Close collaboration between four laboratories at the BIMSB led by Stefan Kempa, Christoph Dieterich, Nikolaus Rajewsky and Wei Chen has led to the identification of thousands of gene products, many of which are expressed and are important in stem cell function. This was achieved by precise characterization of all RNA-molecules expressed in the animals’ cells, the so-called transcriptome, without using the genome sequence (Genome Research, July 2011 21: 1193-1200)*.
Planarians are famous for their almost unlimited ability to regenerate any tissue via pluripotent adult stem cells. Their spectacular regenerative capabilities have been studied for more than 100 years. With the development of new molecular and genetics approaches, planarians have recently re-emerged as a model system for the study of regeneration and stem cells.
The scientists at the BIMSB combined two existing and complementary sequencing methods to decipher the transcriptome of the planarian Schmidtea mediterranea without depending on genome sequences. Their approach is of great practical importance since the genomes of many organisms are known to be extremely difficult to assemble, even with the current sequencing technologies.
Furthermore, they also were able to identify several novel gene products (mRNAs) of which they proved that they are specifically expressed in the stem cells. It is the first proteomics study of such scale in this phylum (Platyhelminthes), as Wei Chen pointed out. The catalogue of transcripts assembled in their study, together with the identified peptides, dramatically expands and refines planarian research.
The Berlin Institute for Medical Systems Biology (BIMSB) was launched by the MDC in 2008, supported by start-up funding from the Federal Ministry of Education and Research (BMBF) and the Senate of Berlin. Medical Systems Biology focuses on molecular networks of genes and proteins, their regulation and interaction with each other and their relevance in disease processes. BIMSB works closely with research institutions and networks in Berlin and beyond, in particular with Humboldt University and Charité – Universitätsmedizin Berlin and also with New York University, USA.
*De novo assembly and validation of Planaria transcriptome by massive parallel sequencing and shotgun proteomics
Catherine Adamidi1*, Yongbo Wang1*, Dominic Gruen1*, Guido Mastrobuoni1*, Xintian You1*, Dominic Tolle1, Matthias Dodt1, Sebastian Mackowiak1, Andreas Gogol-Doering1, Pinar Oenal1, Agnieszka Rybak1, Eric Ross2, Alejandro Sánchez Alvarado2, Stefan Kempa1+, Christoph Dieterich1+, Nikolaus Rajewsky1+, Wei Chen1+
1Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert Rössle Straße 10, Berlin 13125, Germany
2Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University
of Utah, Salt Lake City, UT 84132, USA
* equal contribution
+ corresponding authors SK, CD, NR and WC
Published in Advance May 2, 2011, doi:10.1101/gr.113779.110
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