MCB Accepts, published online ahead of print on 23 July 2007

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Mol. Cell. Biol. doi:10.1128/MCB.00876-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae

Koji Kasahara, Kazushige Ohtsuki, Sewon Ki, Kayo Aoyama, Hiroyuki Takahashi, Takehiko Kobayashi, Katsuhiko Shirahige, and Tetsuro Kokubo^*

Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, 230-0045, Japan; Division of Cytogenetics, National Institute of Genetics and SOKENDAI, Yata, Mishima, 411-8540, Japan; Center for Biological Resources and Informatics, Division of Gene Research, and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan

^* To whom correspondence should be addressed. Email: kokubo{at}tsurumi.yokohama-cu.ac.jp.

HMO1 is a high mobility group B (HMGB) protein that plays a role in transcription of genes encoding rRNA and ribosomal proteins (RPGs) in Saccharomyces cerevisiae. This study uses genome-wide chromatin immunoprecipitation (ChIP) to study the roles of HMO1, FHL1 and RAP1 in transcription of these genes as well as other RNA polymerase II-transcribed genes in yeast. The results show that HMO1 associates with the 35S rRNA gene in an RNA polymerase I (Pol I)-dependent manner and that RPG promoters (138 in total) can be classified into several distinct groups based on HMO1-abundance at the promoter and the HMO1-dependence of FHL1 and/or RAP1 binding to the promoter. FHL1, a key regulator of RPGs, binds to most of the HMO1-enriched and transcriptionally HMO1-dependent RPG promoters in an HMO1-dependent manner whereas it binds to HMO1-limited RPG promoters in an HMO1-independent manner, irrespective of whether or not they are transcribed in an HMO1-dependent manner. Reporter gene assays indicate that these functional properties are determined by the promoter sequence.

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