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J. Biol. Chem., Vol. 281, Issue 14, 9560-9568, April 7, 2006

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Functional Genomic Analysis of CAF-1 Mutants in Arabidopsis thaliana^*

Nicole Schönrock¹, Vivien Exner, Aline Probst, Wilhelm Gruissem, and Lars Hennig²

From the Institute of Plant Sciences, ETH Zurich and Zurich-Basel Plant Science Center, CH-8092 Zurich, Switzerland and the Department of Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland

Duplication of chromatin following DNA replication requires spatial reorganization of chromatin domains assisted by chromatin assembly factor CAF-1. Here, we tested the genomic consequences of CAF-1 loss and the function of chromatin assembly factor CAF-1 in heterochromatin formation. Genes located in heterochromatic regions are usually silent, and we found that this transcriptional repression persists in the absence of CAF-1 in Arabidopsis. However, using microarrays we observed that genes that are active during late S-phase, when heterochromatin is duplicated, were up-regulated in CAF-1 mutants. Arabidopsis CAF-1 mutants also have reduced cytological heterochromatin content; however, DNA methylation of pericentromeric repeats was normal, demonstrating that CAF-1 is not required for maintenance of DNA methylation. Instead, hypomethylation of the genome, which has only mild effects on the development of wild-type plants, completely arrested development of CAF-1 mutants. These results suggest that CAF-1 functions in heterochromatin formation. CAF-1 and DNA methylation, which is also needed for heterochromatin formation, have partially redundant functions that are essential for cell proliferation. Interestingly, transcriptional repression and heterochromatin compaction can be genetically separated, and CAF-1 is required only for the complete compaction of heterochromatin but not to maintain transcriptional repression of heterochromatic genes.

Received for publication, December 16, 2005 , and in revised form, January 31, 2006.

^* This research was supported by Swiss National Science Foundation Project 3100AO-104238 (to L. H.) and by the Functional Genomics Center Zurich. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental material.

¹ Supported by the Roche Research Foundation.

² To whom correspondence should be addressed. Tel.: 41-1-632-2244; Fax: 41-1-632-1044; E-mail: lhennig{at}ipw.biol.ethz.ch.

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