R. Zinzen & N. Rajewsky

Tissue-specific dissection of ncRNAs and their roles in Drosophila nervous system development

Robert P. Zinzen

Berlin Institute for Medical Systems Biology (BIMSB) at the Max Del

Robert-Roessle-Strasse 10 H. 89 Rm. 2.13 13092 Berlin, Germany

Phone : +49 (0) 30 - 9406 18
Fax : +49 (0) 30 - 9406 49

E-Mail : robert.zinzen@mdc-berlin.de

Web : See online here

Prof. Dr. Nikolaus Rajewsky

Robert Rössle Str 10, 13092 Berlin-Buch - Berlin, Germany

Phone : +49 30 9406 2999
Fax :

E-Mail : rajewsky@mdc-berlin.de

Web : See online here

Orderly specification and differentiation of naïve cells into progressively more complex cell types, tissues and organ systems is a fundamental question in developmental and stem cell biology. Many key developmental proteins like transcription factors (TFs) and signaling molecules have been identified over the past decades, primarily by classical forward and reverse genetics. It has become clear over the past few years, however, that a whole other critical regulatory level exists: a multitude of non-coding RNAs (ncRNAs) guide and control gene expression and convey cellular identity.

In order to understand the mechanisms by which ncRNAs drive development of the nervous system, we intend to systematically define several ncRNA species present in early nervous system development of the fruit fly and to dissect their functional roles and modes of action. The Drosophila nervous system derives from a large, continuous swath of cells, which becomes subdivided into several distinct functional domains that give rise to characteristic neuroblasts (NBs). In order to comprehensively understand nervous system development, it is therefore crucial not only to investigate the entirety of the developing nervous system, but to be able to break it into its component parts.

Recently developed technologies such a Batch Isolation of Tissue Specific Chromatin (BiTS) allow for the efficient isolation of tissue specific material from developing embryos and we are now able to isolate the nervous system as well as individual functional domains from within the nervous system. Not only will this yield a map of nervous system ncRNAs with spatial resolution, but we will obtain temporal resolution by investigating consecutive time points covering NS subdivision, specification, and differentiation. These biochemical and genomic approaches will be complemented by bioinformatics for classification and target prediction, and by biochemical and classical genetics analyses to determine the underlying mechanisms and functional roles of ncRNAs in the nervous system components and over the course of development from specification to differentiation.

Some key technologies for internal use :

Zinzen lab :
- BiTS (sorting of tissue-specific material)
- Drosophila genetics and developmental biology

Rajewsky lab :
- computational analysis of ncRNAs:
- miRNA prediction (miRDeep2)
- miRNA target prediction (iPicTar)
- global miRNA effect analysis (miReduce)
- help with ncRNA-focused databases (doRiNA, circBase)

experimental methods for:
- the identification of ncRNAs, e.g. circRNAs
- identification of RNA binding protein targets (iPAR-CLIP)

Last Publications

Grosswendt,S., Filipchyk, A., Manzano, M., Klironomos, F., Schilling, M., Herzog, M., Gottwein, E., Rajewsky, N. (2014). Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell 19;54(6), 1042-54.

Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338.

Zinzen, R., Bonn, S., Girardot, C., Wilczynski, B., and Furlong, E.E. (2012). Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44, 148-156.

Friedlander, M.R., Mackowiak, S.D., Li, N., Chen, W., and Rajewsky, N. (2012). miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40, 37-52.

Bonn, S., Zinzen, R.P., Perez-Gonzalez, A., Riddell, A., Gavin, A.C., and Furlong, E.E. (2012). Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7, 978-994.

Jungkamp, A.C., Stoeckius, M., Mecenas, D., Grun, D., Mastrobuoni, G., Kempa, S., and Rajewsky, N. (2011). In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol Cell 44, 828-840.

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