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Background Hemoglobin is a tetramer consisting of two α-chains and two β-chains of globin. Hereditary aberrations in the synthesis of one of the globin chains are at the root of thalassemia, one of the most prevalent monogenic diseases worldwide. In humans, in addition to α- and β-globins, embryonic zeta-globin and fetal γ-globin are expressed. Immediately after birth, the expression of fetal Aγ- and Gγ-globin ceases, and then adult β-globin is mostly expressed. It has been shown that in addition to erythroid cells, hemoglobin is widely expressed in nonerythroid cells including neurons of the cortex, hippocampus, and cerebellum in rodents; embryonic and adult brain neurons in mice; and mesencephalic dopaminergic brain cells in humans, mice, and rats. Lately, there is growing evidence that different forms of anemia (changes in the number and quality of blood cells) may be involved in (or may accompany) the pathogenesis of various cognitive and mental disorders, such as Alzheimer’s and Parkinson’s diseases, depression of various severity levels, bipolar disorders, and schizophrenia. Higher hemoglobin concentrations in the blood may lead to hyperviscosity, hypovolemia, and lung diseases, which may cause brain hypoxia and anomalies of brain function, which may also result in cognitive deficits. Methods In this study, a search for unannotated single-nucleotide polymorphisms (SNPs) of erythroid genes was initially performed using our previously created and published SNP-TATA_Z-tester, which is a Web service for computational analysis of a given SNP for in silico estimation of its influence on the affinity of TATA-binding protein (TBP) for TATA and TATA-like sequences. The obtained predictions were finally verified in vitro by an electrophoretic mobility shift assay (EMSA). Results On the basis of these experimental in vitro results and literature data, we studied TATA box SNPs influencing both human erythropoiesis and cognitive abilities. For instance, TBP–TATA affinity in the HbZ promoter decreases 6.6-fold as a result of a substitution in the TATA box (rs113180943), thereby possibly disrupting stage-dependent events of “switching” of hemoglobin genes and thus causing erythroblastosis. Therefore, rs113180943 may be a candidate marker of severe hemoglobinopathies with comorbid cognitive and mental disorders associated with cerebral blood flow disturbances. Conclusions The literature data and experimental and computations results suggest that the uncovered candidate SNP markers of erythropoiesis anomalies may also be studied in cohorts of patients with cognitive and/or mental disorders with comorbid erythropoiesis diseases in comparison to conventionally healthy volunteers. Research into the regulatory mechanisms by which the identified SNP markers contribute to the development of hemoglobinopathies and of the associated cognitive deficits will allow physicians not only to take timely and adequate measures against hemoglobinopathies but also to implement strategies preventing cognitive and mental disorders.

Glaucoma is a chronic progressive disease. It involves more than 60 million people worldwide. Primary open-angle glaucoma (POAG) is one of its commonest forms. About 2.71 million people in the United States suffered from POAG in 2011. Currently, POAG is a major cause of irreversible vision loss. The risk of blindness in patients with treated open-angle glaucoma is 27%. It is known that the death of optic nerve cells can be triggered by mechanical stress caused by ocular hypertension, which induces neuronal apoptosis and occurs in patients with POAG. Many scientific publications are dedicated to proteins and genes involved in the development of POAG, including neuronal apoptosis and the cell response to mechanical stress (CRMS). However, the molecular mechanisms underlying the pathophysiology of POAG are still poorly understood. The reconstruction of associative networks describing the functional interactions between these genes/proteins, including biochemical reactions, regulatory interactions, and transport, requires automated knowledge extraction from scientific publications. This work aims to analyze the associative networks describing molecular interactions between proteins and genes involved in CRMS, neuronal apoptosis, and the development of POAG. It has been shown that genes associated with POAG are statistically significantly overrepresented among the genes involved in the interactions between CRMS and neuronal apoptosis in comparison to what is expected on a random basis. This finding may explain how POAG causes the death of the retinal ganglion cell.

The studies of the last decade allow us to look in a new way at the possible association between the aging processes and the circadian rhythm. One of the promising directions in this area appeared thanks to the new data on the involvement of the NAD+-dependent protein deacetylase SIRT1 in the integration of the pathways of the circadian rhythm and metabolism regulation and the new NAD+ function as a “metabolic oscillator”. We present the a modification and extension of the most detailed circadian oscillator (CO) model developed in 2012 by J.K. Kim and D.B. Forger. The additional oscillator feedback with the involvement of NAMPT, SIRT1 genes/proteins, as well as NAM and NAD+, is included in it. The involvement of the CLOCK/BMAL1 transcription factor in regulating the NAMPT gene transcription determines the appropriate rhythm of mRNA expression and the NAMPT protein. Since the enzyme (this gene product) is a key in the pathway of NAD+ biosynthesis and recycling, the circadian rhythm is also typical for the fluctuation of this coenzyme level and the activity of NAD+-dependent protein deacetylase SIRT1. The deacetylation of the CO components by this enzyme closes the feedback mediated by this pathway. In particular, an increase in the Per2 protein degradation, an increase in the Bmal1 gene transcription, and the deacetylation of the chromatin of the regulatory regions of the CO genes in the area of E-boxes with subsequent transcription suppression can be revealed among the SIRT1 effects in the CO. All these processes are presented in the extended CO model that we suggested. Based on the experimental data about changes in the SIRT1 activity and NAD+ level with age, an attempt to study the effect of these age-related changes on the functioning of a CO was made. The modeling data indicate a decrease in the expression level of a number of CO genes (particularly the Bmal1 and Per2) in older age groups. An increase in the period of circadian oscillations was also registered. The results obtained indicate that a decrease in the SIRT1 activity associated with the age-related violation of the NAD+ metabolism can be one of the reasons for the violations of the functioning of a CO in the suprachiasmatic nuclei (SCN). Such violations can also entail violations of the organism’s circadian rhythms in general.

The paper presents the results of a study of the tissue­specificity of the circadian phase characteristics of biological processes in the mouse liver and kidneys. We performed a comparative analysis of the translatomes in these two organs based on experimental data on the daily dynamics of the level of translation of mouse genes from the GEO database (GSE67305 and GSE81283) obtained by ribosome profiling. Genes with a pronounced daily dynamics of translation were revealed (3 358 genes in the liver and 2 938 in the kidneys). Further, for each of the 12 time points (ZT0–ZT22), for each tissue (liver, kidneys), groups of genes that were in a phase with an increased level of translation were identified. It was assumed that the gene is in a phase with an increased level of translation if at a given time point its ribosome profiling rate for both replicas exceeded the daily average value for this gene. The greatest number of rhythmic genes in the liver has an increased level of translation at the beginning of the dark phase of the day corresponding to increased animal activity. In the kidneys, the differences in the distribution of the number of genes in the phase of an elevated translation level by the time of day were less pronounced, and the maximum number of such genes was observed from the middle of the light phase of the day to the middle of the dark one. A statistical analysis of enrichment of Gene Ontology terms in these twelve gene groups in the liver and kidneys was perform ed. Analyzing the processes, the rhythmicity of which is typical of both liver and kidneys, we have identified the processes, the circadian phase characteristics of which in these tissues coincide and the processes having essentially different temporal phase patterns for these tissues. Processes with strict tissue­specific rhythmic translation have also been identified. The approach used in our work allows us to analyze the organo/tissue­specificity of the phase characteristics of biological processes, and the results emphasize the need to take into account the phase circadian characteristics when comparing the features of the course of biological processes in various organs.

Genetic variability in genes of the circadian clock can manifest itself as a phenotypic variability of physiological functions and behavior, as well as functional disorders not only of the clock but also of other systems leading to the development of pathologies. We analyzed the influence of SNPs localized in the [–70,–20] region from the transcription start site on the promoter affinity of the TATA-binding protein (TBP) in two groups of genes that are components of the human circadian clock system. The first group is comprised of the genes of the core of the circadian oscillator (11 genes); the second comprises the genes of nearest regulatory environment of the circadian oscillator components (21 genes).The control comparison group included genes with other functions (31 genes). The SNP_TATA_Comparator web service was used to predict the effects of the SNPs in the regions of the RNA polymerase II positioning on the TBP/promoter dissociation constant. It was shown that the number of SNP markers reducing the TBP/promoter affinity in the first group of genes is significantly lower than the number of SNP markers increasing affinity (α < 10–3). The opposite was true for the comparison group. A significantly greater number of SNP markers reduced the TBP/promoter affinity than increased it (α < 10–6). Thus, this property may represent a characteristic feature of the genes of the circadian oscillator that may ensure its stability during the genetic variability of the analyzed promoter regions. These predictions are important for identifying the candidate SNP markers for various pathologies associated with the dysfunction of the circadian clock genes for further testing in the experimental and clinical studies, as well as for the verification of the mathematical models of the circadian oscillator.

The computational analysis of millions of unannotated SNPs from the 1000 Genomes Project may speed up the search for biomedical SNP markers. We combined the analysis of SNPs at the binding sites of the TATA-binding protein (TBP) using a previously described Web service (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl) with a keyword search for biochemical markers of chronopathologies that correspond to the clinical manifestations of these SNPs. We found 32 known and candidate SNP markers of circadian-rhythm disturbances in the [–70;–20] region of the promoters of 14 human genes (location of proven binding sites of TBP). These SNPs include rs17231520 and rs569033466 (both confer risk of chronopathologies in the liver); rs35036378 (behavioral chronoaberrations); rs549858786 (rheumatoid arthritis with a chronoaberration of IL1B expression); rs563207167, rs11557611, and rs5505 (all three: chronopathologies of the tumor—host balance, blood pressure, and the reproductive system); rs1143627 (bipolar disorder with circadian dependence of diagnosis and treatment); rs16887226 and rs544850971 (both: lowered resistance to endotoxins because of the imbalance between the circadian and immune systems); rs367732974 and rs549591993 (both: circadian dependence of heart attacks); rs563763767 (circadian dependence of myocardial infarction); rs2276109 and rs572527200 (both: circadian dependence of asthma attacks); rs34223104, rs563558831, and rs10168 (circadian optima of treatment with methotrexate and cyclophosphamide); and rs397509430, rs33980857, rs34598529, rs33931746, rs33981098, rs34500389, rs63750953, rs281864525, rs35518301, and rs34166473 (all: neurosensory hearing loss and restless legs syndrome). For these SNPs, we evaluated the α (significance) of changes in the affinity of TBP for promoters, where increased affinity corresponds to overexpression of the genes, and decreased affinity to deficient expression (Z-test). Verification of these 32 SNP markers according to the clinical standards and protocols may advance the field of predictive preventive personalized medicine.

Glaucoma is a chronic and progressive disease, which affects more than 60 million people worldwide. Primary open-angle glaucoma (POAG) is one of the most common forms of glaucoma. For example, about 2.71 million people in the USA had primary open-angle glaucoma in 2011. Currently POAG is a major cause of irreversible vision loss. In patients with treated open-angle glaucoma the risk of blindness reached to be about 27 %. It is known that the death of optic nerve cells can be triggered by mechanical stress caused by increased intraocular pressure, which induces neuronal apoptosis and is observed in patients with POAG. Currently, there is a large number of scientific publications describing proteins and genes involved in the pathogenesis of POAG, including neuronal apoptosis and the cell response to mechanical stress. However, the molecular- genetic mechanisms underlying the pathophysiology of POAG are still poorly understood. Reconstruction of associative networks describing the functional interactions between these genes/proteins, including biochemical reactions, regulatory interactions, transport, etc., requires the use of methods of automated knowledge extraction from texts of scientific publications. The aim of the work was the analysis of associative networks, describing the molecular-genetic interactions between proteins and genes involved in cell response to mechanical stress (CRMS), neuronal apoptosis and pathogenesis of POAG using ANDSystem, our previous development for automated text analysis. It was shown that genes associated with POAG are statistically significantly more often represented among the genes involved in the interactions between CRMS and neuronal apoptosis than it was expected by random reasons, which can be an explanation for the effect of POAG leading to the retinal ganglion cell death.

Studies of the last decade reveal a new sight on the possible link between aging processes and circadian rhythm. New data on the role of the NAD+-dependent histone deacetylase SIRT1 in the integration of regulation pathways for circadian rhythms and metabolism as well as data on a new function of the NAD+ as the ”metabolic oscillator” open a promising direction in this area. In the paper we suggested a modification and extension of the most detailed model for the circadian oscillator developed by Kim and Forger (2012). We included the additional feedback of the oscillator which concerns genes/proteins NAMPT, SIRT1, and also NAM, NAD+. The regulation of transcription for gene NAMPT by transcription factor CLOCK/BMAL1 determine the appropriate rhythm of mRNA and protein NAMPT expression. Since an enzyme product of this gene is a key in the pathway of biosynthesis and recycling of NAD+, therefore the circadian rhythm is also characteristic for the fluctuations in the level of this coenzyme and in the activity of NAD+-dependent histone deacetylase SIRT1. The deacetylation of circadian oscillator components by this enzyme closes the feedback mediated through this pathway. In particular, the effects of SIRT1 in circadian oscillator are the gain of degradation of protein Per2, increasing of the gene Bmal1 transcription, deacetylation of chromatin in regulatory regions of circadian oscillator genes in the E-boxes area with subsequent suppression of transcription. We took into account all of these processes in our extended model of the circadian oscillator. Based on the experimental data on the aging changes in the activity of SIRT1 and the level of NAD+, we attempted to study the effect of these age-related changes on the functioning of the circadian oscillator. Simulation data showed a decrease in expression level of several genes of the circadian oscillator, in particular, Bmal1 and Per2, in the older age groups. In addition, our extended model predicted an increase in the period of oscillations. The results indicate that decrease in SIRT1 activity deal with agerelated NAD+ metabolic disorder may be one of the reasons for the circadian oscillator dysfunctions in the suprachiasmatic nuclei. Such disorders may result in a breaking of the circadian rhythms in the body as a whole.

This paper presents the results of the reconstruction and analysis of the gene regulatory network of the circadian clock in mammals. Application of graph theory methods makes it possible to analyze the structure of the gene network and identify the central component of circadian clock regulation, which includes the basic regulatory loops passing through the key element of the circadian clock, the Clock/Bmal1 protein. Cluster analysis has revealed subsystems with obvious biological interpretation which are involved in the functioning of the circadian clock by interacting with the central component. This structural model, which includes the central component and functional subsystems that interact with the central component, can provide grounds for the construction of a mathematical model of the dynamics of the gene network regulating the circadian rhythm.

The review describes combined experimental and computational approaches to the investigation of the mechanisms of transcriptional regulation of eukaryotic genes and organization of transcription regulatory regions. These include (a) an analysis of the factors affecting the affinity of TBP (TATA-binding protein) for the TATA box; (b) research on the patterns of chromatin mark distributions and their role in the regulation of gene expression; (c) a study of 3D chromatin organization; (d) an estimation of the effects of polymorphisms on gene expression via high-resolution ChIP-seq and DNase-seq techniques. It was demonstrated that combined experimental and computational approaches are very important for the current understanding of transcription regulatory mechanisms and the structural and functional organization of the regulatory regions controlling transcription.

The development of in vitro technologies has produced new experimental information on protein binding onto DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent in vitro selected sequences reflect the actual structures of the real transcription factor (TF) binding sites. The Kullback–Leibler divergence has been applied to the comparison of frequency matrices of TF binding sites constructed on sets of artificially selected sequences and real sites. The similarity of core sequences of real and artificial sites has been observed for 80% of all TFs studied. For 20% of TFs, in vitro selected binding site sequences have a broader range of permissible significant nucleotides not found in real sites. The optimal lengths of DNA sequences containing real binding sites, at which the sites are recognized most accurately, are estimated by the weight matrix method. For approximately 80% of the TFs studied, the optimal binding site length notably exceeds the lengths of the core sequences, as well as the lengths of in vitro selected sites. The detected features of in vitro selected TF binding sites impose constraints on their use in the development of computer-assisted methods of the recognition of candidate sites in genomic sequences.

The circadian clock system coordinates all the processes occurring in the body and controls the rhythmic pattern in metabolic system functioning. The reciprocal relationship between molecular and genetic systems of the circadian clock and the systems responsible for carbohydrate and lipid turnover provide fine tuning both of metabolic processes and the circadian clock regulation system, permitting the body to adapt to a variable environment. NAD-dependent enzymes, protein-kinases, and transcription regulators could serve as presumable molecular components, which are responsible for such a type of relationship. Genetic models and epidemiological studies demonstrate an association between mutations in the circadian clock genes with the risk of a disturbance of metabolic processes regulation, obesity development, and other manifestations of metabolic syndrome.

Recognition of composite elements consisting of two transcription factor binding sites gets behind the studies of tissue-, stage- and condition-specific transcription. Genome-wide data on transcription factor binding generated with ChIP-seq method facilitate an identification of composite elements, but the existing bioinformatics tools either require ChIP-seq datasets for both partner transcription factors, or omit composite elements with motifs overlapping. Here we present an universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented composite elements from a single ChIP-seq dataset. This includes homo- and heterotypic composite elements of four mutual orientations of motifs, separated with a spacer or overlapping, even if recognition of motifs within composite element requires various stringencies. Analysis of 52 ChIP-seq datasets for 18 human transcription factors confirmed that for over 60% of analyzed datasets and transcription factors predicted co-occurrence of motifs implied experimentally proven protein-protein interaction of respecting transcription factors. Analysis of 164 ChIP-seq datasets for 57 mammalian transcription factors showed that abundance of predicted composite elements with an overlap of motifs compared to those with a spacer more than doubled; and they had 1.5-fold increase of asymmetrical pairs of motifs with one more conservative ‘leading’ motif and another one ‘guided’.

Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).

The study systemizes the current state of the mechanisms of the internalization of nanoparticles into living systems at all levels of organization (whole body, organ, tissue, and cell). Based on the data of the biological effects of nanoparticles with different characteristics, i.e., shape, size, composition, etc., it has been revealed that the whole set of physicochemical properties of nanoparticles define their ability to overcome biological barriers, as well as the mechanisms of cellular uptake, biodistribution in the organism, organs and tissues, biocompatibility, and cellular effects.

Reconstruction of an associative network, which represents molecular relationships among proteins, metabolites, and molecular processes associated with myopia and glaucoma was performed with the use of the ANDCell computer system which includes a database of knowledge and facts extracted automatically from PubMed. This network contains over 200 proteins and genes and more than 2000 interactions between them, including proteins and genes associated with both open-angle glaucoma and myopia. Reduction of this network and further analysis of molecular pathways revealed candidate genes for simultaneous genotyping of both myopia and open angle glaucoma.

The review describes integrated experimental and computer approaches to the investigation of the mechanisms of transcriptional regulation of the organization of eukaryotic genes and transcription regulatory regions. These include (a) an analysis of the factors affecting the affinity of TBP (TATA-binding protein) for the TATA box; (b) research on the patterns of chromatin mark distributions and their role in the regulation of gene expression; (c) a study of 3D chromatin organization; (d) an estimation of the effects of polymorphisms on gene expression via high-resolution Chip-seq and DNase-seq techniques. It was demonstrated that integrated experimental and computer approaches are very important for the current understanding of transcription regulatory mechanisms and the structural and functional organization of the regulatory regions controlling transcription.

Computer prediction of nucleosome positioning sites from DNA sequences is of great impor- tance for analyzing eukaryotic gene expression regulation. Investigation of experimentally found nucleosome positioning sites determined statistically significant contexts and revealed symmetry of their distribution about the center of a site. Internet-available software was developed to determine the profile of preference of genomic DNA for nucleosome formation (nucleosome potential) on the basis of Markov mod- els. A correlation of the nucleosome potential with the complexity of the nucleotide sequence text was es- tablished. The nucleosome potential was estimated for transcription factor binding sites, promoters, exons, and introns of eukaryotic genes. A difference in nucleosome potential between promoters of tissue-specific and constitutively expressed eukaryotic genes was shown. The software is available at the website of the In- stitute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences at the address http://wwwmgs.bionet.nsc.ru/programs/VMM/.

Analysis of deletion polymorphism of the humanc-fms gene intron 11 (∼425-bp deletion) is of particular interest because of the increased proportion of the heterozygotes among the children born from parents, one of which lacks the deletion-carrying allele, and the other is heterozygous for this allele. In this study, allele and haplotype frequencies of the polymorphism were assessed in a number of Caucasoid and Mongoloid populations of Russia. In all populations tested, relatively high prevalence of the deletion-bearing allele, ranging from 9.45% in ethnic Germans to 20.75% in Altaians, was detected. Russians and Kazakhs were characterized by intermediate frequencies of the rare allele, constituting in these populations 12.89 and 14.93%, respectively. Hardy–Weinberg expectations were met in all populations examined, pointing to a stable level of polymorphism at the c-fms intron 11. It was established by the contextual analysis of the deleted DNA fragment along with the flanking sequences that this region contained a number of transcription factor motifs (ets, CArG, and myc), potentially capable of the regulation of the M-CSF-dependant c-fms transcription. The deletion breakpoint was localized within the CArG motif, which, together with the neighboring ets motif, form the potential CArG/ets composite element. It was suggested that the allele lacking the fragment of intron 11 might be restricted in its ability to modulate the level of the c-fms transcription in response to M-CSF. The molecular epidemiological survey provided indirect evidence favoring the suggestion on the possible functional value of this gene fragment. It was demonstrated that in the samples from acute bronchitis and trichomoniasis patients allelic and genotype frequencies were significantly different from those in the population sample. In case of trichmoniasis, the frequency of rare allele was 2.4 times lower, and in case of acute bronchitis it was 2.1 times higher than in the control sample.

The GeneNet database is designed for accumulation of information on gene networks. Original technology applied in GeneNet enables description of not only a gene network structure and functional relationships between components, but also metabolic and signal transduction pathways. Specialised software, GeneNet Viewer, automatically displays the graphical diagram of gene networks described in the database. Current release 3.0 of GeneNet database contains descriptions of 25 gene networks, 945 proteins, 567 genes, 151 other substances and 1364 relationships between components of gene networks. Information distributed between 14 interlinked tables was obtained by annotating 968 scientific publications. The SRS-version of GeneNet database is freely available (http://wwwmgs.bionet.nsc.ru/mgs/systems/ genenet/).

Motivation: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation. Results: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression. Availability: The program for nucleosome sites recognition is included into the GeneExpress system; section ‘DNA Nucleosomal Organization’, http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. Contact: levitsky@bionet.nsc.ru * To whom correspondence should be addressed.

The structure of the Transcription Regulatory Regions Database (TRRD) and the principles of describing transcription regulation of eukaryotic genes in TRRD are considered. Formalized description of the structural and functional organization of the regulatory gene regions is illustrated with examples. By now, TRRD is based on 3500 original works and contains data on transcription regulation of more than 1100 genes known to possess more than 5000 transcription factor binding sites and about 1600 regulatory elements (promoters, enhancers, silencers). TRRD is available at http://www.bionet.nsc.ru/trrd/

Development of methods for mathematical simulation of biological systems and building specific simulations is an important trend of bioinformatics. Here we describe the method of generalized chemokinetic simulation generating flexible and adequate simulations of various biological systems. Adequate simulations of complex nonlinear gene networks—control system of cholesterol by synthesis in the cell and erythrocyte differentiation and maturation—are given as examples. The simulations were expressed in terms of unit processes—biochemical reactions. Optimal sets of parameters were determined and the systems were numerically simulated under various conditions. The simulations allow us to study the possible functional conditions of these gene networks, calculate the consequences of mutations, and define optimal strategies for their correction including therapeutic ones. A graphical user interface for these simulations is available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneNet/

The structural and functional organization of locus control regions (LCR) was analyzed using data of the LCR-TRRDatabase. The role of several transcription factors in the LCR function was considered. A study was made of the possible nucleosomal packing of enhancer regions in LCR. The structure and the format of LCR-TRRD are described. The database has been constructed for SRS and is available at http://wwwmgs.bionet.nsc.ru/mgs/dbases/LCR/

A complex approach to recognition of transcription factor binding sites (TFBS) has been developed, based on four methods: (i) weight matrix, (ii) information content, (iii) multidimensional alignment, and (iv) pairwise alignment with the most similar representative of known sites. It has been shown that none of the methods considered is optimal for all kinds of sites, so in each case the appropriate way of recognition should be chosen. The approach proposed allows one to minimize the errors in TFBS recognition. The program available through the Internet (http://www.sgi.sscc.ru/mgs/programs/multalig/) has been created to search for the potential TFBS in nucleotide sequences set by the user.

Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure–function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure–function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. TRRD 4.2.5 is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of the genes. Release 4.1 of TRRD offers a number of significant improvements, in particular, a more detailed description of transcription factor binding sites, transcription factors per se, and gene expression patterns in a computer-readable format. In addition, the new TRRD release provides considerably more references to other molecular biological databases. TRRD 4.1 is installed under SRS and is available through the WWW at http://www.bionet.nsc.ru/trrd/

TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. The databases are accessible via WWW:http://transfac.gbf.de/TRANSFAC orhttp://www.bionet.nsc.ru/TRRD

A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites.

The goal of creation of the Transcription Regulatory Regions Database (TRRD) was to provide a complete and adequate description of the structure-function organization of transcription regulatory regions in eukaryotic genes. TRRD contains only experimentally confirmed data about (i) transcription factor binding sites; (ii) regulatory units (promoter regions, enhancers, and silencers); and (iii) locus control regions. The main tool for searching TRRD and navigation in it is SRS. TRRD has hierarchically organized vocabularies and thesauruses used for developing specialized data retrieval tools. The current TRRD release contains information about 2308 eukaryotic genes (of them, 34 % are human genes) inputted basing on annotation of 7565 scientific papers. For these genes, the largest in the world sets of experimentally confirmed regulatory units (3439) and transcription factor binding sites (10 045) are collected in TRRD. Of them, 37 % of regulatory units and 38 % of binding sites are related to human genes. This paper characterizes groups of experiments basing on which regulatory units and binding sites are annotated. Examples of TRRD entries are given. The database is available at http://www.bionet.nsc.ru/trrd/.

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/.

Nucleosome Positioning Region Database (NPRD), which is compiling the available experimental data on locations and characteristics of nucleosome formation sites (NFSs), is the first curated NFS-oriented database. The object of the database is a single NFS described in an individual entry. When annotating results of NFS experimental mapping, we pay special attention to several important functional characteristics, such as the relationship between type of gene activity and nucleosome positioning, the influence of non-histone proteins on nucleosome formation, type of the variant of nucleosome positioning (translational or rotational), indication of tissue types and states of cell activity, description of experimental methods used and accuracy of nucleosome position determination, and the results of applying theoretical and computer methods to the analysis of contextual and conformational DNA properties. At present, the NPRD database contains 438 entries and integrates the data described in 124 original papers. The database URL: http://srs6.bionet.nsc.ru/srs6/. Then click the button 'Databank' and open the link NUCLEOSOME.