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Assembly of Regulatory Factors on rRNA and Ribosomal Protein Genes in Saccharomyces cerevisiae ^,

Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama 230-0045, Japan,¹ Division of Cytogenetics, National Institute of Genetics and SOKENDAI, Yata, Mishima 411-8540, Japan,² Center for Biological Resources and Informatics, Division of Gene Research, and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8503, Japan³

Received 17 May 2007/ Returned for modification 12 June 2007/ Accepted 17 July 2007

HMO1 is a high-mobility group B 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 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-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 they are transcribed in an HMO1-dependent manner. Reporter gene assays indicate that these functional properties are determined by the promoter sequence.

Published ahead of print on 23 July 2007.

Supplemental material for this article may be found at http://mcb.asm.org/.

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