In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search

Homologous recombination (HR) is a major pathway to repair DNA double-strand breaks (DSB). HR uses an undamaged homologous DNA sequence as a template for copying the missing information, which requires identifying a homologous sequence among megabases of DNA within the crowded nucleus. In eukaryotes, the conserved Rad51-single-stranded DNA nucleoprotein filament (NPF) performs this homology search. Although NPFs have been extensively studied in vitro by molecular and genetic approaches, their in vivo formation and dynamics could not thus far be assessed due to the lack of functional tagged versions of Rad51. Here we develop and characterize in budding yeast the first fully functional, tagged version of Rad51. Following induction of a unique DSB, we observe Rad51-ssDNA forming exceedingly long filaments, spanning the whole nucleus and eventually contacting the donor sequence. Emerging filaments adopt a variety of shapes not seen in vitro and are modulated by Rad54 and Srs2, shedding new light on the function of these factors. The filaments are also dynamic, undergoing rounds of compaction and extension. Our biophysical models demonstrate that formation of extended filaments, and particularly their compaction-extension dynamics, constitute a robust search strategy, allowing DSB to rapidly explore the nuclear volume and thus enable efficient HR.

Repair Foci as Liquid Phase Separation: Evidence and Limitations

In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.

Physical observables to determine the nature of membrane-less cellular sub-compartments

The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of contexts, but the mechanism of their formation is not fully understood. Several competing mechanisms exist that are difficult to distinguish empirically, including liquid-liquid phase separation, and the trapping of molecules by multiple binding sites. Here, we propose a theoretical framework and outline observables to differentiate between these scenarios from single molecule tracking experiments. In the binding site model, we derive relations between the distribution of proteins, their diffusion properties, and their radial displacement. We predict that protein search times can be reduced for targets inside a liquid droplet, but not in an aggregate of slowly moving binding sites. We use our results to reject the multiple binding site model for Rad52 foci, and find a picture consistent with a liquid-liquid phase separation. These results are applicable to future experiments and suggest different biological roles for liquid droplet and binding site foci.

An Inducible System for Silencing Establishment Reveals a Stepwise Mechanism in Which Anchoring at the Nuclear Periphery Precedes Heterochromatin Formation

In eukaryotic cells, silent chromatin is mainly found at the nuclear periphery forming subnuclear compartments that favor silencing establishment. Here, we set up an inducible system to monitor silencing establishment at an ectopic locus in relation with its subnuclear localization in budding yeast. We previously showed that introducing LacI bound lacO arrays in proximity to gene flanked by HML silencers favors the recruitment of the yeast silencing complex SIR at this locus, leading to its silencing and anchoring at the nuclear periphery. Using an inducible version of this system, we show that silencing establishment is a stepwise process occurring over several cell cycles, with the progressive recruitment of the SIR complex. In contrast, we observed a rapid, SIR-independent perinuclear anchoring, induced by the high amount of LacI binding at the lacO array leading to nucleosome eviction at this array and to the phosphorylation of H2A in the neighboring nucleosomes by Mec1 kinase. While the initial phosphorylation of H2A (H2A-P) and perinuclear anchoring are independent of the SIR complex, its latter recruitment stabilizes H2A-P and reinforces the perinuclear anchoring. Finally, we showed that Sir3 spreading stabilizes nucleosomes and limits the access of specific DNA-binding protein to DNA.

Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis

mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N-termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus.

Sir3 mediates long-range chromosome interactions in budding yeast

Physical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3–5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between distant regions, including the rDNA, telomeres, and internal Sir3-bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach, we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, Sir4), Sir2 activity, or chromosome context. Altogether, these data suggest that Sir3 acts as a molecular bridge that stabilizes long-range interactions.

Single molecule microscopy reveals key physical features of repair foci in living cells

In response to double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Here we explored the physical nature of these foci, using single molecule microscopy in living cells. Rad52, the functional homolog of BRCA2 in yeast, accumulates at DSB sites and diffuses ~6 times faster within repair foci than the focus itself, exhibiting confined motion. The Rad52 confinement radius coincides with the focus size: foci resulting from 2 DSBs are twice larger in volume that the ones induced by a unique DSB and the Rad52 confinement radius scales accordingly. In contrast, molecules of the single strand binding protein Rfa1 follow anomalous diffusion similar to the focus itself or damaged chromatin. We conclude that while most Rfa1 molecules are bound to the ssDNA, Rad52 molecules are free to explore the entire focus reflecting the existence of a liquid droplet around damaged DNA.

Time, magnitude and patterns of left ventricular remodeling after MitraClip implantation: clinical implications

Background

The reverse left ventricular remodeling (LV-R) is well known phenomenon that may occurs in a wide spectrum of heart disease, generally associated with an improvement of prognosis. Recently, conflicting data are reported from two randomized trials assessing prognosis after MitraClip implantation.

Purpose

To assess time, magnitude and pattern of LV-R and its relationship with outcome, and to assess the role of ejection fraction (EF) in selection of patients for MitraClip procedure.

Methods and results

Among 47 patients treated with MitraClip for severe mitral regurgitation (MR), 2 switched to surgical intervention. All patients underwent echo before, at discharge, 1 and 6-month after procedure (age 78.2±8.3 years, NYHA 3.74±0.44, LV EF 36.5±12.8%, logistic EuroSCORE I 22.41±8.4, STS-PROM 4.6±1.9, functional MR 82%). From baseline to 6-month reverse LV-R was defined as a ≥15% decrease in LV end-systolic volume (LVESV) and an adverse LV-R as a increase of ≥10% in LVESV, respectively. At 6-month, sustained reduction of MR ≤2 was observed in all patients, but 2; reverse LV-R occurred in 51% (23), adverse LV-R in 18% (8) and no LV-R in 31% (14) patients. In a multivariate regression model, baseline LVEDV were a strong independent predictor of reverse LV remodeling [β −0.564, 95% CI: −0.363 to −0.074; P=0.004], whereas baseline LVEF was not (P=0.126). Furthermore, an LVEDV ≤130 mL was strongly associated with reverse remodeling with an OR: 0.796 (CI: 0.052–0.792, P=0.022). During follow-up (17.5±9.3 months), in adverse/no LV-R patients mortality for any cause and hospitalization for heart failure (HF) occurred in 50% vs. 95.7% (log-rank, P value= 0.006). By Cox analysis, adverse LV-R was strongly associated with mortality for any cause and hospitalization for HF with adjusted OR of 5.6 (95% CI: 1.65–19.00, P=0.006). Finally, combining adverse/no LV-R together the risk of mortality for any cause and hospitalization for HF increased with adjusted OR of 10.08 (95% CI: 1.29–78.6, P=0.027).

Conclusion

The half of real-world patients undergoing percutaneous mitral valve repair for severe MR showed reverse remodeling. However, there was a half of patients in whom afterload mismatch resulted in early and sustained adverse and no remodeling associated with subsequently high mortality and recurrence of HF. Baseline larger LV volumes rather than EF may help us to refine selection patients for MitraClip procedure, avoiding futility.

Funding Acknowledgement

Type of funding source: None

Subtelomeres as Specialized Chromatin Domains

Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. However, current definitions of subtelomeres are generally based on synteny and are largely gene-centered. Taking into consideration both the peculiar gene content and dynamics as well as the chromatin properties of those domains, it is discussed how chromatin features can contribute to subtelomeric properties and functions, and play a pivotal role in the emergence of subtelomeres.

Physical principles and functional consequences of nuclear compartmentalization in budding yeast

One striking feature of eukaryotic nuclei is the existence of discrete regions, in which specific factors concentrate while others are excluded, thus forming microenvironments with different molecular compositions and biological functions. These domains are often referred to as subcompartments even though they are not membrane enclosed. Despite their functional importance the physical nature of these structures remains largely unknown. Here, we describe how the Saccharomyces cerevisiae nucleus is compartmentalized and discuss possible physical models underlying the formation and maintenance of chromatin associated subcompartments. Focusing on three particular examples, the nucleolus, silencing foci, and repair foci, we discuss the biological implications of these different models as well as possible approaches to challenge them in living cells.

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

The eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly, and human. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at varying levels in yeast and found that Sir3 spreads into extended silent domains (ESDs), eventually reaching saturation at subtelomeres. We observed the spread of Sir3 into subtelomeric domains associated with specific histone marks in wild-type cells, and stopping at zones of histone mark transitions including H3K79 trimethylation levels. Our study shows that the conserved H3K79 methyltransferase Dot1 is essential in restricting Sir3 spread beyond ESDs, thus ensuring viability upon overexpression of Sir3. Last, our analyses of published data demonstrate how ESDs unveil uncharacterized discrete domains isolating structural and functional subtelomeric features from the rest of the genome. Our work offers a new approach on how to separate subtelomeres from the core chromosome.

Recombination at subtelomeres is regulated by physical distance, double-strand break resection and chromatin status

Homologous recombination (HR) is a conserved mechanism that repairs broken chromosomes via intact homologous sequences. How different genomic, chromatin and subnuclear contexts influence HR efficiency and outcome is poorly understood. We developed an assay to assess HR outcome by gene conversion (GC) and break-induced replication (BIR), and discovered that subtelomeric double-stranded breaks (DSBs) are preferentially repaired by BIR despite the presence of flanking homologous sequences. Overexpression of a silencing-deficient SIR3 mutant led to active grouping of telomeres and specifically increased the GC efficiency between subtelomeres. Thus, physical distance limits GC at subtelomeres. However, the repair efficiency between reciprocal intrachromosomal and subtelomeric sequences varies up to 15-fold, depending on the location of the DSB, indicating that spatial proximity is not the only limiting factor for HR EXO1 deletion limited the resection at subtelomeric DSBs and improved GC efficiency. The presence of repressive chromatin at subtelomeric DSBs also favoured recombination, by counteracting EXO1-mediated resection. Thus, repressive chromatin promotes HR at subtelomeric DSBs by limiting DSB resection and protecting against genetic information loss.

Late-presenting right congenital diaphragmatic hernia with severe hypotrophy of the right lobe of the liver

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We report an absolute novelty in the extant scientific literature.

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Usually congenital diaphragmatic hernia is prenatally diagnosed.

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This is an autoptic finding of the co-existence of right congenital diaphragmatic hernia and important hypotrophy of the right lobe of the liver.

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We suggest to suspect the presence of congenital diaphragmatic hernia in fetus with disparity in right and left liver lobe at prenatal ultrasound.

Introduction

Congenital diaphragmatic hernia (CDH) presenting after 30 days of life is unusual and has a variant pattern of presentation.

Presentation of case

We present a death case occurred to a 34-days-old infant. The infant arrived to our emergency department in cardiac arrest after having suffered from intermittent acute abdominal pain. Autopsy confirmed the presence of a right CDH, with herniation of the right lobe of the liver into the thorax.

Discussion

Most of the cases of CDH are diagnosed prenatally or in the neonatal period. However, some patients do not develop symptoms until after the neonatal period. The relevance of our case is the co-existence of right CDH and important hypotrophy of the right lobe of the liver.

Conclusions

Evidence of this phenomenon represents an absolute novelty in the extant scientific literature. Even if rare, we suggest to suspect the presence of CDH in fetus with disparity in right and left liver lobe at prenatal ultrasound.

Spatial reorganization of telomeres in long-lived quiescent cells

Background

The spatiotemporal behavior of chromatin is an important control mechanism of genomic function. Studies in Saccharomyces cerevisiae have broadly contributed to demonstrate the functional importance of nuclear organization. Although in the wild yeast survival depends on their ability to withstand adverse conditions, most of these studies were conducted on cells undergoing exponential growth. In these conditions, as in most eukaryotic cells, silent chromatin that is mainly found at the 32 telomeres accumulates at the nuclear envelope, forming three to five foci.

Results

Here, combining live microscopy, DNA FISH and chromosome conformation capture (HiC) techniques, we report that chromosomes adopt distinct organizations according to the metabolic status of the cell. In particular, following carbon source exhaustion the genome of long-lived quiescent cells undergoes a major spatial re-organization driven by the grouping of telomeres into a unique focus or hypercluster localized in the center of the nucleus. This change in genome conformation is specific to quiescent cells able to sustain long-term viability. We further show that reactive oxygen species produced by mitochondrial activity during respiration commit the cell to form a hypercluster upon starvation. Importantly, deleting the gene encoding telomere associated silencing factor SIR3 abolishes telomere grouping and decreases longevity, a defect that is rescued by expressing a silencing defective SIR3 allele competent for hypercluster formation.

Conclusions

Our data show that mitochondrial activity primes cells to group their telomeres into a hypercluster upon starvation, reshaping the genome architecture into a conformation that may contribute to maintain longevity of quiescent cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0766-2) contains supplementary material, which is available to authorized users.

Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae

Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in S. cerevisiae of several lncRNAs within Y′ subtelomeric regions. We have called them subTERRA. These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. subTERRA transcription, carried out mainly by RNAPII, is initiated within the subtelomeric Y’ element and occurs in both directions, towards telomeres as well as centromeres. We show that subTERRA are distinct from TERRA and are mainly degraded by the general cytoplasmic and nuclear 5′- and 3′- RNA decay pathways in a transcription-dependent manner. subTERRA accumulates preferentially during the G1/S transition and in C-terminal rap1 mutant but independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomeres, loss of telomeric clustering in mitotic cells and changes in silencing of subtelomeric regions. Our data suggest that subtelomeric RNAs expression links telomere maintenance to RNA degradation pathways.

VEGF-A clinical significance in gastric cancers: immunohistochemical analysis of a wide Italian cohort

PURPOSE

The clinical significance of VEGF-A expression in gastric cancer (GC) has been reported with contradicting results. We analyzed the expression and clinical significance of VEGF-A in a wide Italian cohort of GC specimens.

METHODS

VEGF-A expression was tested by immunohistochemistry in 507 patients with GC of all clinical stages. The impact of VEGF-A on overall survival (OS) was evaluated in conjunction with clinical and pathological parameters.

RESULTS

In the Italian cohort we studied VEGF-A was not an independent prognostic factor neither at the univariate nor at multivariate analysis.

CONCLUSIONS

Although frequently expressed, in our study VEGF-A was not able to discriminate between groups of patients with different risk.

Scoring and manipulating gene position and dynamics using FROS in budding yeast

The spatial organization of the genome within the nucleus is now seen as a key contributor to genome function. Studying chromatin dynamics in living cells has been rendered possible by the development of fast microscopy coupled with fluorescent repressor operator systems (FROS). In these systems, arrays of protein-binding sites integrated at specific loci by homologous recombination are monitored through the fluorescence of tagged DNA-binding proteins. In the budding yeast, where homologous recombination is efficient, this technique, combined with targeting assay and genetic analysis, has been extremely powerful for studying the determinants and function of chromatin dynamics in living cells. However, issues have been recurrently raised in different species regarding the use of these systems. Here we discuss the different uses of gene tagging with FROS and their limitations, focusing in budding yeast as a model organism.

Estrogen and Progesterone Receptors Expression in Uterine Malignant Smooth Muscle Tumors: Correlation with Clinical Outcome

Uterine leiomyosarcomas are associated with a poor prognosis, although a considerable diversity in behavior may be found, and prolonged survival may occur. The aim of this study was to analyze the expression of estrogen (ER) and progesterone (PR) receptors in tumor specimens from uterine leiomyosarcomas, and to test their correlation with disease-free interval and cause-specific survival. This additional information may help the clinician differentiate between patients who have minimal risk of recurrence and those at greater risk of developing progressive disease. We examined specimens from 31 uterine leiomyosarcoma patients with clinical history and known follow-up. Disease-free interval and cause-specific survival rates were calculated according to the Kaplan-Meier method. According to univariate analysis, with Cox proportional hazards models, the ER expression (P=0.006 and P=0.016, respectively), PR expression (P=0.005 and P=0.016, respectively), and FIGO stage disease (P=0.011 and P=0.007, respectively) were independent predictors of the risk of recurrence and death from disease.

Spatial telomere organization and clustering in yeast Saccharomyces cerevisiae nucleus is generated by a random dynamics of aggregation-dissociation

The 32 telomeres of budding yeast form clusters, yet whether clusters are due to random localization or telomeric interactions is unclear. Data from live-cell imaging are compared with a biophysical model of telomere dynamics. Direct molecular interaction between telomeres is the key parameter that regulates telomere clustering.

Spatial and temporal behavior of chromosomes and their regulatory proteins is a key control mechanism in genomic function. This is exemplified by the clustering of the 32 budding yeast telomeres that form foci in which silencing factors concentrate. To uncover the determinants of telomere distribution, we compare live-cell imaging with a stochastic model of telomere dynamics that we developed. We show that random encounters alone are inadequate to produce the clustering observed in vivo. In contrast, telomere dynamics observed in vivo in both haploid and diploid cells follows a process of dissociation–aggregation. We determine the time that two telomeres spend in the same cluster for the telomere distribution observed in cells expressing different levels of the silencing factor Sir3 protein, limiting for telomere clustering. We conclude that telomere clusters, their dynamics, and their nuclear distribution result from random motion, aggregation, and dissociation of telomeric regions, specifically determined by the amount of Sir3.

Building silent compartments at the nuclear periphery: a recurrent theme

In eukaryotes, the genetic material is stored in the nucleus, which is enclosed in a double lipid bilayer, the nuclear envelope (NE). It protects the genome from physical stress and separates it from the rest of the cell. On top of this physical function, growing evidence shows that the nuclear periphery contributes to the 3D organization of the genome. In turn, tridimensional organization of chromatin in the nuclear space influences genome expression. Here we review recent findings on the function of this physical barrier in gene repression and latest models on how silent subnuclear compartments at the NE are built in yeast as well as in the nematode C. elegans and mammalian cells; trying to draw parallels between the three systems.

Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination

Chromatin in the interphase nucleus moves in a constrained random walk. Despite extensive study, the molecular causes of such movement and its impact on DNA-based reactions are unclear. Using high-precision live fluorescence microscopy in budding yeast, we quantified the movement of tagged chromosomal loci to which transcriptional activators or nucleosome remodeling complexes were targeted. We found that local binding of the transcriptional activator VP16, but not of the Gal4 acidic domain, enhances chromatin mobility. The increase in movement did not correlate strictly with RNA polymerase II (PolII) elongation, but could be phenocopied by targeting the INO80 remodeler to the locus. Enhanced chromatin mobility required Ino80's ATPase activity. Consistently, the INO80-dependent remodeling of nucleosomes upon transcriptional activation of the endogenous PHO5 promoter enhanced chromatin movement locally. Finally, increased mobility at a double-strand break was also shown to depend in part on the INO80 complex. This correlated with increased rates of spontaneous gene conversion. We propose that local chromatin remodeling and nucleosome eviction increase large-scale chromatin movements by enhancing the flexibility of the chromatin fiber.

Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast

A general feature of the nucleus is the organization of repetitive deoxyribonucleic acid sequences in clusters concentrating silencing factors. In budding yeast, we investigated how telomeres cluster in perinuclear foci associated with the silencing complex Sir2-Sir3-Sir4 and found that Sir3 is limiting for telomere clustering. Sir3 overexpression triggers the grouping of telomeric foci into larger foci that relocalize to the nuclear interior and correlate with more stable silencing in subtelomeric regions. Furthermore, we show that Sir3's ability to mediate telomere clustering can be separated from its role in silencing. Indeed, nonacetylable Sir3, which is unable to spread into subtelomeric regions, can mediate telomere clustering independently of Sir2-Sir4 as long as it is targeted to telomeres by the Rap1 protein. Thus, arrays of Sir3 binding sites at telomeres appeared as the sole requirement to promote trans-interactions between telomeres. We propose that similar mechanisms involving proteins able to oligomerize account for long-range interactions that impact genomic functions in many organisms.

Nuclear geometry and rapid mitosis ensure asymmetric episome segregation in yeast

BACKGROUND

Asymmetric cell division drives the generation of differentiated cells and maintenance of stem cells. In budding yeast, autonomously replicating sequence (ARS) plasmids lacking centromere elements are asymmetrically segregated into the mother cell, where they are thought to contribute to cellular senescence. This phenomenon has been proposed to result from the active retention of plasmids through an interaction with nuclear pores.

RESULTS

To investigate the mother-daughter segregation bias of plasmids, we used live-cell imaging to follow the behavior of extrachromosomal DNA. We show that both an excised DNA ring and a centromere-deficient ARS plasmid move freely in the nucleoplasm yet show a strong segregation bias for the mother cell. Computational modeling shows that the geometrical shape of the dividing yeast nucleus and length of mitosis severely restrict the passive diffusion of episomes into daughter nuclei. Predictions based on simulated nuclear division were tested with mutants that extend the length of mitosis. Finally, explaining how various anchors can improve mitotic segregation, we show that plasmid partitioning is improved by tethering the plasmid to segregating structures, such as the nuclear envelope and telomeres.

CONCLUSIONS

The morphology and brevity of mitotic division in budding yeast impose physical constraints on the diffusion of material into the daughter, obviating the need for a retention mechanism to generate rejuvenated offspring.

The budding yeast nucleus

The budding yeast nucleus, like those of other eukaryotic species, is highly organized with respect to both chromosomal sequences and enzymatic activities. At the nuclear periphery interactions of nuclear pores with chromatin, mRNA, and transport factors promote efficient gene expression, whereas centromeres, telomeres, and silent chromatin are clustered and anchored away from pores. Internal nuclear organization appears to be function-dependent, reflecting localized sites for tRNA transcription, rDNA transcription, ribosome assembly, and DNA repair. Recent advances have identified new proteins involved in the positioning of chromatin and have allowed testing of the functional role of higher-order chromatin organization. The unequal distribution of silent information regulatory factors and histone modifying enzymes, which arises in part from the juxtaposition of telomeric repeats, has been shown to influence chromatin-mediated transcriptional repression. Other localization events suppress unwanted recombination. These findings highlight the contribution budding yeast genetics and cytology have made to dissecting the functional role of nuclear structure.

Actin-related protein Arp6 influences H2A.Z-dependent and -independent gene expression and links ribosomal protein genes to nuclear pores

Actin-related proteins are ubiquitous components of chromatin remodelers and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6 binding sites along four yeast chromosomes using chromatin immunoprecipitation from wild-type and swr1 deleted (swr1Delta) cells. We find that a majority of Arp6 binding sites coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1 (H2A.Z) deposited by SWR-C. However, Arp6 binding detected at centromeres, the promoters of ribosomal protein (RP) genes, and some telomeres is independent of Swr1 and Htz1 deposition. Given that RP genes and telomeres both show association with the nuclear periphery, we monitored the ability of Arp6 to mediate the localization of chromatin to nuclear pores. Arp6 binding is sufficient to shift a randomly positioned locus to nuclear periphery, even in a swr1Delta strain. Arp6 is also necessary for the pore association of its targeted RP promoters possibly through cell cycle-dependent factors. Loss of Arp6, but not Htz1, leads to an up-regulation of these RP genes. In contrast, the pore-association of GAL1 correlates with Htz1 deposition, and loss of Arp6 reduces both GAL1 activation and peripheral localization. We conclude that Arp6 functions both together with the nucleosome remodeler Swr1 and also without it, to mediate Htz1-dependent and Htz1-independent binding of chromatin domains to nuclear pores. This association is shown to have modulating effects on gene expression.

Early initiation of a replication origin tethered at the nuclear periphery

Peripheral nuclear localization of chromosomal loci correlates with late replication in yeast and metazoan cells. To test whether peripheral positioning can impose late replication, we examined whether artificial tethering of an early-initiating replication origin to the nuclear periphery delays its replication in budding yeast. We tested the effects of three different peripheral tethering constructs on the time of replication of the early replication origin ARS607. Using the dense-isotope transfer method to assess replication time, we found that ARS607 still replicates early when tethered to the nuclear periphery using the Yif1 protein or a fragment of Sir4, whereas tethering using a Yku80 construct produces only a very slight replication delay. Single-cell microscopic analysis revealed no correlation between peripheral positioning of ARS607 in individual cells and delayed replication. Overall, our results demonstrate that a replication origin can initiate replication early in S phase, even if artificially relocated to the nuclear periphery.

The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion

Budding yeast telomeres and cryptic mating-type loci are enriched at the nuclear envelope, forming foci that sequester silent information regulators (SIR factors), much as heterochromatic chromocenters in higher eukaryotes sequester HP1. Here we examine the impact of such subcompartments for regulating transcription genome-wide. We show that the efficiency of subtelomeric reporter gene repression depends not only on the strength of SIR factor recruitment by cis-acting elements, but also on the accumulation of SIRs in such perinuclear foci. To monitor the effects of disrupting this subnuclear compartment, we performed microarray analyses under conditions that eliminate telomere anchoring, while preserving SIR complex integrity. We found 60 genes reproducibly misregulated. Among those with increased expression, 22% were within 20 kb of a telomere, confirming that the nuclear envelope (NE) association of telomeres helps repress natural subtelomeric genes. In contrast, loci that were down-regulated were distributed over all chromosomes. Half of this ectopic repression was SIR complex dependent. We conclude that released SIR factors can promiscuously repress transcription at nontelomeric genes despite the presence of "anti-silencing" mechanisms. Bioinformatic analysis revealed that promoters bearing the PAC (RNA Polymerase A and C promoters) or Abf1 binding consenses are consistently down-regulated by mislocalization of SIR factors. Thus, the normal telomeric sequestration of SIRs both favors subtelomeric repression and prevents promiscuous effects at a distinct subset of promoters. This demonstrates that patterns of gene expression can be regulated by changing the spatial distribution of repetitive DNA sequences that bind repressive factors.

Re-positioning genes to the nuclear envelope in mammalian cells: impact on transcription

The spatial organization of the genome within the nucleus is thought to contribute to genome functions. A key component of the nuclear architecture is the nuclear envelope, which is often associated with inactive chromatin. Studies in budding yeast indicate that nuclear position can directly affect gene function. However, the causal relationship between gene position and gene activity in mammalian cells has been more elusive. Several groups recently addressed this issue by tethering genes to the inner nuclear membrane. Their studies show that the nuclear periphery is not refractory to gene transcription, but can modulate the activity of certain genes. The 3D organization of the genome might, thus, provide an additional level of regulation necessary for fine-tuning gene expression.

O6-Methylguanine-DNA-methyltransferase in recurring anaplastic ependymomas: PCR and immunohistochemistry

Ependymomas are the third most common brain tumor in children. The post surgical management is controversial. There are no convincing data on an effective role for chemotherapy. O(6)-Methylguanine-DNA-Methyltransferase (MGMT) is a DNA repair protein considered to be a chemosensitivity predictor. Hypermethylation of the MGMT gene promoter is an important cause of MGMT inactivation. We evaluated the MGMT gene promoter methylation and the immunohistochemical MGMT protein expression in 12 recurrent anaplastic ependymomas affecting children. Our purpose was to investigate the molecular rationale of the administration of alkylating agents to children affected by recurrent anaplastic ependymomas. All ependymomas lacked MGMT promoter hypermethylation and 9 (75%) showed high MGMT protein expression (>50% tumoral cells). Differences between different recurrences in the same patient were not observed. These results may indicate MGMT as a factor of chemoresistance to alkylating drugs in anaplastic ependymomas and support the uncertainties regarding the actual benefit of chemotherapy for patients with anaplastic ependymomas.

Geophysical validation of MIPAS-ENVISAT operational ozone data

Abstract. The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), on-board the European ENVIronmental SATellite (ENVISAT) launched on 1 March 2002, is a middle infrared Fourier Transform spectrometer measuring the atmospheric emission spectrum in limb sounding geometry. The instrument is capable to retrieve the vertical distribution of temperature and trace gases, aiming at the study of climate and atmospheric chemistry and dynamics, and at applications to data assimilation and weather forecasting. MIPAS operated in its standard observation mode for approximately two years, from July 2002 to March 2004, with scans performed at nominal spectral resolution of 0.025 cm−1 and covering the altitude range from the mesosphere to the upper troposphere with relatively high vertical resolution (about 3 km in the stratosphere). Only reduced spectral resolution measurements have been performed subsequently. MIPAS data were re-processed by ESA using updated versions of the Instrument Processing Facility (IPF v4.61 and v4.62) and provided a complete set of level-2 operational products (geo-located vertical profiles of temperature and volume mixing ratio of H2O, O3, HNO3, CH4, N2O and NO2) with quasi continuous and global coverage in the period of MIPAS full spectral resolution mission. In this paper, we report a detailed description of the validation of MIPAS-ENVISAT operational ozone data, that was based on the comparison between MIPAS v4.61 (and, to a lesser extent, v4.62) O3 VMR profiles and a comprehensive set of correlative data, including observations from ozone sondes, ground-based lidar, FTIR and microwave radiometers, remote-sensing and in situ instruments on-board stratospheric aircraft and balloons, concurrent satellite sensors and ozone fields assimilated by the European Center for Medium-range Weather Forecasting. A coordinated effort was carried out, using common criteria for the selection of individual validation data sets, and similar methods for the comparisons. This enabled merging the individual results from a variety of independent reference measurements of proven quality (i.e. well characterized error budget) into an overall evaluation of MIPAS O3 data quality, having both statistical strength and the widest spatial and temporal coverage. Collocated measurements from ozone sondes and ground-based lidar and microwave radiometers of the Network for the Detection Atmospheric Composition Change (NDACC) were selected to carry out comparisons with time series of MIPAS O3 partial columns and to identify groups of stations and time periods with a uniform pattern of ozone differences, that were subsequently used for a vertically resolved statistical analysis. The results of the comparison are classified according to synoptic and regional systems and to altitude intervals, showing a generally good agreement within the comparison error bars in the upper and middle stratosphere. Significant differences emerge in the lower stratosphere and are only partly explained by the larger contributions of horizontal and vertical smoothing differences and of collocation errors to the total uncertainty. Further results obtained from a purely statistical analysis of the same data set from NDACC ground-based lidar stations, as well as from additional ozone soundings at middle latitudes and from NDACC ground-based FTIR measurements, confirm the validity of MIPAS O3 profiles down to the lower stratosphere, with evidence of larger discrepancies at the lowest altitudes. The validation against O3 VMR profiles using collocated observations performed by other satellite sensors (SAGE II, POAM III, ODIN-SMR, ACE-FTS, HALOE, GOME) and ECMWF assimilated ozone fields leads to consistent results, that are to a great extent compatible with those obtained from the comparison with ground-based measurements. Excellent agreement in the full vertical range of the comparison is shown with respect to collocated ozone data from stratospheric aircraft and balloon instruments, that was mostly obtained in very good spatial and temporal coincidence with MIPAS scans. This might suggest that the larger differences observed in the upper troposphere and lowermost stratosphere with respect to collocated ground-based and satellite O3 data are only partly due to a degradation of MIPAS data quality. They should be rather largely ascribed to the natural variability of these altitude regions and to other components of the comparison errors. By combining the results of this large number of validation data sets we derived a general assessment of MIPAS v4.61 and v4.62 ozone data quality. A clear indication of the validity of MIPAS O3 vertical profiles is obtained for most of the stratosphere, where the mean relative difference with the individual correlative data sets is always lower than ±10%. Furthermore, these differences always fall within the combined systematic error (from 1 hPa to 50 hPa) and the standard deviation is fully consistent with the random error of the comparison (from 1 hPa to ~30–40 hPa). A degradation in the quality of the agreement is generally observed in the lower stratosphere and upper troposphere, with biases up to 25% at 100 hPa and standard deviation of the global mean differences up to three times larger than the combined random error in the range 50–100 hPa. The larger differences observed at the bottom end of MIPAS retrieved profiles can be associated, as already noticed, to the effects of stronger atmospheric gradients in the UTLS that are perceived differently by the various measurement techniques. However, further components that may degrade the results of the comparison at lower altitudes can be identified as potentially including cloud contamination, which is likely not to have been fully filtered using the current settings of the MIPAS cloud detection algorithm, and in the linear approximation of the forward model that was used for the a priori estimate of systematic error components. The latter, when affecting systematic contributions with a random variability over the spatial and temporal scales of global averages, might result in an underestimation of the random error of the comparison and add up to other error sources, such as the possible underestimates of the p and T error propagation based on the assumption of a 1 K and 2% uncertainties, respectively, on MIPAS temperature and pressure retrievals. At pressure lower than 1 hPa, only a small fraction of the selected validation data set provides correlative ozone data of adequate quality and it is difficult to derive quantitative conclusions about the performance of MIPAS O3 retrieval for the topmost layers.

Liquid-based endometrial cytology: cyto-histological correlation in a population of 917 women

OBJECTIVE

Liquid-based cytology, because of its capacity to reduce the obscuring factors and to provide thin-layer specimens, represents an opportunity to reevaluate endometrial cytology. In order to assess the utility of the liquid-based method in endometrial diagnosis, we evaluated its accuracy in comparison with histology.

METHODS

Nine hundred and seventeen women scheduled for hysteroscopy were enrolled in the study. After providing informed consent, all the women proceeded sequentially to hysteroscopy, endometrial cytology and then biopsy endometrial sampling.

RESULTS

Cyto-histological correlations were possible in 519 cases (57%): in 361 (39%) cases the biopsy was inadequate, in 15 (2%) the cytology was inadequate, and in 22 (2%) both were inadequate. At biopsy 25 (3%) women had adenocarcinoma, 5 (1%) had adenomatous atypical hyperplasia and 21 (2%) had simple non atypical hyperplasia. At cytology two adenocarcinomas and one adenomatous atypical hyperplasia were underrated as atypical hyperplasias and as non-atypical hyperplasia; two simple non-atypical hyperplasias were reported as negative; and eight cases were false positive (non-atypical hyperplasia at cytology, negative at biopsy). In our population, the cytology provided sufficient material more often than biopsy (P < 0.04). Sensitivity was estimated at 96%, specificity at 98%, positive predictive value at 86% and negative predictive value at 99%.

CONCLUSIONS

We concluded that endometrial cytology may be an efficient diagnostic method. It could be applied to selected patients solely or in association with ultrasonography. The combination of these two noninvasive procedures may improve their diagnostic accuracy and reduce unnecessary hysteroscopies, thereby producing benefits for women and society.

Active genes at the nuclear pore complex

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.

Oxaliplatin, 5-fluorouracil/leucovorin and epirubicin as first-line treatment in advanced gastric carcinoma: a phase II study

The association between oxaliplatin and 5-fluorouracil (5-FU) has been extensively reported to improve prognosis of gastric cancer patients. The present study is aimed at evaluating response rate and the toxicity profile of the association with oxaliplatin, 5-FU/lecovorin and epirubicin in gastric cancer patients with locally advanced or metastatic disease. Thirty-six patients have been enrolled and 35 evaluated. The treatment schedule was oxaliplatin (100 mg m(-2)), 5-FU (400 mg m(-2)), leucovorin (40 mg m(-2)) and epirubicin (60 mg m(-2)) intravenously. administered every 3 weeks for 6 months, for a total of 185 therapy cycles . Response rate and toxicity were assessed according to the international WHO criteria. Every patient received a mean of 5.3 therapy cycles in a day-hospital setting. Sixteen of 35 patients (46%) showed an objective response, two complete response and 14 partial response. Median time to progression was 33 weeks with an overall median survival of 49 weeks. During the study, anaemia grade 3 and neutropenia grade 3 were observed in 9 and 11% of patients respectively. A grade 3 periferic sensorial neuropathy was observed in 6% of patients. No life threatening or cardiac toxicity was recorded. The regimen used showed anticancer activity against gastric carcinoma, a tolerable toxicity profile and excellent patient compliance.

Replication foci dynamics: replication patterns are modulated by S-phase checkpoint kinases in fission yeast

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.

In and out of the replication factory

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.

Advanced thyroid carcinoma: An experience of 385 cases

AIMS

To report clinical outcomes of a large series of cases with advanced thyroid cancer.

STUDY DESIGN

Three hundred and eighty-five patients at the UICC stages III and IV were selected for the study with thyroid cancer.

RESULTS

Papillary carcinoma and sclerosing carcinoma have better survival than the Hürthle cell and insular types. Lymphatic metastasis does not appear to worsen the prognosis. All the tumour forms offer the chance of long survival.

CONCLUSIONS

Surgical treatment is the primary treatment of thyroid carcinoma. The combined treatments of surgery, metabolic beam therapy, suppressive hormone therapy, radiotherapy and chemotherapy cure a high percentage of patients with the tumour at an advanced stage.

Nuclear pore association confers optimal expression levels for an inducible yeast gene

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.

Repairing subtelomeric DSBs at the nuclear periphery

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.

Inducible cyclooxygenase (COX-2) in glioblastoma--clinical and immunohistochemical (COX-2-VEGF) correlations

Cyclooxygenase-2 (COX-2) is the inducible form of the enzyme responsible for the first step in the prostaglandin synthesis. COX-2 upregulation is demonstrated in different tumors. COX-2 products may modulate tumoral growth, apoptosis, metastasis, multidrug resistance and angiogenesis. Moreover, the antitumoral effect of the COX inhibitors has been documented. We studied the immunohistochemical expression and the prognostic value of COX-2 on 43 surgical specimens of glioblastoma-affected patients. Furthermore, we evaluated the correlation between the immunohistochemical expression of COX-2 and vascular endothelial growth factor (VEGF). Of the glioblastomas, 63% resulted as COX-2-positive. Median survival of the patients with COX-2-positive lesions was 10 months; median survival of the patients with COX-2 negative glioblastoma was 21 months (NS). All 4 patients who survived longer than 24 months had COX-2 negative lesions (p = 0.017). Concordance between COX-2 and VEGF was documented in 60% of the cases. Our findings show that glioblastoma can immunohistochemically express COX-2 and that its expression is unrelated with VEGF and significantly less frequent in the long survivors. Nevertheless, the absence of statistical correlation with survival time advises further studies on larger series to ascertain the concrete prognostic value of COX-2 in glioblastoma.