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The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

Abstract

Upon transcription, histones can either detach from DNA or transfer behind the polymerase through a process believed to involve template looping. The details governing nucleosomal fate during transcription are not well understood. Our atomic force microscopy images of yeast RNA polymerase II–nucleosome complexes confirm the presence of looped transcriptional intermediates and provide mechanistic insight into the histone-transfer process through the distribution of transcribed nucleosome positions. Notably, we find that a fraction of the transcribed nucleosomes are remodeled to hexasomes, and this fraction depends on the transcription elongation rate. A simple model involving the kinetic competition between transcription elongation, histone transfer and histone-histone dissociation quantitatively explains our observations and unifies them with results obtained from other polymerases. Factors affecting the relative magnitude of these processes provide the physical basis for nucleosomal fate during transcription and, therefore, for the regulation of gene expression.

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Figure 1: Snapshots of transcription.
Figure 2: Nucleosome position.
Figure 3: DNA looping during histone transfer.
Figure 4: Transcription leads to hexamer formation.
Figure 5: Histone transfer outcome depends on the speed of transcription.
Figure 6: Histone transfer model.

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Acknowledgements

We thank M. Dangkulwanich, T. Ishibashi, B. Onoa, P. Visperas and Y. Wu for experimental assistance and helpful discussions, and C. Rivetti for sharing the ALEX code. This work was supported by the Howard Hughes Medical Institute and by US National Institutes of Health grant R01-GM032543-30 (to C.B.).

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L.B., M.Kopaczynska, C.H. and C.B. designed the research. M.Kopaczynska, L.B. and C.H. prepared materials and conducted experiments. L.B. and M.Kopaczynska analyzed the data. L.L. and M.Kashlev contributed materials and discussed the manuscript. L.B., M.Kopaczynska, C.H. and C.B. wrote the paper.

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Correspondence to Carlos Bustamante.

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Bintu, L., Kopaczynska, M., Hodges, C. et al. The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes. Nat Struct Mol Biol 18, 1394–1399 (2011). https://doi.org/10.1038/nsmb.2164

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