In JoVE (1)
Articles by Zuzer Dhoondia in JoVE
Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on (TRO) Approach Zuzer Dhoondia1, Ricci Tarockoff1, Nadra Alhusini1, Scott Medler1, Neha Agarwal1, Athar Ansari1 1Department of Biological Sciences, Wayne State University We describe a basic experimental approach for analysis of termination of transcription by RNA polymerase II in vivo using BrUTP by the strand-specific transcription run-on (TRO) approach in budding yeast. This protocol can be extended to study transcription termination by other RNA polymerases both in yeast and higher eukaryotes.
Other articles by Zuzer Dhoondia on PubMed
Regulated Formation of LncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation Molecular Cell. Feb, 2016 | Pubmed ID: 26833086 Long non-coding (lnc)RNAs, once thought to merely represent noise from imprecise transcription initiation, have now emerged as major regulatory entities in all eukaryotes. In contrast to the rapidly expanding identification of individual lncRNAs, mechanistic characterization has lagged behind. Here we provide evidence that the GAL lncRNAs in the budding yeast S. cerevisiae promote transcriptional induction in trans by formation of lncRNA-DNA hybrids or R-loops. The evolutionarily conserved RNA helicase Dbp2 regulates formation of these R-loops as genomic deletion or nuclear depletion results in accumulation of these structures across the GAL cluster gene promoters and coding regions. Enhanced transcriptional induction is manifested by lncRNA-dependent displacement of the Cyc8 co-repressor and subsequent gene looping, suggesting that these lncRNAs promote induction by altering chromatin architecture. Moreover, the GAL lncRNAs confer a competitive fitness advantage to yeast cells because expression of these non-coding molecules correlates with faster adaptation in response to an environmental switch.