Lukačišin, MartinLandon, MatthieuJajoo, Rishi2017-05-012017Lukačišin, Martin, Matthieu Landon, and Rishi Jajoo. 2017. “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast.” PLoS ONE 12 (3): e0174066. doi:10.1371/journal.pone.0174066. http://dx.doi.org/10.1371/journal.pone.0174066.http://nrs.harvard.edu/urn-3:HUL.InstRepos:32630499RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.en-USBiology and life sciencesMolecular biologyMolecular biology techniquesMolecular probe techniquesProbe hybridizationRNA hybridizationBiology and Life SciencesCell BiologyChromosome BiologyChromatinNucleosomesGeneticsEpigeneticsGene ExpressionMolecular BiologyMolecular Biology TechniquesGene MappingNucleosome MappingPhysical SciencesPhysicsThermodynamicsSequencing TechniquesNucleotide SequencingDatabase and informatics methodsBioinformaticsSequence analysisDNA sequence analysisSequencing techniquesRNA sequencingDatabase and Informatics MethodsSequence AnalysisSequence Motif AnalysisJournal Article2017-05-0110.1371/journal.pone.0174066