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High-resolution genome-wide mapping of histone modifications

Nature Biotechnology volume 22, pages 1013–1016 (2004)Cite this article

Abstract

The expression patterns of eukaryotic genomes are controlled by their chromatin structure, consisting of nucleosome subunits in which DNA of approximately 146 bp is wrapped around a core of 8 histone molecules1. Post-translational histone modifications play an essential role in modifying chromatin structure2. Here we apply a combination of SAGE3 and chromatin immunoprecipitation (ChIP) protocols to determine the distribution of hyperacetylated histones H3 and H4 in the Saccharomyces cerevisiae genome. We call this approach genome-wide mapping technique (GMAT). Using GMAT, we find that the highest acetylation levels are detected in the 5′ end of a gene's coding region, but not in the promoter. Furthermore, we show that the histone acetyltransferase, GCN5p, regulates H3 acetylation in the promoter and 5′ end of the coding regions. These findings indicate that GMAT should find valuable applications in mapping target sites of chromatin-modifying enzymes.

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Figure 1: Schematic of the genome-wide mapping technique (GMAT).
Figure 2: Acetylation map of yeast chromosome III.
Figure 3: Distribution of tags in the promoter regions and along the open reading frames.

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Acknowledgements

We thank David Clark, Gerald Crabtree, Warren Leonard and Carl Wu for their comments on the manuscript. The wild-type yeast W303 was provided by David Clark and Carl Wu. The GCN5-deleted yeast strain was provided by Rohinton Kamakaka. The flag-H2B yeast strain was provided by Zu-wen Sun and David Allis. The Long-SAGE software was provided by Kenneth W. Kinzler. The work was supported by National Heart, Lung, and Blood Institute (K.Z.)/ National Library of Medicine, National Center for Biotechnology Information (D.L.).

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Authors and Affiliations

  1. Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, 20892, Maryland, USA

    Tae-young Roh, Kairong Cui & Keji Zhao

  2. Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, Maryland, USA

    Wing Chi Ngau & David Landsman

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Correspondence to Keji Zhao.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Anti-diacetylated K9/K14 histone H3 and anti-tetraacetylated histone H4 antibodies specifically recognized acetylated histones in yeast chromatin. (PDF 175 kb)

Supplementary Fig. 2

AcH3 distribution on all chromosomes. (PDF 423 kb)

Supplementary Fig. 3

AcH4 distribution on all chromosomes. (PDF 419 kb)

Supplementary Fig. 4

Inducible genes are marked by acetylation under non-inducible conditions. (PDF 218 kb)

Supplementary Fig. 5

AcH4 distribution on all telomeres. (PDF 227 kb)

Supplementary Fig. 6

Telomeric Position Effect (TPE) is inversely correlated with the level of histone hyperacetylation. (PDF 20 kb)

Supplementary Fig. 7

Distribution of tags in the promoter region and along the open reading frames for histone H4 of wild type (a) and GCN5-deleted (b) yeast (PDF 116 kb)

Supplementary Table 1

Tag Density (PDF 54 kb)

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Roh, Ty., Ngau, W., Cui, K. et al. High-resolution genome-wide mapping of histone modifications. Nat Biotechnol 22, 1013–1016 (2004). https://doi.org/10.1038/nbt990

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