Biotechnology approach to determination of genetic and epigenetic control in cells

A series of studies aimed at developing methods and systems for analyzing epigenetic information in cells are presented. The role of the epigenetic information of cells, which is complementary to their genetic information, was inferred by comparing the predictions of genetic information with the cell behaviour observed under conditions chosen to reveal adaptation processes and community effects. Analysis of epigenetic information was developed starting from the twin complementary viewpoints of cells regulation as an 'algebraic' system (emphasis on the temporal aspect) and as a 'geometric' system (emphasis on the spatial aspect). The knowlege acquired from this study will lead to the use of cells for fully controlled practical applications like cell-based drug screening and the regeneration of organs.     

An integrated approach to Phoma systematics

Physiological and morphological characters were recorded from 55 strains of 17 Phoma taxa and one Pyrenochaeta. The results were subjected to numerical analysis and UPGMA dendrograms produced. The full results were compared with TLC profiles of secondary metabolites. Seven distinct clusters were recovered from dendrograms based on full and partial character sets and the grouping of strains within each cluster discussed. The new combination Phoma sambuci-nigrae (Sacc.) Monte, Bridge & Sutton is proposed for P. herbarum f. sambuci-nigrae Sacc.     

An integrated approach to hydropower impact assessment

The submerged aquatic vegetation of 17 Norwegian lakes is described and related to the environmental impacts that result from hydro-electric power (HEP) use of these lakes. Largely based upon physiognomical features, three main community types are discerned. These are denoted as (a) shallow-water, (b) mid-depth, and (c) deep-water community, respectively. The aquatic macrophytes are classified into a plant strategy framework. This classification suggests that these macrophytes frequently exhibit combined traits of the S (stress-tolerating), R (ruderal), and C (competitive) strategies. A plant-strategy index for the lakes is derived from the species classification and related to their HEP use.Broadly, the response features of hydrolake vegetation are: (1) a decline in species richness; (2) the gradual disappearance of the shallow-water and mid-depth communities; (3) a conspicuous absence of vascular submerged macrophytes in storage hydrolakes when lake levels change more than 7 m annually, and; (4) an increased incidence of species possessing plant strategies of the ruderal (R) type. The implications of these results for an environmental impact assessment of hydropower schemes are discussed.     

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits

SUMMARY: Investigators conducting studies of the molecular genetics of complex traits in humans often need rationally to select a set of single nucleotide polymorphisms (SNPs) from the hundreds or thousands available for a candidate gene. Accomplishing this requires integration of genomic data from distributed databases and is both time-consuming and error-prone. We developed the TAMAL (Technology And Money Are Limiting) web site to help identify promising SNPs for further investigation. For a given list of genes, TAMAL identifies SNPs that meet user-specified criteria (e.g. haplotype tagging SNPs or SNP predicted to lead to amino acid changes) from current versions of online resources (i.e. HapMap, Perlegen, Affymetrix, dbSNP and the UCSC genome browser). AVAILABILITY: TAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal. SUPPLEMENTARY INFORMATION: http://neoref.ils.unc.edu/tamal/.     

An integrated approach to uncover drivers of cancer

Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set. Our analysis correctly identified known drivers of melanoma and predicted multiple tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify candidate drivers with biological, and possibly therapeutic, importance in cancer.     

An integrated epigenetic and genetic analysis of DNA methyltransferase genes (DNMTs) in tumor resistant and susceptible chicken lines

Both epigenetic alterations and genetic variations play essential roles in tumorigenesis. The epigenetic modification of DNA methylation is catalyzed and maintained by the DNA methyltransferases (DNMT3a, DNMT3b and DNMT1). DNA mutations and DNA methylation profiles of DNMTs themselves and their relationships with chicken neoplastic disease resistance and susceptibility are not yet defined. In the present study, we analyzed the complexity of the DNA methylation variations and DNA mutations in the first exon of three DNMTs genes over generations, tissues, and ages among chickens of two highly inbred White Leghorn lines, Marek's disease-resistant line 6(3) and -susceptible line 7(2), and six recombinant congenic strains (RCSs). Among them, tissue-specific methylation patterns of DNMT3a were disclosed in spleen, liver, and hypothalamus in lines 6(3) and 7(2). The methylation level of DNMT3b on four CpG sites was not significantly different among four tissues of the two lines. However, two line-specific DNA transition mutations, CpG-->TpG (Chr20:10203733 and 10203778), were discovered in line 7(2) compared to the line 6(3) and RCSs. The methylation contents of DNMT1 in blood cell showed significant epimutations in the first CpG site among the two inbred lines and the six RCSs (P<0.05). Age-specific methylation of DNMT1 was detected in comparisons between 15 month-old and 2 month-old chickens in both lines except in spleen samples from line 7(2). No DNA mutations were discovered on the studied regions of DNMT1 and DNMT3a among the two lines and the six RCSs. Moreover, we developed a novel method that can effectively test the significance of DNA methylation patterns consisting of continuous CpG sites. Taken together, these results highlight the potential of epigenetic alterations in DNMT1 and DNMT3a, as well as the DNA mutations in DNMT3b, as epigenetic and genetic factors to neoplastic diseases of chickens.     

Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression

The recent development of whole genome association studies has lead to the robust identification of several loci involved in different common human diseases. Interestingly, some of the strongest signals of association observed in these studies arise from non-coding regions located in very large introns or far away from any annotated genes, raising the possibility that these regions are involved in the etiology of the disease through some unidentified regulatory mechanisms. These findings highlight the importance of better understanding the mechanisms leading to inter-individual differences in gene expression in humans. Most of the existing approaches developed to identify common regulatory polymorphisms are based on linkage/association mapping of gene expression to genotypes. However, these methods have some limitations, notably their cost and the requirement of extensive genotyping information from all the individuals studied which limits their applications to a specific cohort or tissue. Here we describe a robust and high-throughput method to directly measure differences in allelic expression for a large number of genes using the Illumina Allele-Specific Expression BeadArray platform and quantitative sequencing of RT-PCR products. We show that this approach allows reliable identification of differences in the relative expression of the two alleles larger than 1.5-fold (i.e., deviations of the allelic ratio larger than 6040) and offers several advantages over the mapping of total gene expression, particularly for studying humans or outbred populations. Our analysis of more than 80 individuals for 2,968 SNPs located in 1,380 genes confirms that differential allelic expression is a widespread phenomenon affecting the expression of 20% of human genes and shows that our method successfully captures expression differences resulting from both genetic and epigenetic cis-acting mechanisms.     

Connections between epigenetic gene silencing and human disease

Alterations in epigenetic gene regulation are associated with human disease. Here, we discuss connections between DNA methylation and histone methylation, providing examples in which defects in these processes are linked with disease. Mutations in genes encoding DNA methyltransferases and proteins that bind methylated cytosine residues cause changes in gene expression and alterations in the patterns of DNA methylation. These changes are associated with cancer and congenital diseases due to defects in imprinting. Gene expression is also controlled through histone methylation. Altered levels of methyltransferases that modify lysine 27 of histone H3 (K27H3) and lysine 9 of histone H3 (K9H3) correlate with changes in Rb signaling and disruption of the cell cycle in cancer cells. The K27H3 mark recruits a Polycomb complex involved in regulating stem cell pluripotency, silencing of developmentally regulated genes, and controlling cancer progression. The K9H3 methyl mark recruits HP1, a structural protein that plays a role in heterochromatin formation, gene silencing, and viral latency. Cells exhibiting altered levels of HP1 are predicted to show a loss of silencing at genes regulating cancer progression. Gene silencing through K27H3 and K9H3 can involve histone deacetylation and DNA methylation, suggesting cross talk between epigenetic silencing systems through direct interactions among the various players. The reversible nature of these epigenetic modifications offers therapeutic possibilities for a wide spectrum of disease.     

An integrated system for genetic analysis

Background  

Large-scale genetic mapping projects require data management systems that can handle complex phenotypes and detect and correct high-throughput genotyping errors, yet are easy to use.     

An integrated approach to life-cycle evolution using selective landscapes

A model which defines fitness in terms of the intrinsic rate of increase of phenotypes is used to analyse which life cycles are appropriate to which ecological circumstances. The following predictions are made for asexual animals and those sexual animals producing on average more than one daughter per brood. If there are no behavioural or physiological interactions between variables, then number of offspring per breeding should be maximized, survival until first/next breeding should be maximized, and time to first/next breeding should be minimized. If interactions occur such that altering one life-cycle variable affects another, then there are trade-offs between variables and the optimum trade-off will maximize fitness.Number of offspring per breeding will generally affect adult survivorship until next breeding. Given certain reasonable assumptions about this trade-off, high juvenile survivorship selects towards semelparity (many offspring per brood), low juvenile survivorship selects towards iteroparity (few offspring per brood). If juvenile survival depends on adult feeding, as in altricial birds, then juvenile survivorship declines as clutch size is increased. Optimal clutch size maximizes the number of surviving offspring per brood.Two trade-offs involve parental care. If parents guard their offspring they should take more risks if brood size is larger. The amount that parents feed their offspring should depend on how effective feeding is in enhancing growth. Growth may also be enhanced by taking risks, in juveniles or adults. The extent of risk-taking should depend on how effective risk-taking is in enhancing growth.If the number of offspring per brood is related to growing conditions for offspring, the prediction is that more offspring per brood should be produced if growing conditions for offspring are better. If the adult can protect the offspring, for example by encapsulating them, the amount of protection provided should depend on how effective the protection is in increasing offspring survivorship.     

Beyond neo-Darwinism--an epigenetic approach to evolution

We argue that the basic neo-Darwinian framework—the natural selection of random mutations—is insufficient to account for evolution. The role of natural selection is itself limited: it cannot adequately explain the diversity of populations or of species; nor can it account for the origin of new species or for major evolutionary change. The evidence suggests on the one hand that most genetic changes are irrelevant to evolution; and on the other, that a relative lack of natural selection may be the prerequisite for major evolutionary advance.Contrary to the neo-Darwinian view, we point out that the variations of the phenotype, on which natural selection could act, do not arise at random; they are produced by interactions between the organism and the environment during development. We propose, therefore, that the intrinsic dynamical structure of the epigenetic system itself, in its interaction with the environment, is the source of non-random variations which direct evolutionary change, and that a proper study of evolution consists in the working out of the dynamics of the epigenetic system and its response to environmental stimuli as well as the mechanisms whereby novel developmental responses are canalized.We postulate that “large” evolutionary changes could be the result of the canalization of novel developmental responses which arose from environmental challenges under conditions of relaxed natural selection, and moreover, that the canalization of novel developmental responses might involve cytoplasmic inheritance or maternal effects at least in the initial stages.     

An integrated approach to the prediction of domain-domain interactions

Background  

The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain interactions, it is crucial to understand protein interactions at the level of the domains. The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets.     

An integrated modelling approach to forecast the impact of human pressure in the Seine estuary

Within the framework of the European Water Framework Directive, the Seine-Normandie Water Agency has defined prospective scenarios describing possible trends of evolution of the pressures on water resources. In order to evaluate the resulting water quality improvement or degradation of water bodies in the Seine river basin, an integrated modelling was proposed. The approach consisted in coupling three models, the seneque model for upstream sub-basins, the ProSe model for the Seine river and main tributaries and finally the s i am1d model for the downstream estuary. After consistency verification, the integrated model was applied to scenarios proposed by the Seine-Normandie Water Agency. As a result of improvement in the nitrogen treatment by waste water treatment plants, the annual load of ammonia at the basin scale will be reduced by 65%. The oxygen and ammonia criteria in the estuary will improve from “bad” to “good”. However the nitrate criteria will remain “poor”, given the strong influence of non-point sources. Despite a 70–75% drop of the point orthophosphate loads, the criteria for this variable will also remain “poor”. The nutrient levels will be high enough to maintain eutrophication in the system; a general trend to a shift from N-limitation to P-limitation will be accentuated.     

An integrated genetics approach for identifying protein signal pathways of Alzheimer's disease

Alzheimer's disease (AD) is considered one of the most common age-associated neurodegenerative disorders, affecting millions of senior people worldwide. Combination of protein-protein interaction (PPI) network analysis and gene expression studies provides a better insight into AD. A computational approach was developed in our work to identify protein signal pathways between amyloid precursor proteins and tau proteins, which are well known as important proteins for AD. First, a modified LA-SEN method, called the network-constrained regularisation analysis, was applied to microarray data from a transgenic mouse model and AD patients. Then protein pathways were constructed based on an integer linear programming model to integrate microarray data and the PPI database. Important pathways of AD, including some cancer-related pathways, were identified finally.