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2008

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome.

Author(s) : Hanriot L, Keime C, Gay N, Faure C, Dossat C, Wincker P, Scote-Blachon C, Peyron C, Gandrillon O,
Journal : BMC Genomics
2008
BACKGROUND: "Open" transcriptome analysis methods allow to study gene expressionwithout a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. RESULTS: In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. CONCLUSION: We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.

A differential fluctuation theorem.

Author(s) : Maragakis P, Spichty M, Karplus M,
Journal : J Phys Chem B
2008
We derive a nonequilibrium thermodynamics identity (the "differential fluctuation theorem") that connects forward and reverse joint probabilities of nonequilibrium work and of arbitrary generalized coordinates corresponding to states of interest. This identity allows us to estimate the free energy difference betweendomains of these states. Our results follow from a general symmetry relation between averages over nonequilibrium forward and backward path functions derivedby Crooks [Crooks, G. E. Phys. Rev. E 2000, 61, 2361-2366]. We show how several existing nonequilibrium thermodynamic identities can be obtained directly from the differential fluctuation theorem. We devise an approach for measuring conformational free energy differences, and we demonstrate its applicability to the analysis of molecular dynamics simulations by estimating the free energy difference between two conformers of the alanine dipeptide model system. We anticipate that these developments can be applied to the analysis of laboratory experiments.

A novel role for the SMG-1 kinase in lifespan and oxidative stress resistance in Caenorhabditis elegans.

Author(s) : Masse I, Molin L, Mouchiroud L, Vanhems P, Palladino F, Billaud M, Solari F,
Journal : PLoS One
2008
The PTEN tumour suppressor encodes a phosphatase, and its daf-18 orthologue in Caenorhabditis elegans negatively regulates the insulin/IGF-1 DAF-2 receptor pathway that influences lifespan in worms and other species. In order to identify new DAF-18 regulated pathways involved in aging, we initiated a candidate RNAi feeding screen for clones that lengthen lifespan. Here, we report that smg-1 inactivation increases average lifespan in a daf-18 dependent manner. Genetic analysis is consistent with SMG-1 acting at least in part in parallel to the canonical DAF-2 receptor pathway, but converging on the transcription factor DAF-16/FOXO. SMG-1 is a serine-threonine kinase which plays a conserved role in nonsense-mediated mRNA decay (NMD) in worms and mammals. In addition, human SMG-1 has also been implicated in the p53-mediated response to genotoxic stress. The effect of smg-1 inactivation on lifespan appears to be unrelated to its NMD function, but requires the p53 tumour suppressor orthologue cep-1. Furthermore, smg-1 inactivation confers a resistance to oxidative stress in a daf-18-, daf-16- and cep-1-dependent manner. We propose that the role of SMG-1 in lifespan regulation is at least partly dependent on its function in oxidative stress resistance. Taken together, our results unveil a novel role for SMG-1 in lifespan regulation.

Adding self-renewal in committed erythroid progenitors improves the biological relevance of a mathematical model of erythropoiesis.

Author(s) : Crauste F, Pujo-Menjouet L, Genieys S, Molina C, Gandrillon O,
Journal : J Theor Biol
2008
We propose a new mathematical model of erythropoiesis that takes a positive feedback of erythrocytes on progenitor apoptosis into account, and incorporates a negative feedback of erythrocytes on progenitor self-renewal. The resulting model is a system of age-structured equations that reduces to a system of delay differential equations where the delays account for progenitor compartment duration and cell cycle length. We compare this model with experimental data on an induced-anemia in mice that exhibit damped oscillations of the hematocrit before it returns to equilibrium. When we assume no self-renewal of progenitors,we obtain an inaccurate fitting of the model with experimental data. Adding self-renewal in the progenitor compartment gives better approximations, with themain features of experimental data correctly fitted. Our results indicate the importance of progenitor self-renewal in the modelling of erythropoiesis. Moreover, the model makes testable predictions on the lifespan of erythrocytes confronted to a severe anemia, and on the progenitors behavior.

Cell-cycle regulation of cohesin stability along fission yeast chromosomes.

Author(s) : Bernard P, Schmidt C, Vaur S, Dheur S, Drogat J, Genier S, Ekwall K, Uhlmann F, Javerzat J,
Journal : EMBO J
2008
Sister chromatid cohesion is mediated by cohesin, but the process of cohesion establishment during S-phase is still enigmatic. In mammalian cells, cohesin binding to chromatin is dynamic in G1, but becomes stabilized during S-phase. Whether the regulation of cohesin stability is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behavior. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, suggesting that repeated loading cycles maintain cohesin binding. Cohesin instability in G1 depends on wpl1, the fission yeast ortholog of mammalian Wapl, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl1 is nonessential, indicating that a change in wpl1-dependent cohesin dynamics is dispensable for cohesion establishment. Instead, we find that cohesin stability increases at the time of S-phase in a reaction that can be uncoupled from DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence.

Cell-to-cell stochastic variation in gene expression is a complex genetic trait.

Author(s) : Ansel J, Bottin H, Rodriguez-Beltran C, Damon C, Nagarajan M, Fehrmann S, Francois J, Yvert G,
Journal : PLoS Genet
2008
The genetic control of common traits is rarely deterministic, with many genes contributing only to the chance of developing a given phenotype. This incompletepenetrance is poorly understood and is usually attributed to interactions between genes or interactions between genes and environmental conditions. Because many traits such as cancer can emerge from rare events happening in one or very few cells, we speculate an alternative and complementary possibility where some genotypes could facilitate these events by increasing stochastic cell-to-cell variations (or 'noise'). As a very first step towards investigating this possibility, we studied how natural genetic variation influences the level of noise in the expression of a single gene using the yeast S. cerevisiae as a model system. Reproducible differences in noise were observed between divergent genetic backgrounds. We found that noise was highly heritable and placed under a complexgenetic control. Scanning the genome, we mapped three Quantitative Trait Loci (QTL) of noise, one locus being explained by an increase in noise when transcriptional elongation was impaired. Our results suggest that the level of stochasticity in particular molecular regulations may differ between multicellular individuals depending on their genotypic background. The complex genetic architecture of noise buffering couples genetic to non-genetic robustness and provides a molecular basis to the probabilistic nature of complex traits.

Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.

Author(s) : Pantalacci S, Chaumot A, Benoit G, Sadier A, Delsuc F, Douzery E, Laudet V,
Journal : Mol Biol Evol
2008
It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of speciesto their environment. We benefited from the large amount of genomic data now available to explore the evolution of the upstream genes of the EDA pathway. In mammals, these genes are eda (encoding 2 ligands, EDA-A1 and EDA-A2), edar (EDA-A1 receptor), edaradd (EDA receptor [EDAR] adapter), xedar (EDA-A2 receptor), and troy (a XEDAR-related receptor). We show that the evolution of EDA pathway genes combines both strongly conserved features and evolutionary shifts.These shifts are found at different signaling levels (from the ligand to intracellular signaling) and at different taxonomic levels (class, suborder, andgenera). Although conserved features likely participate to the similarities found in the early development of vertebrate skin appendages, these shifts might account for innovations and specializations. Moreover, our study demonstrates that we can now benefit from the large number of sequenced vertebrate genomes toexplore the evolution of specific signaling pathways and thereby to open new perspectives for developmental biology and evolutionary developmental biology.

Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.

Author(s) : Pantalacci S, Chaumot A, Benoit G, Sadier A, Delsuc F, Douzery E, Laudet V,
Journal : Mol Biol Evol
2008
It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of speciesto their environment. We benefited from the large amount of genomic data now available to explore the evolution of the upstream genes of the EDA pathway. In mammals, these genes are eda (encoding 2 ligands, EDA-A1 and EDA-A2), edar (EDA-A1 receptor), edaradd (EDA receptor [EDAR] adapter), xedar (EDA-A2 receptor), and troy (a XEDAR-related receptor). We show that the evolution of EDA pathway genes combines both strongly conserved features and evolutionary shifts.These shifts are found at different signaling levels (from the ligand to intracellular signaling) and at different taxonomic levels (class, suborder, andgenera). Although conserved features likely participate to the similarities found in the early development of vertebrate skin appendages, these shifts might account for innovations and specializations. Moreover, our study demonstrates that we can now benefit from the large number of sequenced vertebrate genomes toexplore the evolution of specific signaling pathways and thereby to open new perspectives for developmental biology and evolutionary developmental biology.

Constraint-based knowledge discovery from SAGE data.

Author(s) : Klemal J, Blachon S, Soulet A, Cremilleux B, Gandrillon O,
Journal : In Silico Biol
2008
Current analyses of co-expressed genes are often based on global approaches suchas clustering or bi-clustering. An alternative way is to employ local methods and search for patterns--sets of genes displaying specific expression properties in a set of situations. The main bottleneck of this type of analysis is twofold--computational costs and an overwhelming number of candidate patterns which can hardly be further exploited. A timely application of background knowledge available in literature databases, biological ontologies and other sources can help to focus on the most plausible patterns only. The paper proposes, implements and tests a flexible constraint-based framework that enables the effective mining and representation of meaningful over-expression patterns representing intrinsic associations among genes and biological situations. The framework can be simultaneously applied to a wide spectrum of genomic data and we demonstrate that it allows to generate new biological hypotheses with clinical implications.

Cross talk between expression of the human T-cell leukemia virus type 1 Tax transactivator and the oncogenic bHLH transcription factor TAL1.

Author(s) : Terme J, Wencker M, Favre-Bonvin A, Bex F, Gazzolo L, Duc Dodon M, Jalinot P,
Journal : J Virol
2008
The human T-cell leukemia virus type 1 (HTLV-1) Tax transactivator is known to induce or repress various cellular genes, several of them encoding transcriptionfactors. As Tax is known to deregulate various basic bHLH factors, we looked more specifically at its effect on TAL1 (T-cell acute lymphoblastic leukemia 1), alsoknown as SCL (stem cell leukemia). Indeed, TAL1 is deregulated in a high percentage of T-cell acute lymphoblastic leukemia cells, and its oncogenic properties are well-established. Here we show that Tax induces transcription of this proto-oncogene by stimulating the activity of the TAL1 gene promoter 1b, through both the CREB and NF-kappaB pathways. It was also observed that TAL1 upregulates HTLV-1 promoter activity, in either the presence or the absence of Tax. The viral promoter is inhibited in trans by expression of the E2A protein E47, and TAL1 is able to abrogate this inhibition. These data show the existenceof a positive feedback loop between Tax and TAL1 expression and support the notion that this proto-oncogene participates in generation of adult T-cell leukemia/lymphoma by increasing the amount of the Tax oncoprotein but also possibly by its own transforming activities.

Displayed correlation between gene expression profiles and submicroscopic alterations in response to cetuximab, gefitinib and EGF in human colon cancer cell lines

Author(s) : Solmi R, Lauriola M, Francesconi M, Martini D, Voltattorni M, Ceccarelli C, Ugolini G, Rosati G, Zanotti S, Montroni I, Mattei G, Taffurelli M, Santini D, Pezzetti F, Ruggeri A, Castellani G, Guidotti L, Coppola D, Strippoli P,
Journal : BMC cancer
2008

Expression levels of estrogen receptor beta are modulated by components of the molecular clock.

Author(s) : Cai W, Rambaud J, Teboul M, Masse I, Benoit G, Gustafsson J, Delaunay F, Laudet V, Pongratz I,
Journal : Mol Cell Biol
2008
Circadian regulation of gene expression plays a major role in health and disease. The precise role of the circadian system remains to be clarified, but it is known that circadian proteins generate physiological rhythms in organisms by regulating clock-controlled target genes. The estrogen receptor beta (ERbeta) is, together with ERalpha, a member of the nuclear receptor superfamily and a key mediator ofestrogen action. Interestingly, recent studies show that disturbed circadian rhythmicity in humans can increase the risk of reproductive malfunctions, suggesting a link between the circadian system and ER-mediated transcription pathways. Here, we identify a novel level of regulation of estrogen signaling where ERbeta, but not ERalpha, is controlled by circadian clock proteins. We show that ERbeta mRNA levels fluctuate in different peripheral tissues following a robust circadian pattern, with a peak at the light-dark transition, which is maintained under free-running conditions. Interestingly, this oscillation is abolished in clock-deficient BMAL1 knockout mice. Circadian control of ERbeta expression is exerted through a conserved E-box element in the ERbeta promoter region that recruits circadian regulatory factors. Furthermore, using small interfering RNA-mediated knockdown assays, we show that the expression levels ofthe circadian regulatory factors directly influence estrogen signaling by regulating the intracellular levels of endogenous ERbeta.

Hedgehog and Wingless stabilize but do not induce cell fate during Drosophila dorsal embryonic epidermal patterning.

Author(s) : Vincent S, Perrimon N, Axelrod J,
Journal : Development
2008
A fundamental concept in development is that secreted molecules such as Wingless(Wg) and Hedgehog (Hh) generate pattern by inducing cell fate. By following markers of cellular identity posterior to the Wg- and Hh-expressing cells in theDrosophila dorsal embryonic epidermis, we provide evidence that neither Wg nor Hh specifies the identity of the cell types they pattern. Rather, they maintain pre-existing cellular identities that are otherwise unstable and progress stepwise towards a default fate. Wg and Hh therefore generate pattern by inhibiting specific switches in cell identity, showing that the specification and the patterning of a given cell are uncoupled. Sequential binary decisions without induction of cell identity give rise to both the groove cells and their posterior neighbors. The combination of independent progression of cell identity and arrest of progression by signals facilitates accurate patterning of an extremely plastic developing epidermis.

Heterobimetallic Bisphosphonate Titanium Complexes: Carbene-Like Carbanions?

Author(s) : Spichty M, Kulicke K, Neuburger M, Schaffner S, Mueller J,
Journal : European journal of inorganic chemistry
2008
A new class of carbene-like titanium complexes is easily accessible by means of a dilithiation–transmetallation sequence of a bisphosphonate. The X-ray structure of the dimeric, organometallic compound 3 reveals a nano-sized, multi-layer aggregate with titanium-metallated, trigonal planar carbon centers being devoid of Li contacts. DFT calculations show that the metallated carbon is a carbanion with only a slight carbene portion (10 %); the carbene character can be easily strengthened or weakened by varying the counterion. We anticipate that the sensitivity and flexibility to influence the electronic character of these carbene-like carbanions offers a way to design new versatile reagents with variable chemical properties.

In vitro expression of the HIV-2 genomic RNA is controlled by three distinct internal ribosome entry segments that are regulated by the HIV protease and the Gag polyprotein.

Author(s) : Ricci E, Herbreteau C, Decimo D, Schaupp A, Datta S, Rein A, Darlix J, Ohlmann T,
Journal : RNA
2008
The HIV-2 genomic RNA serves both as a messenger for protein synthesis and as a genome for viral assembly and particle production. Our previous work has shown that the HIV-2 genomic RNA encodes two additional Gag proteins that are N-terminal truncated isoforms of the p57 Gag polyprotein. In this study, by the use of mono- and bicistronic RNAs we show that translation at the three AUGs is driven by three distinct and independent internal ribosome entry segments both in vitro and ex vivo. Furthermore we used the recombinant Gag and HIV-2 protease toshow that, in vitro, translation is tightly regulated by these two viral proteins. This regulation is exerted both at the level of protein production andalso on the selection of the AUG initiation site which changes the ratio at which the three different Gag isoforms are produced.

Intracellular delivery of peptides via association with ubiquitin or SUMO-1 coupled to protein transduction domains.

Author(s) : Vitte A, Jalinot P,
Journal : BMC Biotechnol
2008
BACKGROUND: We previously developed small hybrid proteins consisting of SUMO-1 linked to an heptapeptide fused to the Tat protein transduction domain (PTD). The heptapeptide motif was selected from a library of random sequences to specifically bind HIV-1 regulatory proteins Tat or Rev. These constructs, named SHP, are able to enter primary lymphocytes and some of them inhibit HIV-1 replication. Considering these positive results and other data from the literature, we further tested the ability of ubiquitin or SUMO-1 linked to various PTD at their N-terminus to deliver within cells proteins or peptides fused downstream of their diglycine motif. In this system it is expected that the intracellular ubiquitin or SUMO-1 hydrolases cleave the PTD-Ub or PTD-SUMO-1 modules from the cargo polypeptide, thereby allowing its delivery under an unmodified form. RESULTS: Several bacterial expression vectors have been constructed to produce modular proteins containing from the N- to the C-terminus: the FLAG epitope, a cleavage site for a protease, a PTD, human ubiquitin or SUMO-1, and either GFP or the HA epitope. Nine different PTDs were tested, including the Tat basic domain, wild type or with various mutations, and stretches of arginine or lysine. It was observed that some of these PTDs, mainlythe Tat PTD and seven or nine residues long polyarginine motifs, caused association of the hybrid proteins with cells, but none of these constructs weredelivered to the cytosol. This conclusion was derived from biochemical and immunofluorescence studies, and also from the fact that free cargo protein resulting from cleavage by proteases after ubiquitin or SUMO-1 was never observed. However, in agreement with our previous observations, mutation of the diglycine motif into alanine-arginine, as in the SHP constructs, allows cytosol entry demonstrated by immunofluorescence observations on living cells and by cell fractionation analyses. This process results from a non-endocytic pathway. CONCLUSION: Our observations indicate that fusion of SUMO-1 to a peptide-PTD module allows generation of a stable hybrid protein that is easily produced in bacteria and which efficiently enters into cells but this property necessitates mutation of the diglycine motif at the end of SUMO-1, thereby impairing deliveryof the peptide alone.

Involvement of the TGF-beta and mTOR/p70S6Kinase pathways in the transformation process induced by v-ErbA.

Author(s) : Gonin-Giraud S, Bresson-Mazet C, Gandrillon O,
Journal : Leuk Res
2008
v-ErbA is the oncogenic form of TRalpha/c-ErbA which transforms chicken erythrocytic progenitors by blocking differentiation. The oncogenic property of v-ErbA has been correlated with its ability to antagonize ligand-dependent gene activation by TRalpha/c-ErbA and retinoic acid receptors. Nevertheless, its cytoplasmic retention suggests that v-ErbA could interfere with intracellular signaling pathways. We demonstrate that only the transforming form of v-ErbA confers to chicken erythroid progenitors a TGF-beta independency and induces an activation of the mTOR/p70S6K pathway. In these cells, TGF-beta and mTOR/p70S6K pathways regulate the expression of a known target gene of v-ErbA, band3. This is the first demonstration that v-ErbA is able to modulate specifically some signaling pathways leading to changes in the expression level of a gene involvedin transformation.

Large multiprotein structures modeling and simulation: the need for mesoscopic models.

Author(s) : Coulon A, Beslon G, Gandrillon O,
Journal : Methods Mol Biol
2008
Recent observational techniques based upon confocal microscopy make it possible to observe cells at a scale that has never been probed before: the mesoscopic scale. In the eukaryotic cell nucleus, many objects demonstrating phenomena occurring at this scale, such as nuclear bodies, are current subjects of investigations. But from a modeling perspective, this scale has not been widely explored, and hence there is a lack of suitable models for such studies. By reviewing higher and lower scale modeling techniques, we analyze their relevancein the context of mesoscale phenomena. We emphasize important characteristics that should be included in a mesoscopic model: an explicit continuous three-dimensional space with discrete simplified molecules that still have the characteristics of steric volume exclusion and realistic distant interaction forces. Then we present 3DSPI, a model dedicated to studies of nuclear bodies based on a simple formalism inspired from molecular dynamics and coarse-grained models: particles interacting through a potential energy function and driven by an overdamped Langevin equation. Finally, we present the features expected to beincluded in the model, pointing out the difficulties that might arise.

Lentiviral RNAs can use different mechanisms for translation initiation.

Author(s) : Ricci E, Soto Rifo R, Herbreteau C, Decimo D, Ohlmann T,
Journal : Biochem Soc Trans
2008
The full-length genomic RNA of lentiviruses can be translated to produce proteins and incorporated as genomic RNA in the viral particle. Interestingly, both functions are driven by the genomic 5'-UTR (5'-untranslated region), which harbours structural RNA motifs for the replication cycle of the virus. Recent work has shown that this RNA architecture also functions as an IRES (internal ribosome entry site) in HIV-1 and -2, and in SIV (simian immunodeficiency virus). In addition, the IRES extends to the gag coding region for all these viruses andthis leads to the synthesis of shorter isoforms of the Gag polyprotein from downstream initiation codons. In the present study, we have investigated how different members of the lentivirus family (namely HIV-1 and -2, and SIV) can initiate protein synthesis by distinct mechanisms. For this, we have used the competitive reticulocyte lysate that we have recently described. Our results show that HIV-1 is able to drive the synthesis of the Gag polyprotein both by a classical cap-dependent mechanism and an IRES, whereas HIV-2 and SIV appear to use exclusively an IRES mechanism.

Nuclear hormone receptor signaling in amphioxus.

Author(s) : Schubert M, Brunet F, Paris M, Bertrand S, Benoit G, Laudet V,
Journal : Dev Genes Evol
2008
The nuclear hormone receptors (NRs) form a superfamily of transcription factors unified by conserved protein structure and mode of function. While most members of this superfamily are activated by ligands, such as thyroid hormones, steroids, vitamin D or retinoic acid, other NRs are called orphan receptors because they have no known ligand. NR-dependent signaling is crucial for vertebrate development with the majority of receptors being expressed in the developing embryo. Due to massive gene duplications during vertebrate diversification, there are usually more NRs in vertebrates than in invertebrates. In this study, we examine the evolutionary diversification of the NR superfamily and of NR-dependent signaling in chordates (vertebrates, tunicates, and amphioxus). We take advantage of the unique features of the genome of the invertebrate amphioxus, which is characterized by a vertebrate-like gene content without having undergone massive duplications, to assess the NR signaling complement (NRs and NR coregulators) of the ancestral chordate. We find 33 NRs in amphioxus, which are more NRs than originally anticipated. This increase is mainly due to an amphioxus-specific duplication of genes encoding receptors of the NR1H group. Inaddition, there are three heterologous NRs in amphioxus that could not be placedwithin the framework of the NR superfamily. Apart from these exceptions, there is usually one amphioxus NR or NR signaling coregulator for each paralogous group of two, three, or four human receptors suggesting that the ancestral chordate had aset of 22 different NRs plus one copy of each NR coregulator.

Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis.

Author(s) : Semon M, Wolfe K,
Journal : Proc Natl Acad Sci U S A
2008
As paleopolyploid genomes evolve, the expression profiles of retained gene pairsare expected to diverge. To examine this divergence process on a large scale in a vertebrate system, we compare Xenopus laevis, which has retained approximately 40% of loci in duplicate after a recent whole-genome duplication (WGD), with itsunduplicated relative Silurana (Xenopus) tropicalis. This comparison of ingroup pairs to an outgroup allows the direction of change in expression profiles to beinferred for a set of 1,300 X. laevis pairs, relative to their single orthologs in S. tropicalis, across 11 tissues. We identify 68 pairs in which X. laevis is inferred to have undergone a significant reduction of expression in at least twotissues since WGD. Of these pairs, one-third show evidence of subfunctionalization, with decreases in the expression levels of different gene copies in two different tissues. Surprisingly, we find that genes with slow rates of evolution are particularly prone to subfunctionalization, even when the tendency for highly expressed genes to evolve slowly is controlled for. We interpret this result to be an effect of allopolyploidization. We then compare the outcomes of this WGD with an independent one that happened in the teleost fish lineage. We find that if a gene pair was retained in duplicate in X. laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs.

Reconstructing networks of pathways via significance analysis of their intersections

Author(s) : Francesconi M, Remondini D, Neretti N, Sedivy J, Cooper L, Verondini E, Milanesi L, Castellani G,
Journal : BMC Bioinformatics
2008
Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically approached by applying post hoc corrections to control the false discovery rate, without taking into account prior biological knowledge. Pathway or gene ontology analysis can provide an alternative way to relax the significance threshold applied to single genes and may lead to a better biological interpretation.

SQUAT: A web tool to mine human, murine and avian SAGE data.

Author(s) : Leyritz J, Schicklin S, Blachon S, Keime C, Robardet C, Boulicaut J, Besson J, Pensa R, Gandrillon O,
Journal : BMC Bioinformatics
2008
BACKGROUND: There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns. DESCRIPTION: We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: http://bsmc.insa-lyon.fr/squat/. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situationsis my favorite gene expressed?" as well as much more complex queries like: <<what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?>>. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated. CONCLUSION: SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.

Stem cell antigen 2: a new gene involved in the self-renewal of erythroid progenitors.

Author(s) : Bresson-Mazet C, Gandrillon O, Gonin-Giraud S,
Journal : Cell Prolif
2008
OBJECTIVES: Stem cell antigen 2 (SCA2), also known as TSA1 and LY6E, is a glycosylphosphatidylinositol-anchored molecule that belongs to the Ly-6 family and whose function remains largely unknown. We have previously shown that SCA2 is overexpressed in self-renewing avian erythroid progenitors (T2ECs) as opposed todifferentiating T2ECs. The aim of this study was to define the role of SCA2 in the switch between self-renewal and differentiation of erythroid progenitors. MATERIALS AND METHODS: We have investigated the cellular processes controlled bySCA2 in T2ECs by RNA interference and overexpression approaches. Moreover, we have used a SAGE Querying and analysis tools developed in our laboratory, to investigate the expression level of SCA2 gene in different human cell types. RESULTS: We demonstrate the regulation of SCA2 expression by TGF-beta, a growth factor essential for self-renewal of T2ECs. We establish that SCA2 knockdown by RNA interference reduced the proliferation and promoted the differentiation of T2ECs. In contrast, SCA2 overexpression inhibited differentiation of T2ECs only.Furthermore, by using a bioinformatic approach, we found that SCA2 is highly expressed in a variety of human cancer cells. We confirmed this result by quantitative PCR on human colon and kidney tissues. CONCLUSIONS: Altogether, these findings imply that SCA2 may function in a dose-dependent manner to support the self-renewal state and that its deregulation might contribute to the development of some human cancers.