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RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA

Nature Structural & Molecular Biology volume 14, pages 123–130 (2007)Cite this article

Abstract

RNA polymerase (Pol) I–transcribed ribosomal genes of budding yeast exist as a tandem array (about 150 repeats) with transcription units separated by spacer sequences. Half of these rDNAs are inactivated by repressive chromatin structure, whereas the rest exist in an open conformation transcribed by closely spaced Pol I elongation complexes. Whereas previous studies have suggested that active rDNA is devoid of nucleosomal structure, we demonstrate that active rDNA has nucleosomal structure, according to chromatin immunoprecipitation and biochemical fractionation. Using a yeast strain with reduced numbers of all actively transcribed rDNA repeats, we show that rDNA exists in a dynamic chromatin structure of unphased nucleosomes. Furthermore, it is associated with chromatin-remodeling enzymes Chd1p, Isw1p and Isw2p, whose inactivation causes defects in transcription termination. We suggest that Pol I transcription, like that of Pol II, may be modulated by specific chromatin structures.

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Figure 1: Histones H2B and H3 are present across active rDNA repeats.
Figure 2: Biochemical analysis of Pol I–associated nucleosomes.
Figure 3: Chromatin-remodeling factors are associated with the entire rDNA repeat.
Figure 4: Chromatin remodeling factors Chd1p, Isw1p and Isw2p modulate Pol I's transcription termination profile.

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Acknowledgements

We thank members of N.J.P.'s laboratory for useful discussions. We are grateful to A. Johnson (University of California, San Francisco), J. Mellor (University of Oxford), M. Nomura (McGill University), M. Riva (Centre National de la Recherche Scientifique, Campus de Gif sur Yvette) and T. Tsukiyama (Fred Hutchinson Cancer Center) for providing the strains used in this work. We thank D. Bentley (University of Colorado, School of Medicine) for providing the H2B antibody. H.S.J. was supported by a Wellcome Trust Prize Studentship and J.K. by a fellowship from the Japan Heart Foundation. This work was supported by a Wellcome Trust Programme grant to N.J.P.

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Author notes

  1. Claudia M Alen & Nicholas A Kent

    Present address: Present addresses: National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Royal Brompton Campus, Dove House, London SW3 6LY, UK (C.M.A.) and School of Biosciences, Cardiff Universiy, Cardiff CF10 3XT, UK (N.A.K.).,

  2. Hannah S Jones and Junya Kawauchi: These authors contributed equally to this work.

Authors and Affiliations

  1. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK

    Hannah S Jones, Junya Kawauchi, Priscilla Braglia, Claudia M Alen, Nicholas A Kent & Nick J Proudfoot

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Correspondence to Nick J Proudfoot.

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Supplementary information

Supplementary Figure 1

Transcription run-on titration. (PDF 142 kb)

Supplementary Table 1

Primers for chromatin immunoprecipitation. (PDF 70 kb)

Supplementary Table 2

Primers for biochemical chromatin analysis. (PDF 68 kb)

Supplementary Methods

PCR primer locations. (PDF 55 kb)

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Jones, H., Kawauchi, J., Braglia, P. et al. RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol 14, 123–130 (2007). https://doi.org/10.1038/nsmb1199

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