title: Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast.
abstract: RNA 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.
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.|IST Austria, Klosterneuburg, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Lukačišin
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.|Department of Genetics, Harvard Medical School, Boston, MA, United States of America.|Ecole des Mines de Paris, Mines Paristech, Paris, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Landon
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.
authors.forename: Rishi
authors.identifier: http://orcid.org/0000-0002-9836-8967
authors.initials: R
authors.lastname: Jajoo
mesh_terms: D020029:Base Pairing; D005800:Genes, Fungal; D009696:Nucleic Acids / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D009696:Nucleic Acids