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Team Publications Compartmentalization and Dynamics of Nuclear Functions

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Team Publications Compartmentalization and Dynamics of Nuclear Functions Team Publications Compartmentalization and Dynamics of Nuclear Functions Year of publication 2007 Angela Taddei (2007 May 1) Active genes at the nuclear pore complex. Current opinion in cell biology : 305-10 Summary The nucleus is spatially and functionally organized and its architecture is now seen as a key contributor to genome functions. A central component of this architecture is the nuclear envelope, which is studded with nuclear pore complexes that serve as gateways for communication between the nucleoplasm and cytoplasm. Although the nuclear periphery has traditionally been described as a repressive compartment and repository for gene-poor chromosome regions, several recent studies in yeast have demonstrated that repressive and activating domains can both be positioned at the periphery of the nucleus. Moreover, association with the nuclear envelope favors the expression of particular genes, demonstrating that nuclear organization can play an active role in gene regulation. Peter Meister, Angela Taddei, Aaron Ponti, Giuseppe Baldacci, Susan M Gasser (2007 Feb 17) Replication foci dynamics: replication patterns are modulated by S-phase checkpoint kinases in fission yeast. The EMBO journal : 1315-26 Summary Although the molecular enzymology of DNA replication is well characterised, how and why it occurs in discrete nuclear foci is unclear. Using fission yeast, we show that replication takes place in a limited number of replication foci, whose distribution changes with progression through S phase. These sites define replication factories which contain on average 14 replication forks. We show for the first time that entire foci are mobile, able both to fuse and re-segregate. These foci form distinguishable patterns during S phase, whose succession is reproducible, defining early-, mid- and late-S phase. In wild-type cells, this same temporal sequence can be detected in the presence of hydroxyurea (HU), despite the reduced rate of replication. In cells lacking the intra-S checkpoint kinase Cds1, replication factories dismantle on HU. Intriguingly, even in the absence of DNA damage, the replication foci in cds1 cells assume a novel distribution that is not present in wild-type cells, arguing that Cds1 kinase activity contributes to the spatio-temporal organisation of replication during normal cell growth. Year of publication 2006 Peter Meister, Angela Taddei, Susan M Gasser (2006 Jul 4) In and out of the replication factory. Cell : 1233-5 INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 1 Team Publications Compartmentalization and Dynamics of Nuclear Functions Summary In this issue of Cell, use live-fluorescence microscopy to monitor individual genomic loci as they replicate in budding yeast. They confirm that DNA is recruited to replication factories and show that sister replication forks initiated from the same origin are held together within a single replication factory. Angela Taddei, Griet Van Houwe, Florence Hediger, Veronique Kalck, Fabien Cubizolles, Heiko Schober, Susan M Gasser (2006 Jun 9) Nuclear pore association confers optimal expression levels for an inducible yeast gene. Nature : 774-8 Summary The organization of the nucleus into subcompartments creates microenvironments that are thought to facilitate distinct nuclear functions. In budding yeast, regions of silent chromatin, such as those at telomeres and mating-type loci, cluster at the nuclear envelope creating zones that favour gene repression. Other reports indicate that gene transcription occurs at the nuclear periphery, apparently owing to association of the gene with nuclear pore complexes. Here we report that transcriptional activation of a subtelomeric gene, HXK1 (hexokinase isoenzyme 1), by growth on a non-glucose carbon source led to its relocalization to nuclear pores. This relocation required the 3′ untranslated region (UTR), which is essential for efficient messenger RNA processing and export, consistent with an accompanying report. However, activation of HXK1 by an alternative pathway based on the transactivator VP16 moved the locus away from the nuclear periphery and abrogated the normal induction of HXK1 by galactose. Notably, when we interfered with HXK1 localization by either antagonizing or promoting association with the pore, transcript levels were reduced or enhanced, respectively. From this we conclude that nuclear position has an active role in determining optimal gene expression levels. Angela Taddei, Susan M Gasser (2006 Apr 20) Repairing subtelomeric DSBs at the nuclear periphery. Trends in cell biology : 225-8 Summary Nuclear organization creates microenvironments favoring distinct nuclear functions. In budding yeast, silent chromatin regions such as telomeres are clustered at the nuclear periphery, creating zones of transcriptional repression. Recently, in the Journal of Cell Biology, Therizols et al. report that “telomere tethering at the nuclear periphery is essential for DNA double strand break repair in subtelomeric regions”. Here, we discuss these results and their functional implications. INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 2 Team Publications Compartmentalization and Dynamics of Nuclear Functions Year of publication 2005 Peter Meister, Angela Taddei, Laurence Vernis, Mickaël Poidevin, Susan M Gasser, Giuseppe Baldacci (2005 Feb 14) Temporal separation of replication and recombination requires the intra-S checkpoint. The Journal of cell biology : 537-44 : DOI : 10.1083/jcb.200410006 Summary In response to DNA damage and replication pausing, eukaryotes activate checkpoint pathways that prevent genomic instability by coordinating cell cycle progression with DNA repair. The intra-S-phase checkpoint has been proposed to protect stalled replication forks from pathological rearrangements that could result from unscheduled recombination. On the other hand, recombination may be needed to cope with either stalled forks or double-strand breaks resulting from hydroxyurea treatment. We have exploited fission yeast to elucidate the relationship between replication fork stalling, loading of replication and recombination proteins onto DNA, and the intra-S checkpoint. Here, we show that a functional recombination machinery is not essential for recovery from replication fork arrest and instead can lead to nonfunctional fork structures. We find that Rad22-containing foci are rare in S-phase cells, but peak in G2 phase cells after a perturbed S phase. Importantly, we find that the intra-S checkpoint is necessary to avoid aberrant strand-exchange events during a hydroxyurea block. Angela Taddei, Danièle Roche, Wendy A Bickmore, Geneviève Almouzni (2005 Jan 21) The effects of histone deacetylase inhibitors on heterochromatin: implications for anticancer therapy? EMBO reports : 520-4 Summary Histone acetylation regulates many chromosome functions, such as gene expression and chromosome segregation. Histone deacetylase inhibitors (HDACIs) induce growth arrest, differentiation and apoptosis of cancer cells ex vivo, as well as in vivo in tumour-bearing animal models, and are now undergoing clinical trials as anti-tumour agents. However, little attention has been paid to how HDACIs function in these biological settings and why different cells respond in different ways. Here, we discuss the consequences of inhibiting histone deacetylases in cycling versus non-cycling cells, in light of the dynamics of histone acetylation patterns with a specific emphasis on heterochromatic regions of the genome. Year of publication 2004 Angela Taddei, Susan M Gasser (2004 Mar 17) INSTITUT CURIE, 20 rue d’Ulm, 75248 Paris Cedex 05, France | 3 Team Publications Compartmentalization and Dynamics of Nuclear Functions Multiple pathways for telomere tethering: functional implications of subnuclear position for heterochromatin formation. Biochimica et biophysica acta : 120-8 Summary Technical advances in the imaging of GFP derivatives in living cells have improved our ability to determine the position and dynamics of specific chromatin loci. This approach, combined with genetics and functional assays, has shed new light on how nuclear compartments facilitate gene repression in yeast. Angela Taddei, Florence Hediger, Frank R Neumann, Christoph Bauer, Susan M Gasser (2004 Mar 12) Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. The EMBO journal : 1301-12 Summary In budding yeast, the nuclear periphery forms a subcompartment in which telomeres cluster and SIR proteins concentrate. To identify the proteins that mediate chromatin anchorage to the nuclear envelope, candidates were fused to LexA and targeted to an internal GFP-tagged chromosomal locus. Their ability to shift the locus from a random to a peripheral subnuclear position was monitored in living cells. Using fusions that cannot silence, we identify YKu80 and a 312-aa domain of Sir4 (Sir4(PAD)) as minimal anchoring elements, each able to relocalize an internal chromosomal locus to the nuclear periphery. Sir4(PAD)-mediated tethering requires either the Ku complex or Esc1, an acidic protein that is localized to the inner face of the nuclear envelope even in the absence of Ku, Sir4 or Nup133. Finally, we demonstrate that Ku- and Esc1-dependent pathways mediate natural telomere anchoring in vivo. These data provide the first unambiguous identification of protein interactions that are both necessary and sufficient to localize chromatin to the nuclear envelope. Florence Hediger, Angela Taddei, Frank R Neumann, Susan M Gasser (2004 Feb 12) Methods for visualizing
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