Analysis of the circadian rhythm of biological processes in mouse liver and kidney

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

GeneNet in 2005

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/

Detection and analysis of dynamic patterns of diurnal expression of mammalian genes

The purpose of the study is to identify and analyze patterns of the diurnal dynamics of the expression of genes that differ in the shape of the curve. It can be expected that the similarity of the patterns of daily expression (shape of the curve) of genes is a reflection of the synchronization of gene expression by common external and internal signals or participation in similar biological processes. Different signals that have daily dynamics (light, activity, nutrition, stress, temperature, etc.) can affect different levels of expression regulation, which can be manifested in various forms of patterns of daily gene expression. In our research, we used experimental data on gene expression at the level of translation (ribosome profling) in the liver and kidney of a mouse (GSE67305 and GSE81283). To identify genes with a daily rhythm of expression, we used a oneway analysis of variance. To identify similar­in­shape curves of the daily dynamics of gene expression, we propose an approach based on cluster analysis. The distance between the genes was calculated by aligning the phases and fnding the maximum cross­correlation between the patterns of the daily expression of these genes by the cyclic shift. This approach allowed us to identify genes that have not only expression patterns with a single maximum (sinusoidal, asymmetrical, shifted to the left or right, pulsed), but also complex composite signals with several extremes. As a result, the groups of genes united by the similarity of the shape of the daily expression curve without regard to their phase characteristics were identifed. GO enrichment analysis of groups of genes with sharply different patterns of daily expression (sinusoidal and pulsed) in the mouse kidneys and liver showed that the group of genes with a sinusoidal pattern was more associated with regulation of circadian rhythm and metabolism. The group of genes with a pulsed pattern is largely associated with the protective functions of the organism, which require the quick response. Thus, our studies have confrmed the effectiveness of the proposed approach to the analysis of the diurnal dynamics of gene expression. The identifed dynamic patterns of diurnal expression are important for the further study of complex circadian regulation, synchronization and interaction of biological processes with diurnal dynamics in mammals

Computational model for mammalian circadian oscillator: interacting with NAD+/SIRT1 pathway and age-related changes in gene expression of circadian oscillator

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

Ontologies in bioinformatics and systems biology

Computer simulation is now becoming a central scientific paradigm of systems biology and the basic tool for the theoretical study and understanding of the complex mechanisms of living systems. The increase in the number and complexity of these models leads to the need for their collaborative development, reuse of models, and their verification, and the description of the computational experiment and its results. Ontological modeling is used to develop formats for knowledge-oriented mathematical modeling of biological systems. In this sense, ontology associated with the entire set of formats, supporting research in systems biology, in particular, computer modeling of biological systems and processes can be regarded as a first approximation to the ontology of systems biology. This review summarizes the features of the subject area (bioinformatics, systems biology, and biomedicine), the main motivation for the development of ontologies and the most important examples of ontological modeling and semantic analysis at different levels of the hierarchy of knowledge: the molecular genetic level, cellular level, tissue levels of organs and the body. Bioinformatics and systems biology is an excellent ground for testing technologies and efficient use of ontological modeling. Several dozens of verified basic reference ontologies now represent a source of knowledge for the integration and development of more complex domain models aimed at addressing specific issues in biomedicine and biotechnology. Further formalization and ontological accumulation of knowledge and the use of formal methods of analysis can take the entire cycle of research in systems biology to a new technological level

The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock

Genetic variability in the genes of circadian clock is manifested as the phenotypic variability of physiological functions and behavior as well as disorders of the function of not only the clock but also other systems, leading to the development of a pathologies. We analyzed the influence of SNPs localized in the [–70, –20] region from the transcription start site of the gene on TBP / promoter affinity in two groups of genes that are components of the system of human circadian clock. The first group comprises the genes of the circadian oscillator core (11 genes); the second, the genes of the nearest regulatory environment of the circadian oscillator (21 genes). A group for comparison included genes with another function (31 genes). The SNP_TATA_Comparator web service was used for prediction of the effect of SNPs in the regions of positioning of RNA polymerase II on the dissociation constant for TBP / promoter. It was shown that the number of SNP markers reducing the TBP / promoter affinity in the first group of genes significantly lower than the number of SNP markers increasing affinity (α < 10–3). The reverse was true of the comparison group: SNP markers reduced TBP / promoter affinity to a significantly greater extent than the SNP marker increased affinity (α < 10–6). This property may be a characteristic feature of genes  of the circadian oscillator. These predictions are important for identification of candidate SNP markers of various pathologies associated with the dysfunction of circadian clock genes for further testing them in experimental and clinical studies, as well as for verification of mathematical models of the circadian oscillator

Biomedical and candidate SN P markers of chronopathologies can significantly change affinity of ТАТА -binding protein for human gene promoters

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 in the binding sites of ТАТА - binding protein (ТВР) using a previously described W eb service (http://beehive.bionet.nsc.ru/cgi-bin/mgs/ tatascan/start.pl) with a keyword search for biochemicalmarkers of chronopathologies, which correspond to clinical manifestations of these SNPs. In the [–70; –20] region of promoters of 14 human genes (location of proven binding sites of ТВР), we found 32 known and candidate SNP markers of circadian- rhythm disturbances, including rs17231520 and rs569033466 (both: risk of chronopathologies in 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 α (significance) of changes in the affinity of ТВР 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 clinical standards and protocols may advance the field of predictive preventive personalized medicine

Molecular-genetic mechanisms of the interaction between processes of cell response to mechanical stress and neuronal apoptosis in primary open-angle glaucoma

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

THE MAMMALIAN CIRCADIAN CLOCK: GENE REGULATORY NETWORK AND THEIR COMPUTER ANALYSIS

This paper presents the results of the reconstruction and analysis of 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 circuits passing through the key element of the circadian clock, the Clock/Bmal1 protein. Cluster analysis has revealed subsystems with clear 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

INFORMATION SUPPORT OF RESEARCH ON TRANSCRIPTIONAL REGULATORY MECHANISMS: AN ONTOLOGICAL APPROACH

By now, a huge body of experimental data on gene transcription regulation has been accumulated. Transcription is controlled by a great number of proteins acting at various steps of the process; thus, a diversity of regulatory mechanisms can be realized. This paper presents approaches to building knowledge domain ontology, formalized description of the mechanisms of transcriptional regulation and the development of methods for integration of heterogeneous information on the features of the regulation of gene expression on this base. The pilot version of the knowledge base on the transcriptional regulation of eukaryotic genes includes: (1) description of basic terms related to transcription regulation and relationships between them; (2) hierarchical classification of transcription regulators; (3) classification of phases and steps of transcription; (4) a database of transcriptional regulators of three mammalian species (human, mouse, and rat); and (5) dictionaries for molecular processes involved in transcriptional regulation. The knowledge base is designed for information support of computer analysis of transcriptional regulatory mechanisms. Approaches to reconstruction of eukaryotic transcriptional regulatory mechanisms with the new knowledge base are presented