Assembly of Regulatory Factors on rRNA and Ribosomal Protein Genes in <i>Saccharomyces cerevisiae</i>

Koyamada, Koji; Ohtsuki, Kazuhiro; Ki, Sewon; Aoyama, Kayo; Takahashi, Hiroyuki; Kobayashi, Takehiko; Shirahige, Katsuhiko; Kokubo, Tetsuro

doi:10.1128/mcb.00876-07

Cited by 74 publications

(126 citation statements)

References 79 publications

(146 reference statements)

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“…In contrast to the spreading observed along rDNA, Hmo1-mediated cleavage was restricted to the RPS23A promoter. No significant cleavage was observed at another ribosomal gene locus, RPS22B (data not shown), in agreement with the published data (Hall et al 2006;Berger et al 2007;Kasahara et al 2007).…”

Section: Resultssupporting

confidence: 92%

“…Hmo1 association with the 35S rDNA locus has been observed in ChIP experiments (Hall et al 2006;Berger et al 2007;Kasahara et al 2007). In these studies, Hmo1 interaction with the promoters of many ribosomal protein genes (RPs), transcribed by RNA Pol II, was also reported.…”

Section: Resultsmentioning

confidence: 93%

“…Association of Hmo1 with rDNA has been described (Hall et al 2006;Berger et al 2007;Kasahara et al 2007), but apart from the observation that it genetically interacts with the Pol I subunit Rpa49 (Gadal et al 2002), little is known about its function.…”

Section: Hmo1 Is a Structural Component Of Active Rrna Genesmentioning

confidence: 99%

“…In the study by Kasahara et al (2007) it was shown that Hmo1 associated with 35S rDNA in a Pol I-dependent manner. To address the question of whether Hmo1 travels with the polymerase or if it is a rDNA-associated factor, Hmo1-MNase and Rpa43-MNase fusion proteins were expressed in two different genetic backgrounds: a strain carrying a temperature-sensitive allele of the Pol I-specific transcription initiation factor Rrn3 (Ycc95-rrn3-8) (rrn3-ts in Fig.…”

Section: Hmo1 Is a Structural Component Of Active Rrna Genesmentioning

confidence: 99%

“…A more recent ChIP study demonstrated that actively transcribed rRNA genes are assembled into a dynamic chromatin structure of unphased nucleosomes (Jones et al 2007), challenging the interpretation of the psoralen cross-linking analyses. Hmo1 was found to bind throughout the entire 35S rDNA sequence, suggesting that it may be implicated in the formation of rDNAspecific chromatin (Hall et al 2006;Berger et al 2007; Kasahara et al 2007). Although cells can survive in the absence of Hmo1, they are compromised in their growth.…”

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confidence: 99%

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Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules

Merz¹,

Hondele²,

Goetze³

et al. 2008

Genes Dev.

169

215

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Synthesis of ribosomal RNAs (rRNAs) is the major transcriptional event in proliferating cells. In eukaryotes, ribosomal DNA (rDNA) is transcribed by RNA polymerase I from a multicopy locus coexisting in at least two different chromatin states. This heterogeneity of rDNA chromatin has been an obstacle to defining its molecular composition. We developed an approach to analyze differential protein association with each of the two rDNA chromatin states in vivo in the yeast Saccharomyces cerevisiae. We demonstrate that actively transcribed rRNA genes are largely devoid of histone molecules, but instead associate with the high-mobility group protein Hmo1.[Keywords: Chromatin; transcription; ribosomal DNA] Supplemental material is available at http://www.genesdev.org. Received December 11, 2007; revised version accepted February 29, 2008. In the yeast Saccharomyces cerevisiae (hereafter called yeast), >60% of total cellular transcripts are produced from the ribosomal DNA (rDNA) locus by a specific multiprotein enzyme, RNA Polymerase I (Pol I), and an assorted set of additional transcription factors (Reeder 1999;Moss and Stefanovsky 2002;Russell and Zomerdijk 2006). The basal Pol I transcription machinery has been largely defined and consists of two multiprotein complexes, the upstream activating factor (UAF) , and the core factor (CF) (Keys et al. 1994), as well as the TATA-box-binding protein (TBP) (Steffan et al. 1996).The template of RNA Pol I transcription, the yeast ribosomal RNA (rRNA) genes are located on the right arm of chromosome XII in a tandem array of 150-200 copies (Fig. 1), representing almost 10% of the yeast genome. Each of the repeats contains the Pol I-transcribed 35S rRNA gene (precusor of the 5.8S, 18S, and 25S rRNAs) and the RNA Polymerase III (Pol III)-transcribed 5S rRNA gene (Fig. 1). Three different regulatory DNA elements have been identified within the 35S rRNA gene sequence, two of which are located at the 5Ј end of the 35S rDNA, spanning only ∼170 base pairs (bp) (Musters et al. 1989;Kulkens et al. 1991): the upstream element (UE), which is the binding site for the UAF; and the core promoter (CP), where CF can be recruited (Fig. 1). The third element, called the enhancer (ENH), is located at the 3Ј end of the 35S transcription unit (Fig. 1) and was originally identified as exhibiting a stimulatory effect on Pol I transcription in experiments using episomal reporter systems Warner 1984, 1986). However, this sequence has been shown subsequently to be dispensable for RNA Pol I transcription in the chromosomal context (Wai et al. 2001).In each cell, Pol I-transcribed rDNA coexists in two different chromatin states (Conconi et al. 1989). In these studies, cells were treated with the DNA cross-linking drug psoralen, and it was shown that actively transcribed and transcriptionally inactive rRNA genes differed substantially in their degree of psoralen incorporation. The different migration behavior of the corresponding restriction fragments in agarose gel electrophoresis led to the terms s-ban...

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 93%

Section: Hmo1 Is a Structural Component Of Active Rrna Genesmentioning

confidence: 99%

Section: Hmo1 Is a Structural Component Of Active Rrna Genesmentioning

confidence: 99%

mentioning

confidence: 99%

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Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules

Merz¹,

Hondele²,

Goetze³

et al. 2008

Genes Dev.

169

215

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Regulation of ribosomal protein genes: An ordered anarchy

et al. 2020

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Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under: Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation

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Current awareness on yeast

2008

Yeast

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (4 weeks journals ‐ search completed 6th. Feb. 2008)

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

Cited by 74 publications

References 79 publications

Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules

Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules

Regulation of ribosomal protein genes: An ordered anarchy

Current awareness on yeast

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