Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing

Huang, Jinxiu; Moazed, Danesh

doi:10.1101/gad.1108403

Cited by 210 publications

(358 citation statements)

References 58 publications

(117 reference statements)

Supporting

Mentioning

322

Contrasting

Order By: Relevance

“…FOB1 codes for a protein that binds to DNA elements within the rDNA enhancer region defining the so-called replication fork barrier (Kobayashi and Horiuchi 1996). It has been shown that FOB1 is required for regional Pol II silencing in the intergenic spacer region and thus seems to influence local chromatin structure at this locus (Huang and Moazed 2003). Furthermore, it has been reported recently that Pol II can transcribe intergenic spacer DNA from a bidirectional promoter (E-pro) located within IGS1 Kobayashi and Ganley 2005).…”

Section: Discussionmentioning

confidence: 99%

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

View full text Add to dashboard Cite

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...

show abstract

Section: Discussionmentioning

confidence: 99%

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

View full text Add to dashboard Cite

show abstract

Section: Esa1 Function Within the Rdnamentioning

confidence: 98%

“…That enrichment at these sites was specific was established by comparison to the control POL1 locus, where no differences were observed between tagged and untagged strains. Recovery of Esa1p from these sites in the rDNA thus demonstrates that Esa1p maps to the site of its effects on silencing, as observed for targeting of Sir2p (Huang and Moazed, 2003).Because esa1 mutants affect global levels of histone H4 acetylation , we tested the effect of esa1 mutants on the levels of acetylation in the rDNA at specific lysine residues on histone tails. We performed ChIP analysis using modification specific antisera at the 25S, 5S, and NTS regions within the rDNA, comparing ESA1 and esa1-414 strains at 33°C where both strains have complete viability ( Figure 3C).…”

mentioning

confidence: 99%

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

Clarke

Samal

Pillus

2006

MBoC

View full text Add to dashboard Cite

Among acetyltransferases, the MYST family enzyme Esa1p is distinguished for its essential function and contribution to transcriptional activation and DNA double-stranded break repair. Here we report that Esa1p also plays a key role in silencing RNA polymerase II (Pol II)-transcribed genes at telomeres and within the ribosomal DNA (rDNA) of the nucleolus. These effects are mediated through Esa1p's HAT activity and correlate with changes within the nucleolus. Esa1p is enriched within the rDNA, as is the NAD-dependent protein deacetylase Sir2p, and the acetylation levels of key Esa1p histone targets are reduced in the rDNA in esa1 mutants. Although mutants of both ESA1 and SIR2 have enhanced rates of rDNA recombination, esa1 effects are more modest yet result in distinct structural changes of rDNA chromatin. Surprisingly, increased expression of ESA1 can bypass the requirement for Sir2p in rDNA silencing, suggesting that these two enzymes with seemingly opposing activities both contribute to achieve optimal nucleolar chromatin structure and function. INTRODUCTIONHistone modifications such as phosphorylation, methylation, acetylation, and deacetylation provide a mechanism by which chromatin structure is modulated to affect gene expression both positively and negatively (for reviews see Strahl and Allis, 2000;Iizuka and Smith, 2003;Kurdistani and Grunstein, 2003). The acetylation of lysine residues on histone N-terminal tails is classically linked to increases in gene expression and more directly to roles in transcriptional activation. By contrast, deacetylation of histones is most frequently correlated with transcriptionally silent chromatin. As more is learned about the enzymes catalyzing these modifications, the histone acetyltransferases (HATs) and histone deacetylases (HDACs), simple functional distinctions between acetylation and deacetylation of histones do not hold (Iizuka and Smith, 2003). For example, in several organisms, mutations in RPD3, a gene encoding a deacetylase, lead to increases in silencing rather than the expected decreases (DeRubertis et al., 1996;Rundlett et al., 1996). This brings forward the possibility that histone acetylation may play an important part in both silent and active chromatin. In addition, coactivator proteins, such as the histone acetyltransferases p300 and CBP and nuclear hormone receptors, appear to have roles in transcriptional repression through acetylation and association with particular binding partners (for examples, see Chen and Li, 1998;Waltzer and Bienz, 1998;Baluchamy et al., 2003;Girdwood et al., 2003;Rajabi et al., 2005). Thus, understanding of multiple roles for acetylation in controlling gene expression is expanding.In Saccharomyces cerevisiae, there are three regions of the genome controlled by chromatin-mediated transcriptional silencing: telomeres, the silent mating-type loci HMR and HML, and the rDNA array. Many factors are important for transcriptional silencing at subsets of these loci including the four core histones, the repressor activator protein Rap1...

show abstract

“…Taqman assays confirmed an increase in rDNA-Ty1b interactions in the absence of Sir2p ( Figure 4A). Moreover, deletion of the replication fork blocking site protein, Fob1 (Kobayashi, 2003), which is involved in the localization of the Sir2p-containing RENT complex to the ETS2 domain (Huang and Moazed, 2003b), also caused an increase Figure 4A). Intriguingly, deleting either SIR2 or FOB1 reduced the frequency of intra-rDNA repeat interactions ( Figure 4B, C).…”

Section: S 25s Its1 and It2 Rrnas) Mspi Restriction Sites Are Depmentioning

confidence: 99%

“…Intriguingly, the trf4 strain also showed an increase in the frequency of the intrarDNA interactions between the ETS2 domain and 25S rRNA (Figure 6). This is simply explained by the Sir2- (Houseley et al, 2007b; and Fob1 (Huang and Moazed, 2003a)-dependent silencing of RNA polymerase II promoters within and adjacent to the ETS2 domain. In contrast, the removal of the Trf4 protein does not alter the number of E-pro regions that are being transcribed, but rather causes an increase in the number of Epro CUTs by stabilizing those that have already been produced (Houseley et al, 2007b).…”

Section: S 25s Its1 and It2 Rrnas) Mspi Restriction Sites Are Depmentioning

confidence: 99%

Repeated elements coordinate the spatial organization of the yeast genome

O’Sullivan

Sontam

Grierson

et al. 2009

Yeast

View full text Add to dashboard Cite

The spatial organization of the chromosomes is crucial for gene expression and development. Inter-and intrachromosomal interactions form a crucial part of this epigenomic regulatory system. Here we use circular chromosome conformation capture-on-chip (4C) to identify interactions between repetitive and non-repetitive loci within the yeast genome. The interacting regions occur in non-randomly distributed clusters. Furthermore, the SIR2 histone deacetylase has opposing roles in the organization of the inter-or intrachromosomal interactions. These data establish a dynamic domain model for yeast genome organization. Moreover, they point to the repeated elements playing a central role in the dynamic organization of genome architecture.

show abstract

Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing

Cited by 210 publications

References 58 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

Distinct Roles for the Essential MYST Family HAT Esa1p in Transcriptional Silencing

Repeated elements coordinate the spatial organization of the yeast genome

Contact Info

Product

Resources

About