A06: Vascular gene expression control through DNA:DNA:RNA triplex-formation by lncRNAs

Research Details

  • Project Leaders  
    Prof. Dr. Ralf P. Brandes
    Institute of Cardiovascular Physiology
    Goethe University Frankfurt
    brandes@vrc.uni-frankfurt.de

    Prof. Dr. Harald Schwalbe
    Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ)
    Goethe University Frankfurt
    schwalbe@nmr.uni-frankfurt.de
  • Research Staff Dr. James Oo (Postdoc)
    oo@vrc.uni-frankfurt.de

    Julius Blechar (PhD Student)
    blechar@nmr.uni-frankfurt.de

    Jasleen Kaur Bains (PhD Student)
    bains@nmr.uni-frankfurt.de

    Nina Krause (PhD Student)
    krause@nmr.uni-frankfurt.de

    Tianfu Li (PhD student)
    tianfu@vrc.uni-frankfurt.de

    Julia Stötzel (PhD student)
    stoetzel@med.uni-frankfurt.de

    Timothy Warwick (PhD Student)
    warwick@vrc.uni-frankfurt.de

Biogenesis, function and the rate of occurrence of DNA:DNA:RNA triplices in vivo is poorly understood. In the previous funding period, we identified how triplex formation of the long non-coding RNA (lncRNA) HIF1α- AS1 recruits the HUSH silencing complex to DNA sites in endothelial cells. By NMR analysis, we studied the biophysical specifics of triplices and uncovered that the established rule sets for triplex formation are only partially applicable. Based on this, we developed the bioinformatics tool TriplexAligner, employing machine learning and triplex-sequencing data to identify a substantially improved triplex code operative in cells. In the upcoming funding period, we will extend this tool to include RNA secondary structure information. We will use NMR and other biophysical methods to understand how the local environment within a triplex influences hydrogen bonding, i.e. we will identify the conditions which determine the relative stabilities of Watson-Crick base pairing within the two DNA strands and Hoogsteen base pairing between the RNA and the DNA for each nucleotide quantitatively. Moreover, based on the endothelial triplexome generated in the previous funding period, we will identify how triplex-forming lncRNAs control endothelial to mesenchymal transition (EndMT). A specific focus of the upcoming period is to determine whether triplices require proteins for formation or stabilization. Using different technologies (RADICL-MS, IDAP, dCas13-APEX), we will identify triplex-associated proteins and subsequently use NMR to identify the structure of the protein-DNA:DNA:RNA complex. Finally, we will identify disease-relevant single nucleotide polymorphisms, which impact on triplex formation and thus lncRNA function in cardiovascular disease.

Team A06