Report

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Science  31 Jul 2009:
Vol. 325, Issue 5940, pp. 626-628
DOI: 10.1126/science.1172926

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Gradual Unpacking

Eukaryotic DNA is packaged onto nucleosomes, which form the main constituent of chromatin. This packaging material presents a barrier to accessing the genome by the various machineries that need to deal with the DNA: replication, recombination, repair, and transcription complexes, for example. Hodges et al. (p. 626; see the Perspective by Otterstrom and van Oijen) use single-molecule techniques to analyze how a yeast RNA polymerase II ternary elongation complex copes when it encounters a single nucleosome directly in its path. The polymerase does not actively peel the DNA from the nucleosome's surface but, instead, waits patiently until the DNA fluctuates off the nucleosome and then advances, increment by increment, until the nucleosome is destabilized. Under certain conditions the destabilized nucleosome, rather than being lost entirely from the DNA, can be passed back to the DNA behind the polymerase.

Abstract

RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes during transcription elongation. We have developed an optical tweezers assay to follow individual Pol II complexes as they transcribe nucleosomal DNA. Our results indicate that the nucleosome behaves as a fluctuating barrier that locally increases pause density, slows pause recovery, and reduces the apparent pause-free velocity of Pol II. The polymerase, rather than actively separating DNA from histones, functions instead as a ratchet that rectifies nucleosomal fluctuations. We also obtained direct evidence that transcription through a nucleosome involves transfer of the core histones behind the transcribing polymerase via a transient DNA loop. The interplay between polymerase dynamics and nucleosome fluctuations provides a physical basis for the regulation of eukaryotic transcription.

  • * These authors contributed equally to this work.

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