Article abstract

Nature Methods 6, 745 - 751 (2009)
Published online: 6 September 2009 | doi:10.1038/nmeth.1370

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

Caenorhabditis elegans is one of the most prominent model systems for embryogenesis, but collecting many precisely staged embryos has been impractical. Thus, early C. elegans embryogenesis has not been amenable to most high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect staged C. elegans embryos by fluorescence-activated cell sorting (eFACS). In a proof-of-principle experiment, we found that a single eFACS run routinely yielded tens of thousands of almost perfectly staged 1-cell stage embryos. As the earliest embryonic events are driven by posttranscriptional regulation, we combined eFACS with second-generation sequencing to profile the embryonic expression of small, noncoding RNAs. We discovered complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including microRNAs and 26G-RNAs, during embryogenesis.

  1. Max Delbrück Center for Molecular Medicine, Berlin, Germany.
  2. New York University, Department of Biology and Center for Genomics and Systems Biology, New York, New York, USA.
  3. Present address: Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università La Sapienza, Rome, Italy.
  4. These authors contributed equally to this work.

Correspondence to: Fabio Piano2 e-mail:

Correspondence to: Nikolaus Rajewsky1 e-mail:


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