Peter Stadler & Katja Nowick

Long Non-Coding RNAs in Primate Brain Evolution



Prof Peter Stadler

Universität Leipzig

Haertelstr. 16-18
D-04107 Leipzig

Phone : +49 (0)341-9716691 o
Fax : +49 (0)341-9716679

E-Mail : studla@bioinf.uni-leipzig.de

Web : See online here



PI Katja Nowick

Universität Leipzig

Haertelstr. 16-18
D-04107 Leipzig

Phone : +49 (0)341-9716684
Fax : +49 (0)341-9716679

E-Mail : nowick@bioinf.uni-leipzig.de

Web : See online here

Long non-coding RNAs (lncRNAs) are emerging as key players in the nervous system. Many of the about 15.000 human lncRNAs are expressed in the brain and multiple lines of evidence have linked them to important brain functions, such as neurogenesis and behavior, or have associated them with neurodegenerative and psychiatric diseases. Although several databases for lncRNAs exist, there is still a large gap in the structural and functional annotation of lncRNAs hindering a full understanding of their role in the nervous system. Many characteristics of the brain are human specific. Genes that evolve quickly, as lncRNAs do, are therefore the best candidates to be primarily responsible for the evolution of these innovations. Since biological function has to be studied in the light of evolution, we aim here at establishing a full catalog of human lncRNAs, including an annotation of their sequence, structure, expression, and evolutionary changes by collating and coherently re-analyzing the wealth of already available high throughout data. We will experimentally determine target genes for one selected lncRNA and for the other lncRNA genes provide insights into their function and involvement in gene regulatory networks using computational methods. These results, together with the custom brain-lncRNA chip we plan to develop, will set the stage for thorough functional characterization of lncRNAs in the brain.

Key technologies :

- Functional annotation of lncRNAs
- lncRNA conservation analysis
- lncRNA evolution analysis
- Gene Regulatory Networks
- Genome alignment
- Transcriptome mapping
- Differential expression analysis

Last Publications

Hackerm uller, J., Reiche, K., Otto, C., Hosler, N., Blumert, C., Brocke-Heidrich, K., B ohlig, L., Nitsche, A., Kasack, K., Ahnert, P., Krupp, W., Engeland, K., Stadler, P. F., Horn, F. (2014) Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein coding RNAs. Genome Biol., 15, R48.

Perdomo-Sabogal, A., Kanton, S., Walter, M.B.C., Nowick, K. (2014) The roles of gene regulatory factors in the history of human evolution, Current Opinion in Genetics and Development 10.1016/j.gde.2014.08.007.

Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P. F. (2015) Comparison of splice sites reveals that long non-coding RNAs are evolutionarily well conserved. RNA. accepted.

Nowick, K., Fields, C., Gernat, T., Caetano-Anolles, C., Kholina, N., Stubbs, L. (2011) Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. PLoS One 6: e21553.

Otto, C., Stadler, P. F., Hoffmann, S. (2014) Lacking alignments? The versatile and accurate next generation sequencing mapper segemehl revisited. Bioinformatics, 30, 1837-1843.

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