Research Report 2010 - MDC

Figure 2. Planariato experimentally assay, genome-wide, the impact ofmiRNAs on protein synthesis (see pSILAC website). Amajor ongoing effort is currently to use and developseveral key high throughput technologies for in vivostudies in C. elegans and planaria: high-throughputproteomics (SILAC), RNA sequencing, and new methodsthat allow the genome wide identification of bindingsites if RNA binding proteins.These projects involved or involve, in part, collaborationswith the following labs: Markus Stoffel lab (ETHZurich), Fabio Piano and Kris Gunsalus (NYU), MatthiasSelbach (MDC), Markus Landthaler (MDC).Early embryogenesis in C. elegansMarlon Stoeckius, Jonas Maaskola, Nadine ThierfelderAlthough C. elegans is one of the most famous modelsystems for developmental biology, it has been impossibleto use most high-throughput technologies to studydifferential gene expression and networks during veryearly embryogenesis (for example the oocyte to onecellembryo transition upon fertilization). However,high-throughput technologies are needed to solve severalfundamental problems in embryogenesis, forexample how post-transcriptional and later transcriptionalregulatory networks drive development. One keyproblem is that the state of the art method to obtainprecisely staged early embryos consists of sortingembryos via mouth pipetting, thus making it impracticalto obtain large samples. To overcome this problem,we have developed a novel method (“eFACS”) thatallows us to sort embryos at precise stages duringembryogenesis via FACS sorting (Stoeckius, Maaskola etal, Nature Methods 2009). For example, we can nowroutinely obtain ~60,000 one-cell stage embryos (at apurity of >98%) in one FACS run, enough to apply virtuallyany high throughput method of interest (Figure 3).We have used eFACS to assay the dynamics of smallRNA expression during embryogenesis. We discovered awealth of orchestrated, specific changes between andwithin virtually all classes of small RNAs. These findingsopen the door for many computational and functionalfollow up studies. For example, we are proceeding todevelop and use in vivo SILAC to study the functionalimpact of certain small RNAs on the post-transcriptionallevel. These projects involve collaborations with the F.Piano lab (NYU), M. Selbach (MDC), W. Chen (MDC) andothers.Small RNAs in planarian stem cell biologyCatherine Adamidi, Marc Friedlaender, Pinar Oenal,Sebastian MackowiakWe used massive next generation sequencing to identifymiRNAs and piRNAs in S. mediterranea. We also identifiedmiRNAs that seem specifically linked to stem cellbiology. A number of these miRNAs are conserved inhumans (Friedlaender & Adamidi et al.PNAS 2009). Weare currently starting to functionally follow up some ofthese results. We are also starting to systematicallyidentify the proteome of planarian stem cells and areinterested to use these data to identify and characterizekey genes involved in regeneration mediated by28 Cardiovascular and Metabolic Disease Research