Nup-PI: The Nucleopore-Promoter Interaction of Genes in Yeast

Schmid, Manfred; Arib, Ghislaine; Laemmli, Caroline; Nishikawa, J; Durussel, Thérèse; Laemmli, Ulrich Karl

doi:10.1016/j.molcel.2005.12.012

Cited by 231 publications

(248 citation statements)

References 26 publications

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“…Examples of this in yeast are the preference of telomeres (Hediger et al 2002), centromeres (Heun et al 2001a), and silenced chromatin (Maillet et al 1996;Feuerbach et al 2002) for the nuclear periphery, the localization of various highly expressed and inducible genes to nuclear pores (Brickner and Walter 2004;Casolari et al 2004Casolari et al , 2005Schmid et al 2006), and the colocalization of ribosomal DNA and a majority of tRNA genes at the nucleolus. To accommodate each of these known levels of organization, there are likely to be multiple collaborating mechanisms.…”

Section: Discussionmentioning

confidence: 99%

“…The long-range movement of at least one inducible gene requires actin/myosin (Chuang et al 2006). The transcription-dependent tethering of some genes at the nuclear pore depends on interactions between the gene promoters and the basket of the nuclear pore complex (Schmid et al 2006). Centromere clustering at the spindle pole body requires microtubules (Bystricky et al 2004), as does homologous recombination, which requires spatial proximity of the two loci (Thrower et al 2003).…”

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confidence: 99%

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Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

et al. 2008

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The 274 tRNA genes in Saccharomyces cerevisiae are scattered throughout the linear maps of the 16 chromosomes, but the genes are clustered at the nucleolus when compacted in the nucleus. This clustering is dependent on intact nucleolar organization and contributes to tRNA gene-mediated (tgm) silencing of RNA polymerase II transcription near tRNA genes. After examination of the localization mechanism, we find that the chromosome-condensing complex, condensin, is involved in the clustering of tRNA genes. Conditionally defective mutations in all five subunits of condensin, which we confirm is bound to active tRNA genes in the yeast genome, lead to loss of both pol II transcriptional silencing near tRNA genes and nucleolar clustering of the genes. Furthermore, we show that condensin physically associates with a subcomplex of RNA polymerase III transcription factors on the tRNA genes. Clustering of tRNA genes by condensin appears to be a separate mechanism from their nucleolar localization, as microtubule disruption releases tRNA gene clusters from the nucleolus, but does not disperse the clusters. These observations suggest a widespread role for condensin in gene organization and packaging of the interphase yeast nucleus.[Keywords: tRNA gene; condensin; microtubules; nuclear organization; nucleolus] Supplemental material is available at http://www.genesdev.org.

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Section: Discussionmentioning

confidence: 99%

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Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

et al. 2008

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“…It has been suggested that chromatin loops are formed through association of insulator elements with the nuclear pores (32,33,52). It is therefore possible that the barrier elements flanking HMR (21,22) or the hypersensitive sites at this locus (45) associate with nuclear pores or active chromatin hubs and cluster in the nucleus, the consequence of which would be to align HMR-E and HMR-I in close proximity.…”

Section: Discussionmentioning

confidence: 99%

“…Similarly, in yeast the promoters and terminators of genes are in close proximity to one another (3,48) and tethered to the nuclear pore (10,52). The consequence of this spatial organization is that the DNA between these regulatory elements is looped out.…”

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Long-Range Communication between the Silencers of HMR

Valenzuela

Dhillon

Dubey

et al. 2008

Molecular and Cellular Biology

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Gene regulation involves long-range communication between silencers, enhancers, and promoters. In Saccharomyces cerevisiae, silencers flank transcriptionally repressed genes to mediate regional silencing. Silencers recruit the Sir proteins, which then spread along chromatin to encompass the entire silenced domain. In this report we have employed a boundary trap assay, an enhancer activity assay, chromatin immunoprecipitations, and chromosome conformation capture analyses to demonstrate that the two HMR silencer elements are in close proximity and functionally communicate with one another in vivo. We further show that silencing is necessary for these long-range interactions, and we present models for Sir-mediated silencing based upon these results.Gene activation and gene repression are central to the proper development and differentiation of organisms. DNA elements such as promoters, enhancers, and silencers play a central role in eukaryotic gene regulation. These elements are separated from each other by several kilobase pairs of DNA but are able to communicate with one another to regulate the activation or repression of genes. The exact mechanism by which distally located elements communicate with one another is not clear and is one of the key questions in gene regulation. Long-range communication between distantly located elements in chromosomes is thought to occur by one of two principal mechanisms (8). One class of models postulate that a signal emanating from a distal regulatory element spreads along the DNA fiber until it encounters a proximal regulatory element. A second class of models postulate that distal and proximal regulatory elements interact with one another directly, with the intervening DNA forming a loop. Both mechanisms must function within the context of the global chromosome structure, which appears to be composed of large chromosome loops that attach to a proteinaceous superstructure (11). The nucleus appears to be divided further into distinct chromatin compartments, with heterochromatic domains being present in regions near the nuclear periphery while euchromatic domains are found mainly in the interior of the nucleus, although a significant portion of euchromatin is located near nuclear pores.It has been suggested that the functionally and structurally defined chromatin domains may be coincident (36). Enhancers and locus control regions (LCRs) are long-range regulatory elements that activate promoters in a distance-and orientation-independent manner, and recent studies indicate that enhancers and LCRs often cluster together in three-dimensional space to form an "active chromatin hub" (23,49,58,59).Similarly, in yeast the promoters and terminators of genes are in close proximity to one another (3, 48) and tethered to the nuclear pore (10, 52). The consequence of this spatial organization is that the DNA between these regulatory elements is looped out. It is thought that the formation of these nuclear substructures aids in transcription activation.Silencers are negative regulatory element...

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“…These transcribed genes interact with components of the nuclear pore complex (NPC) 4 (5,(7)(8)(9)(10), perhaps facilitating efficient mRNA processing and export. Although this phenomenon of locus association with the nuclear periphery has been reproducibly observed in yeast (5)(6)(7)(8)(9)(10), critical questions remain unanswered regarding the mechanism of locus recruitment to the NPC. Transcription factors, chromatin modifying complexes, and the transcription machinery itself have each been independently implicated in directing active loci to the NPC (8 -12), perhaps suggesting a recruitment mechanism dependent upon transcription initiation.…”

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confidence: 99%

Actively Transcribed GAL Genes Can Be Physically Linked to the Nuclear Pore by the SAGA Chromatin Modifying Complex

Luthra

Kerr

Harreman

et al. 2007

Journal of Biological Chemistry

119

112

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Recent work has demonstrated that some actively transcribed genes closely associate with nuclear pore complexes (NPC) at the nuclear periphery. The Saccharomyces cerevisiae Mlp1 and Mlp2 proteins are components of the inner nuclear basket of the nuclear pore that mediate interactions with these active genes. To investigate the physical link between the NPC and active loci, we identified proteins that interact with the carboxyl-terminal globular domain of Mlp1 by tandem affinity purification coupled with mass spectrometry. This analysis led to the identification of several components of the Spt-Ada-Gcn5-acetyltransferase (SAGA) histone acetyltransferase complex, Gcn5, Ada2, and Spt7. We utilized co-immunoprecipitation and in vitro binding assays to confirm the interaction between the Mlp proteins and SAGA components. Chromatin immunoprecipitation experiments revealed that Mlp1 and SAGA components associate with the same region of the GAL promoters. Critically, this Mlp-promoter interaction depends on the integrity of the SAGA complex. These results identify a physical association between SAGA and the NPC, and support previous results that relied upon visualization of GAL loci at the nuclear periphery by microscopy (Cabal, G. G. Genovesio, A., Rodriguez-Navarro, S., Zimmer, C., Gadal, O., Lesne, A., Buc, H., Feuerbach-Fournier, F., Olivo-Marin, J.-C., Hurt, E. C., and Nehrbass, U. (2006) Nature 441, 770 -773). We propose that a physical interaction between nuclear pore components and the SAGA complex can link the actively transcribed GAL genes to the nuclear pore.

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Nup-PI: The Nucleopore-Promoter Interaction of Genes in Yeast

Cited by 231 publications

References 26 publications

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

Long-Range Communication between the Silencers of HMR

Actively Transcribed GAL Genes Can Be Physically Linked to the Nuclear Pore by the SAGA Chromatin Modifying Complex

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