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Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast

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5354634.pdf (3.27 MB)

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2017

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10.1371/journal.pone.0174066

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Public Library of Science
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Lukačišin, 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.

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.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354634/pdf/

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Biology and life sciences, Molecular biology, Molecular biology techniques, Molecular probe techniques, Probe hybridization, RNA hybridization, Biology and Life Sciences, Cell Biology, Chromosome Biology, Chromatin, Nucleosomes, Genetics, Epigenetics, Gene Expression, Molecular Biology, Molecular Biology Techniques, Gene Mapping, Nucleosome Mapping, Physical Sciences, Physics, Thermodynamics, Sequencing Techniques, Nucleotide Sequencing, Database and informatics methods, Bioinformatics, Sequence analysis, DNA sequence analysis, Sequencing techniques, RNA sequencing, Database and Informatics Methods, Sequence Analysis, Sequence Motif Analysis

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http://nrs.harvard.edu/urn-3:HUL.InstRepos:32630499

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