期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：47
页码：E7409-E7417
DOI：10.1073/pnas.1607760113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceHow does RNA polymerase (RNAP) accurately and orderly control elongation of RNA in nanosystems dominated by random thermal fluctuations? Our statistical approach challenges this open question by identifying a linkage between thermal fluctuations, repetitive DNA sequences encoded in a genome, and RNAP pausing during elongation. Until now, it has been reasonably assumed that the structure of an elongation complex (EC) at any given location along DNA ultimately controls its enzymatic function. Contrary to this assumption, we show that nonlocal thermal fluctuations of the EC on repetitive DNA sequence elements statistically and robustly affect RNAP elongation by stabilizing pausing. This study also provides a proof of concept for the significance of thermal fluctuations in a wide variety of enzymatic systems. In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations.
关键词：repetitive DNA sequence elements ; nonconsensus protein–DNA binding ; RNA polymerase ; backtracking ; thermal fluctuations
