Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species
- Hye-Ran Lee†,
- Wenli Zhang‡,
- Tim Langdon§,
- Weiwei Jin†,
- Huihuang Yan†,
- Zhukuan Cheng‡, and
- Jiming Jiang†,¶
- †Department of Horticulture, University of Wisconsin–Madison, Madison, WI 53706; ‡Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; and §Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth SY23 3EB, United Kingdom
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Edited by Susan R. Wessler, University of Georgia, Athens, GA (received for review May 10, 2005)
Abstract
The functional centromeres of rice (Oryza sativa, AA genome) chromosomes contain two key DNA components: the CRR centromeric retrotransposons and a 155-bp satellite repeat, CentO. However, several wild Oryza species lack the CentO repeat. We developed a chromatin immunoprecipitation-based technique to clone DNA fragments derived from chromatin containing the centromeric histone H3 variant CenH3. Chromatin immunoprecipitation cloning was carried out in the CentO-less species Oryza rhizomatis (CC genome) and Oryza brachyantha (FF genome). Three previously uncharacterized genome-specific satellite repeats, CentO-C1, CentO-C2, and CentO-F, were discovered in the centromeres of these two species. An 80-bp DNA region was found to be conserved in CentO-C1, CentO, and centromeric satellite repeats from maize and pearl millet, species which diverged from rice many millions of years ago. In contrast, the CentO-F repeat shows no sequence similarity to other centromeric repeats but has almost completely replaced other centromeric sequences in O. brachyantha, including the CRR-related sequences that normally constitute a significant fraction of the centromeric DNA in grass species.
Footnotes
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↵ ¶ To whom correspondence should be addressed. E-mail: jjiang1{at}wisc.edu.
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Author contributions: J.J. designed research; H.-R.L., W.Z., W.J., H.Y., and Z.C. performed research; H.-R.L., W.Z., T.L., Z.C., and J.J. analyzed data; and H.-R.L., T.L., and J.J. wrote the paper.
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This paper was submitted directly (Track II) to the PNAS office.
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Abbreviation: ChIP, chromatin immunoprecipitation.
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Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ058468–DQ058600).
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See Commentary on page 11573.
- Copyright © 2005, The National Academy of Sciences
