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Prof Peter Stadler
Phone : +49 (0)341-9716691 o
Fax : +49 (0)341-9716679
E-Mail : firstname.lastname@example.org
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
Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1. See here. Walter Costa MB, Höner Zu Siederdissen C, Tulpan D, Stadler PF,*Nowick K*. J Theor Biol. 2018 Feb 7;438:143-150. doi: 10.1016/j.jtbi.2017.11.015. Epub 2017 Nov 23. PMID: 29175608
A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. See here. Voigt A,*Nowick K*, Almaas E. PLoS Comput Biol. 2017 Sep 28;13(9):e1005739. doi: 10.1371/journal.pcbi.1005739. eCollection 2017 Sep. PMID: 28957313
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. See here. Berto S, Perdomo-Sabogal A, Gerighausen D, Qin J,*Nowick K*. Front Genet. 2016 Mar 8;7:31. doi: 10.3389/fgene.2016.00031. eCollection 2016. PMID: 27014338
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.