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Chromatin remodelling at promoters suppresses antisense transcription

Abstract

Chromatin allows the eukaryotic cell to package its DNA efficiently. To understand how chromatin structure is controlled across the Saccharomyces cerevisiae genome, we have investigated the role of the ATP-dependent chromatin remodelling complex Isw2 in positioning nucleosomes. We find that Isw2 functions adjacent to promoter regions where it repositions nucleosomes at the interface between genic and intergenic sequences. Nucleosome repositioning by Isw2 is directional and results in increased nucleosome occupancy of the intergenic region. Loss of Isw2 activity leads to inappropriate transcription, resulting in the generation of both coding and noncoding transcripts. Here we show that Isw2 repositions nucleosomes to enforce directionality on transcription by preventing transcription initiation from cryptic sites. Our analyses reveal how chromatin is organized on a global scale and advance our understanding of how transcription is regulated.

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Figure 1: Definition of Isw2 function using high-density microarrays.
Figure 2: Distinct nucleosome organization at the 5′ end of genes.
Figure 3: Loss of Isw2 leads to directional nucleosome repositioning at the 5′ end and 3′ end of genes.
Figure 4: Loss of Isw2 leads to noncoding transcription at the 3′ end of genes.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Raw data are deposited at GEO with accession numbers GSE8813, GSE8814 and GSE8815.

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Acknowledgements

We thank members of the Tsukiyama and Henikoff laboratories for discussions, R. Basom for help with data analysis, and S. Henikoff, S. Biggins, S. Hahn and T. Owen-Hughes for critical reading of the manuscript. This work was supported by funds from NIGMS and the Leukemia and Lymphoma Society to T.T, from the Burroughs Wellcome Fund and Human Frontier Science Program to O.J.R, and from the NCI to J.D.

Author Contributions Experimental strategy was designed by I.W. and T.T., and experiments were performed by I.W. Preliminary nucleosome mapping was performed in collaboration with O.J.R. Data were analysed by I.W., with technical assistance from J.D. The paper was written by I.W., with assistance from T.T. All authors discussed the results and experiments, and edited the manuscript.

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Correspondence to Toshio Tsukiyama.

Supplementary information

Supplementary Information

This file contains Supplementary Table S1and Supplementary Figures S1-S18 with Legends. (PDF 4886 kb)

Supplementary Table

This file contains Supplementary Table with summary data of regions bound by Isw2, sites of chromatin remodelling and lists of nucleosome positions. (XLS 25913 kb)

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Whitehouse, I., Rando, O., Delrow, J. et al. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450, 1031–1035 (2007). https://doi.org/10.1038/nature06391

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