No. 22 /September 7, 2009

A Rapid and Efficient Cell Sorting Method Allows New Insights into Early Animal Embryogenesis - Close Collaboration between Max Delbrück Center and New York University

Caenorhabditis elegans (C. elegans) is one of the most important model systems in biology. A technique to collect large numbers of embryos of the animals, all precisely the same age, has been developed in a collaborative effort by researchers from the Max Delbrück Center (MDC) in Berlin, Germany and New York University (NYU), USA. This new technique (termed eFACS) and subsequent molecular analysis of small RNAs are reported online this week in Nature Methods (DOI 10.1038/nmeth.1370). eFACS opens the door for detailed and quantitative high-throughput studies of early events during embryogenesis of C. elegans, a prerequisite for Systems Biology approaches. Using eFACS, the researchers were already able to reveal that small RNA expression during early embryogenesis is a highly orchestrated and complex process.

 

C. elegans is an important animal model for biologists and many genes essential for the early events in mammalian embryo development have been identified in the worm.

 

Yet, to date, it has not been possible to collect large numbers of embryos at the same developmental stage, a prerequisite to studying gene expression and protein interactions on a genome-wide scale with novel high-throughput genomics or biochemistry assays, which in term are necessary for Systems Biology approaches.

 

“The current method of choice is collecting embryos by hand”, Marlon Stoeckius, one of the two lead authors from the MDC-research group of Nikolaus Rajewsky explains. “This is very time consuming and does not yield adequate sample size for large-scale studies.”

 

Nikolaus Rajewsky and colleagues together with Fabio Piano at New York University established a method (termed eFACS), using fluorescence-activated cell sorting (FACS), to efficiently and rapidly collect tens of thousands of embryos at the same stage within a few hours. They use embryos that express a stage-specific protein fused to a fluorescent marker; when the embryo reaches the particular stage, it fluoresces.

 

Making use of eFACS, the scientists carried out high-throughput sequencing to profile small RNA populations in various embryonic stages, and gained insight into how gene expression changes during the first cell cycles in a worm embryo.

 

They discovered complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including microRNAs, during embryogenesis. Small RNA molecules play an important role in the regulation of genes.

 

The researchers are convinced that eFACS will make a contribution towards a more complete understanding of gene regulatory networks during early animal development.

 

PhD Exchange Program between MDC and NYU

Marlon Stoeckius is the first PhD-student in the new program the MDC and NYU have set up to train PhD-students. Nikolaus Rajewsky was a Professor at NYU before he joined the MDC.

 

This program is a collaboration between the new Berlin Institute for Medical Systems Biology (BIMSB), headed by Nikolaus Rajewsky at the MDC and the new Center for Genomics and Systems Biology at New York University, headed by Fabio Piano. It will support scientific exchange between the two complementary institutions on either side of the Atlantic Ocean.

 

The basic concept of this new program is that collaborative PhD projects are performed in Berlin and New York and that each graduate student is jointly supervised by a Principal Investigator from each of the two research institutions. PhD students have the opportunity to divide their time between Berlin and New York, as Marlon Stoeckius has done for his research on C. elegans.

 

The BIMSB is funded within the program “Advanced Research and Innovation in the New States” by Germany’s Federal Research Ministry (BMBF). In 2008, the BIMSB received a kick-off funding of 7.5 Million euros by the BMBF and 4.4 million euros by the Senate of Berlin.

 

*Large scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.

Marlon Stoeckius1,4, Jonas Maaskola1,4, Teresa Colombo1,3, Hans-Peter Rahn1, Marc R. Friedländer1, Na Li1, Wei Chen1, Fabio Piano2,* & Nikolaus Rajewsky1,*

1 Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany

2 New York University, Department of Biology and Center for Comparative Functional Genomics, 100 Washington Square East, New York, NY 10003, USA.

3 present address: Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università La Sapienza, Rome, Italy

4 equal contributions

*corresponding authors: fp1@nyu.edu and rajewsky@mdc-berlin.de

 

Barbara Bachtler

Press and Public Affairs

Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch

Robert-Rössle-Straße 10; 13125 Berlin; Germany

Phone: +49 (0) 30 94 06 - 38 96

Fax:  +49 (0) 30 94 06 - 38 33

e-mail: presse@mdc-berlin.de

http://www.mdc-berlin.de/

 

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