A high-resolution map of nucleosome positioning on a fission yeast centromere
- Jun S. Song1,2,4,
- Xingkun Liu3,4,
- X. Shirley Liu1, and
- Xiangwei He3,5
- 1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA;
- 2 The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540, USA;
- 3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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↵4 These authors contributed equally to this work.
Abstract
A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence.
Footnotes
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↵5 Corresponding author.
↵5 E-mail xhe{at}bcm.tmc.edu; fax (713) 798-8142.
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[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to Gene Expression Omnibus under accession no. GSE10742.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.075374.107.
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- Received December 7, 2007.
- Accepted April 3, 2008.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
