High-resolution genome-wide mapping of histone modifications

Tae Young Roh, Wing Chi Ngau, Kairong Cui, David Landsman, Keji Zhao

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180 Scopus citations


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 molecules. Post-translational histone modifications play an essential role in modifying chromatin structure. Here we apply a combination of SAGE 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.

Original languageEnglish
Pages (from-to)1013-1016
Number of pages4
JournalNature Biotechnology
Issue number8
StatePublished - Aug 2004

Bibliographical note

Funding Information:
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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