23. February 2017, 16:15 p.m.
Ernst-Abbe-Platz 2, seminar room 3423
RNA:DNA triple helices: A new twist in epigenetic regulation by non-coding RNAs
Dr. Holger Bierhoff
(Interim Professorship for Genetics, Department of Genetics, Faculty of Biology and Pharmacy, FSU Jena)
Non-coding RNAs (ncRNAs) regulate gene expression transcriptionally and post-transcriptionally. At the transcriptional level, ncRNAs impact the epigenetic signature of distinct genomic regions, however, little is known about how target sites are recognized. In this regard, RNA:DNA triple helices (triplexes) have attracted interest as a direct and sequence-specific interface between ncRNAs and DNA. In a triplex structure, 12-30 nucleotides of an ncRNA insert into the major groove of the DNA double helix and form so-called forward or reverse Hoogsteen hydrogen bonds with the purine-rich DNA strand. Such purine-rich tracks are frequently found in gene regulatory regions, suggesting that ncRNAs commonly contact DNA by triplex formation. To elucidate existence and functional relevance of RNA:DNA triplexes, we have developed a synthetic triplex-binding protein termed Stm1TBD. Upon ectopic expression in cells, Stm1TBD binds to endogenous RNA:DNA triplexes, thus facilitating their immunopurification and subsequent identification. Using this approach, we have detected a novel RNA:DNA triplex in the mouse Kras gene promoter and have characterized its role in regulating Kras expression. Moreover, deep sequencing data will be presented showing that Stm1TBD is suitable to globally identify triplex-forming ncRNAs. Together, the results corroborate that ncRNAs engage into triplexes to regulate gene activity.