan Ellenberg's homepage

Rainer Pepperkok's homepage

MANUFACTURER INFORMATION

Applied Precision

BD (BD Biosciences)

Beckman Coulter

BioConductor

Cellomics

CellProfiler

CompuCyte

Definiens

Evotec Technologies

GE Healthcare, Life Sciences (formerly Amersham Biosciences)

Molecular Devices

Olympus: Microscopy

TTP LabTech

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pepperkok, R., Ellenberg, J. High-throughput fluorescence microscopy for systems biology. Nat Rev Mol Cell Biol 7, 690–696 (2006). https://doi.org/10.1038/nrm1979

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm1979

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing