RNA polymerase II determines the area of nucleosome loss in transcribed gene loci Signe Va ¨rv, Kersti Kristjuhan, Arnold Kristjuhan * Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia Received 29 April 2007 Available online 7 May 2007 Abstract Upon transcriptional activation, nucleosomes are removed from not only promoters but also coding regions of highly transcribed genes. However, the mechanisms and factors determining the borders of nucleosome-depleted loci are not known. Here, we identify elon- gating RNA polymerase II as a major factor for defining the region of nucleosome removal in transcribed genes. We also show that upon shut-down of transcription, newly synthesised histones are used for formation of nucleosomes in the coding region of recently transcribed gene locus. Ó 2007 Elsevier Inc. All rights reserved. Keywords: Transcription; RNA polymerase II; Chromatin; Removal of nucleosomes All DNA-related processes in eukaryotic cells encoun- ter chromatin as a barrier to their activity. In order to gain access to DNA, cells have developed several mecha- nisms to contend with the structure of chromatin. While the short promoter regions of genes are opened by various chromatin modifying and remodelling factors recruited to the site by transcriptional activators, the opening of the much longer coding regions of genes during transcription is less clearly understood. Different modifications of his- tones in the coding regions of genes have been shown to correlate with gene’s transcriptional activity [1–4], and as an alternative for histone modifications, transcrip- tion-coupled disassembly of nucleosomes from both pro- moter and coding regions of genes has been reported [5–10,13]. The extent of nucleosome loss varies in different loci: genes induced by heat-shock or regulated by galact- ose-responsible promoters lose the nucleosomes from entire gene loci, while transcriptional induction of PHO5 leads to eviction of nucleosomes only from the promoter region of the gene [8–10,13]. Differences in the extent of nucleosome removal suggest that diverse molec- ular mechanisms or protein complexes might be responsi- ble for eviction and reassembly of nucleosomes on promoter and coding regions of genes. For example, chro- matin remodelling complex SWI/SNF and histone chaper- one Asf1 are required for removal of nucleosomes from PHO5 promoter, while the loss of nucleosomes from the coding regions of HSP82 and GAL10 is only marginally affected in the absence of these factors [5,8,10,11]. Studies of PHO5 promoter-specific dynamics of nucleosomes have revealed that new nucleosomes, formed from the free pool of histones, are loaded onto PHO5 promoter region upon repression of transcription [12]. However, the mechanisms and source of nucleosomes leading to restoration of nucleosomal structure in the coding regions of genes are not known. In this study we present data indicating that the elongat- ing RNA polymerase II (RNAPII) is a major determinant of the area of nucleosome loss in the coding region of a highly transcribed gene locus. We also show that pre-exist- ing nucleosomes are expelled from the coding region of the gene and upon shut-down of transcription new nucleo- somes are formed from the free pool of histones. 0006-291X/$ - see front matter Ó 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2007.05.003 * Corresponding author. Fax: +372 742 0286. E-mail address: arnoldk@ebc.ee (A. Kristjuhan). www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 358 (2007) 666–671