MAY 12, 2016 10:30 AM PDT

DNA methylation analysis by multiplexed reduced representation bisulfite sequencing

Speaker
  • PhD Student, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
    Biography
      Paul Datlinger is a PhD student in the lab of Christoph Bock at the Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, and developer of a high-throughput RRBS protocol, available as a kit from Diagenode. He studied Molecular Biology at the Universities of Vienna, Manchester and at Imperial College London. Besides developing new technologies for next-generation sequencing, his research interests revolve around epigenetic modifier networks, and epigenome editing by exploiting the CRISPR/Cas9 system.

    Abstract

    DNA methylation is an essential mechanism of epigenetic gene regulation with broad relevance in development and disease. Its localization on genomic DNA and general stability make this epigenetic mark an attractive target for large-scale studies in cancer research, developmental biology and ecology. In recent years, microarray-based technologies have been gradually replaced by more robust, accurate and versatile next generation sequencing-based methods. 
        
    This presentation will introduce highly-multiplexed reduced representation bisulfite sequencing as a cost-effective means for large DNA methylation studies. The protocol provides a single-base resolution read-out of 5-methylcytosine, while avoiding the cost of whole-genome sequencing. Based on an enzymatic enrichment step, the method is cost-effective, but provides excellent coverage of promoter regions, CpG islands, and other genomic elements such as enhancers and CpG island shores. At the same time, the protocol supports high-throughput applications, is suitable for any vertebrate species and has been optimized specifically for formalin-fixed, paraffin-embedded samples.

    In our lab, we have successfully used RRBS on over 2000 samples comprising many different vertebrate species, various cancers, FFPE and low-input samples, and are happy to share our experience with the epigenomics community.

    Learning objectives:

    • the talk will introduce highly multiplexed reduced representation bisulfite sequencing as a cost-effective means for large DNA methylation studies
    • get an overview of the required bioinformatic workflow, for an easy transition from microarrays to next generation sequencing-based analyses

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