Research Report 2010 - MDC

Technical AssistantsClaudia LangnickMirjam FeldkampRegine SchwartzStart of group: January 2009overcome these limitations, we have developed novelmethods based on new sequencing technology to characterizethe breakpoints in an efficient manner. We arenow implementing our method in large-scale breakpointmapping and gene finding.De novo transcriptome sequencing using 454pyrosequencingYongbo WangNew sequencing technologies are not only robust toolsfor the investigation of transcriptome in model organisms,but also manifest great potential in studying nonmodelorganisms. To facilitate comprehensive transcriptomecharacterization, we are developing methodsfor transcriptome sequencing using 454 pyrosequencing.With long read length and high accuracy, it is particularlysuitable for de novo sequence assembly. To befit for 454 sequencing, our methods consist of steps toremove poly A+ tails and cDNA library normalization.The sequencing data would provide a comprehensivereference resource for further functional studies.Selected publicationsFu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W*, Li Y, Zeng R,Khaitovich P*. (2009). Estimating accuracy of RNA-Seq and microarrayswith proteomics. BMC Genomics. 10, 161-169*shared corresponding authorEnder C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W,Pfeffer S, Rajewsky N, Meister G. (2008). A Human snoRNA withMicroRNA-Like Functions. Mol Cell. 32(4), 519-528Kuss AW, Chen W. (2008) MicorRNAs in brain function and disease. CurrNeurol Neurosci Rep. 3, 190-197.Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,Rajewsky N. (2008). Discovering microRNAs from deep sequencing datausing miRDeep Nat Biotechnol. 26(4), 407-415.Chen W, Kalscheu V, Tzschach A, Menzel C, Ullmann R, Schulz M, ErdoganF, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U,Rost I, Dufke A, Grasshoff U, Glaeser BG, Vingron M, Ropers HH.(2008)Mapping translocation breakpoints by next-generation sequencing.Genome Res. 18: 1143-1149Berlin Institute of Medical Systems Biology 195