International conference on bioinformatics of genome regulation
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Key words: postgenome medicine, diagnostic patterns, molecular profiling N-of-one science is destined to serve a particular individual who is considered as an “uber-client” but not a “patient”. Normally we observe n-of-one science in connection with gadgets and Internet-services for non-obtrusive life couching. For example, num- ber of steps taken a day is counted by owners of the wearable devices. The postgeno- me medicine rests upon the application of multi-omics technologies to observe human physiology at the molecular level. Instead of searching a singe-molecule biomarkers of disease, the postgenome medicine operates with an ensembles of molecules, which comprise the diagnostic patterns of health and disease. By definition the molecular si- gnatures are surrogate, as the specific disease-related biomarkers cannot be revealed due to analytical limit of detection. We observed that molecular profiling could specifically characterize the human health in case it is collected sequentially over a period of time. That provides a technology challenge to collect these profiles 100 times faster and at least 10 times cheaper in comparison to the biochemical blood-tests. The methods of direct mass-spectrometry coupled with novelties in technology of ionization and ion separation are described as a possible solution of n-of-one challenge for the sake of the postgenome medicine. 176 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY DNA DUPLEX STRUCTURE AND THERMODYNAMICS BY MOLECULAR DYNAMICS SIMULATION A.A. Lomzov*, D.V. Pyshnyi Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia * Corresponding author: lomzov@niboch.nsc.ru Key words: DNA, molecular dynamics simulation, hybridization thermodynamics Motivation and Aim: Prediction of the thermal stability of double stranded DNA is use- ful in basic research (e.g. protein – nucleic acid interaction) and in a number of applica- tions (e.g. PCR, biosensing). The development of new derivatives and analogs of nucleic acid with improved characteristics for purposes of molecular biology, biotechnology and biomedicine is still of current interests. New derivatives not always have the same physico-chemical and molecular-biological properties as were proposed at development. The essential problem is the reliable prediction of hybridization properties of nucleic acids derivatives and analogues. The nearest-neighbor model is the only one which al- lows calculating enthalpy, entropy and Gibbs free energy changes only for experimen- tally well-studied native nucleic acid and for a limited number of their derivatives. The development of new tools for reliable prediction of nucleic acids complex properties is a serious challenge. Recently we have shown the possibility of high accuracy calculation of hybridization enthalpy for native fully complementary DNA duplex [1]. In this work we have evaluate the hybridization enthalpy and Gibbs free energy. Methods and Algorithms: Molecular dynamics simulations of a set of oligonucleotides and its complexes were performed in implicit and explicit solvent shell using parmbsc0 force field in AMBER12 software package. Conformational contribution in hybridiza- tion entropy was evaluated using normal mode analysis and quasi-harmonic calculations. Results: Calculated values of conformational entropy correlate well with experimental data and values calculated using nearest neighbor model [2]. The linear correlation be- tween the values calculated using quasi-harmonic and nearest-neighbor models has a slope 1.05, intercept -84.0 cal/mol/K and R2=0.97 for 305 DNA complexes of different length (4-20 bp) and GC-content (0-100%). Conclusion: The use of combination of molecular dynamic simulation in explicit solvent with MM/PBSA and Quasi-harmonic calculation allows good evaluation of thermody- namic parameters of formation perfectly matched DNA duplexes. Availability: This is a first step in prognostic calculations of physico-chemical proper- ties of nucleic acids derivatives and development of new analogs with predetermined characteristics. Acknowledgements: This work was supported by RFBR #16-04-01029. References: 1. A.A.Lomzov et al. (2015) Evaluation of Gibbs free energy changes and melting temperatures of DNA/ DNA duplexes using hybridization enthalpy calculated by molecular dynamics simulation, The Journal of Physical Chemistry B, 119: 15221–15234. 2. A.A.Lomzov et al. (2006) Thermodynamic parameters for calculating the stability of complexes of bridged oligonucleotides, Doklady Biochemistry Biophysics, 409: 211-215. 177 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY EVOLUTION OF PHENOTYPIC CONTROL BY NEW GENES THROUGH INTEGRATING AND REWIRING OF ANCESTRAL EXPRESSION NETWORKS M. Long* Department of Ecology and Evolution, University of Chicago, Chicago, USA Key words: evolution, gene networks We have observed that new genes quickly evolved essential functions in mammals and fruit flies.These observations, while overturning the conventional notion of evolutionar- ily static protein coding gene functions, raised a new question of how a new gene ac- quires essential functions.We proposed a hypothesis that a new gene may be integrated into and reshape ancestral gene-gene interaction (GGI) networks and thus subsequently create a hub topological structure with essential genetic control of a phenotype distinct from the new gene absent species that maintain ancestral networks. We examined the network topological and functional evolution of new genes that originated at various stages in humans, mouse and fruit flies, by constructing and analyzing various GGI net- works. We computationally and experimentally identified a large number of new genes in various topological positions in GGI networks, showing distinct evolutionary patterns in mammalian and Drosophila lineages. These genes experienced a stepwise integra- tion process into GGI networks, starting on the network periphery and eventually be- coming highly connected hubs, and acquiring pleiotropic and essential functions. We identified species-specific hub genes that have evolved critical or essential functions in development, brains and behaviors, supported by increasing mechanistic analyses of young genes in literatures. We explored the possible underlying mechanisms driving the GGI network evolution and the observed patterns of new gene integration process and identified certain mechanisms distinct from interpretations of general network scientific theories. We propose that the difference in effective population sizes in humans and fruit flies plays a significant role in shaping their strikingly different evolutionary patterns. References: 1. Chen et al, 2013. Nature Reviews Genetics. 14: 645–60. 2. Zhang et al, 2015. Genome Biology. 16:202. 3. Krinsky et al, 2016. bioRxiv.dx.doi.org/10.1101/045385 4. Andrea R Gschwend 178 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY TARGETED SPATIAL GENOME MODIFICATION IN TOPOLO-GICALLY ASSOCIATING DOMAINS STRUCTUREIN MOUSE EMBRYONIC STEM CELLS V.A. Lukyanchikova*, N.R. Battulin, O.L. Serov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia * Corresponding author: lukyanchikova_varvara@mail.ru Key words: 3D-genome organization, TADs, CTCF sites, genomic deletions, CRISPR/Cas9, mESCs Motivation and Aim: it was recently shown that genomes of higher eukaryotes are parti- tioned at a sub-megabase self-interacting units termed topologically associating domains (TADs) (Dixon et al., 2012). Molecular basis of TADs structure, the mechanism of its maintenance, and the role in regulation of gene expression are still important funda- mental questions. Due to the latest reports, cohesin complex and CTCF protein are key players of TADs formation (Guo et al. 2015, Nichols et al., 2015), whilst dislocations in domain boundaries and disruptions of CTCF-binding sites can lead to faults in gene regulation and to activation of oncogenes (Lupiáñez et al., 2015, Hnisz et al., 2016). So, generation of cell lines and animal models with modified TADs boundaries can reveal the natural meaning of TADs integrity and mechanisms of TADs maintenance in general. Methods and Algorithms: we were focused on the murine genomic locus between Kdr and c-Kit, chr5:76,240,000-76,280,000 (UCSC Genome Browser on Mouse July 2007 (NCBI37/mm9) Assembly). This region contains well-defined TAD boundary co-local- ized with CTCF-binding sites, while neighboring Kdr and c-Kit genes are mainly in- volved in embryonic development and have a detectable level of expression in mESCs. To remove the chosen region from mESC genome we utilized CRISPR/Cas9 editing tool (Mali et al., 2013b). Real-time PCR was used to characterize alterations in gene expres- sion pattern. Results and Conclusion: we have produced mESCs lines with genomic deletions of 1, 2 and 4 CTCF-binding sites in Kdr/c-Kit-region. Karyotype screening of all obtained cell clones has been performed, and gene expression from only ones which have balanced karyotype was analyzed with real-time PCR. Data analysis has demonstrated the signifi- cant shift in expression patterns of neighboring genes which can be evidence of gene regulation impairment due to deletion of TAD boundary. Acknowledgements: This project was supported by the Russian Foundation for Basic Research (grant 16-04-01453 А). References: 1. Dixon, Jesse R., et al. “Topological domains in mammalian genomes identified by analysis of chroma- tin interactions.”Nature 485.7398 (2012): 376-380; 2. Guo, Ya, et al. “CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter func- tion.” Cell 162.4 (2015): 900-910; 3. Nichols, Michael H., and Victor G. Corces. “A CTCF code for 3d genome architecture.” Cell 162.4 (2015): 703-705; 4. Lupiáñez, Darío G., et al. “Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.” Cell 161.5 (2015): 1012-1025; 5. Hnisz, Denes, et al. “Activation of proto-oncogenes by disruption of chromosome neighborhoods.”Science 351.6280 (2016): 1454-1458; 6. Mali, Prashant, et al. “RNA-guided human genome engineering via Cas9.” Science 339.6121 (2013): 823-826. 179 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY THE DENSITY OF WOLBACHIA STRAIN wMELPOP IN DROSOPHILA MELANOGASTER BRAIN IS INVERSELY RELATED TO THE LEVEL OF HSP67BC GENE EXPRESSION D.A. Malkeyeva 1, 2 *, E.V. Kiseleva 1 1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia * Corresponding author:malkeyeva@bionet.nsc.ru Key words: Wolbachia, heat shock proteins, hsp67Bc Motivation and Aim: Wolbachia are the widespread endosymbionts of arthropods and nematodes. These bacteria are known for having a significant impact on hosts’ repro- ductive functions, longevity and gene expression. Wolbachia down-regulates 41% of heat shock protein genes, including hsp67Bc, in Drosophila melanogaster S2 cells [1]. Hsp67Bc was shown to stimulate macroautophagy [2], a mechanism by which Wolba- chia bacteria are removed from host cells [3]. In this study, we investigated the interrela- tion between the expression of hsp67Bc gene and the density of pathogenic Wolbachia strain wMelPop in D. melanogaster brain. Methods and Algorithms: To obtain D. melanogaster with down-regulated hsp67Bc gene expression we used the imprecise excision of the P-element from hsp67Bc pro- moter region, which resulted in a deletion in hsp67Bc gene. In this work, flies with one (mutants) of two (control) copies of the gene were used. Overexpression of hsp67Bc in D. melanogaster was obtained using GAL4-driven expression of UAS-hsp67Bc con- struct. Wolbachia in fly brains were visualized by fluorescence in situ hybridization with Cy3-labeled W2 probes specific to Wolbachia 16S rRNA. The quantity of endosymbi- onts was measured as Wolbachia-occupied area/brain area (S w /S b ) ratio on brain optical sections with the use of ImageJ 1.48 software. Results: In our study, an inverse relation between hsp67Bc expression and the quantity of pathogenic wMelPop strain of Wolbachia bacteria was determined. In D. melanogas- ter with one copy of hsp67Bc the S w /S b ratio was 2.7 times higher than in control flies (4.82±1.69 % compared to 1.75±1.00 %), whereas in flies overexpressing hsp67Bc the S w /S b ratio was 2.4 times lower than in control animals (1.21±0.29 % in comparison with 2.97±0.65 %). Conclusion: Deletion of one of two copies of the host’s hsp67Bc gene results in the over- replication of Wolbachia wMelPop strain in D. melanogaster brain. Overexpression of hsp67Bc not only retains the endosymbionts’ titer, but also reduces the titer of Wolbachia in the host’s brain to below the native (control) level. These results suggest that Wolba- chia strain wMelPop is recognized by the host organism as a pathogen. Acknowledgements: This work was supported by RFBR grant № 15-04-08993 and the State project of ICG SB RAS № 0324-2015-0003. References: 1. Z. Xi et al. (2008) Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host, BMC Genomics, 9:1. 2. S. Carra et al. (2010) Identification of the Drosophila ortholog of HSPB8: implication of HSPB8 loss of function in protein folding diseases, J Biol Chem, 285: 37811-37822. 3. D. Voronin et al. (2012) Autophagy regulates Wolbachia populations across diverse symbiotic associa- tions, Proc Natl Acad Sci USA, 109: E1638-1646. 180 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY PREDICTION OF FUNCTIONAL EFFECTS OF REGULATORY SEQUENCE VARIATIONS M. Malkowska 1 *, J. Zubek 2, 3 , D. Plewczynski 3 , L.S. Wyrwicz 1 1 Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland 2 Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland 3 Center of New Technologies, University of Warsaw, Warsaw, Poland * Corresponding author: bioinfo@coi.waw.pl Key words: regulatory variation, function prediction, machine learning Motivation and Aim: In the era of huge amounts of data from high-throughput DNA sequencing is necessary to search for more effective methods of analysis of functional regions of genomes, in particular regulatory regions, that may be crucial in the search for single-nucleotide polymorphisms potentially responsible for the development of the diseases. Our research aims to create and evaluate an integrative machine-learning model for regulatory variants identification within promoter regions of genes. We intend to utilize various gene annotations and DNA shape features, which have recently become avail- able and determine the significance of these new components. Methods and Algorithms: To improve the accuracy of predicting the functional conse- quences of regulatory variants we are implementing machine learning algorithms using newly available features. Our positive examples dataset was constructed using regu- latory mutations from the Human Gene Mutation Database 1 . Negative examples were derived using single nuclear variations from the 1000 Genomes Project 2 . The annotation data include the local DNA 3D shape, phylogenetic conservation, transcriptomic and epigenetic measurements. The model prediction performance will be evaluated across human genome to determine potential, not reported, true functional variants and com- pared to existing methods. Results: Currently, we are in process of model selection and optimization. There are strong indications that chosen features will improve the accuracy and precision of func- tional effects of regulatory sequence variations predictions. Conclusion: The results of the project will improve our understanding of the molecular mechanisms of disease pathogenesis and complex traits. Availability: The machine-learning model and variant predictions will be available through GitHub repository (project in progress). References: 1. P.D. Stenson at el. (2014) The human gene mutation database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine, Human Genetics, 133:1-9. 2. 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes, Nature, 491(7422):56-65. 181 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY MOLECULAR EVOLUTION AND SYSTEMATICS OF FLAT LEECHES (HIRUDINEA: GLOSSIPHONIIDAE) N.B. Mandzyak 1 *, I.A. Kaygorodova 1, 2 1 Limnological Institute SB RAS, Irkutsk, Russia 2 Irkutsk State University, Irkutsk, Russia * Corresponding author: mandzyak@lin.irk.ru Key words: species divergence, species delimitation, genetic distances Motivation and Aim: Species as a basic unit of evolution have to be identifiable. Mean- while, the presence of cryptic species poses significant challenges for the accurate as- sessment of biodiversity. Increasingly, molecular data are being used to evaluate spe- cies boundaries and to assist in the identification of groups such as hirudinids in which morphological characters often do not distinguish species reliably [1]. However, the development of species-specific DNA barcodes for leeches has lagged behind that of other groups. Methods and Algorithms: To study species-specific DNA barcodes, leech samples were collected during multiple expeditions in 2003-2015. Sequences of universal for Meta- zoan barcoding fragment (CoxI) of 73 leech specimens from different sites of Northern Eurasia were newly generated for the present study. Bioinformatic analyses were con- ducted in MEGA V6.06 [2]. The evolutionary distances were computed separately for both intraspecific and congeneric comparisons using the Kimura two-parameter (K2P) model in accordance with DNA barcode techniques [3]. Results: The molecular phylogenetic analysis of barcoding fragment of the Glossiphonia representatives allowed to reveal four evolutionary branches among glossifonias inhab- iting Siberian and Far Eastern freshwater bodies. On the resulting phylogenetic tree, each group of nucleotide sequences belonging to Glossiphonia sp.1, Glossiphonia sp.2, Glossiphonia sp.3 and Glossiphonia sp.4 was clustered apart of each other and separate- ly from homologous sequences of the rest world fauna representatives. Genetic distances between Siberian leeches and phylogenetically close lineages exceed significantly the threshold of 3% [3] that could indicate their independent taxonomic position and assume that four potentially new species exist. In addition, intraspecific genetic polymorphism varies within the range of 0-0.73% and confirms this supposition. Moreover, due to im- pressive barcoding gap (over 5%), a long branch attraction phenomenon observed in this group of parasitic organisms [4] becomes clear. Conclusion: Thus, the use of barcoding thresholds bode well for delineating closely re- lated species and taxonomically understudied groups within Hirudinea. This work was supported by the Russian Foundation for Basic Research (14-04- 00345). References: 1. A.E. Bely, D.A. Weiseblat (2006) Evolution & Development, 8: 491-501. 2. K. Tamura et al. (2013) Molecular Biology and Evolution, 30: 2725-2729. 3. P. Hebert et al. (2003) Proc. Royal Soc. B: Biological Sciences, 270:313–321. 4. P. Martin et al. (2000) Mol. Phyl. Evol., 15: 355-368. 182 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY PREDICTION OF STRUCTURAL PROPERTIES OF UNCHARACTERIZED PROTEINS FROM THEIR POST-CLEAVAGE MASS SPECTRA BY A MULTIVARIATE STATISTICAL MODEL O.A. Markelov 1 *, A.R. Kayumov 2 , M.I. Bogachev 1 1 St. Petersburg Electrotechnical University, St. Petersburg, Russia 2 Kazan (Volga region) Federal University, Kazan, Russia * Corresponding author: OAMarkelov@etu.ru Key words: protein structure prediction, mass spectrometry, multivariate regression model Motivation and Aim: Successful prediction of structural and structure-associated proper- ties of uncharacterized proteins currently requires the knowledge of the sequence either of the studied protein itself or of its homologous counterparts. We aimed to characterize proteins directly from their post-cleavage mass distribution shapes without reconstruc- tion of their primary sequences. Methods and Algorithms: We used Kolmogorov statistics to compare the simulated post- cleavage mass distribution shapes of various proteins from the UniProtKB/Swiss-Prot, RSCB PDB, DisProt, Ideal, PDBTM and VFPB databases. To combine results for several cleavages, we suggest a solution based on the multivariate logistic regression. Results: We found that various structural and structure-associated properties of proteins are explicitly reflected in the shapes of their post-cleavage mass distributions. In par- ticular, proteins carrying presumably α-helixes in their secondary structure exhibit broad mass distributions, while for proteins with β-sheet structures mass distributions decay by a simple exponential, allowing to distinguish between them with 90% accuracy by using a single Thermolysin cleavage. For membrane-associated proteins with specific structural properties we could properly predict their location (membrane vs soluble) as well as localization in the membrane (monotopic vs transmembrane, single-pass vs multi- pass transmembrane) with 80% accuracy for each pairwise comparison by combining 3-4 different cleavages. Other prominent examples included 3 out of 4 successful predictions of intrinsically disordered proteins vs fixed-structure proteins as well as membrane-asso- ciated proteins by their functional group and host bacteria phylum. Remarkably, the best prediction accuracy of structural and localization properties was achieved by Thermolysin and GluC(phosphate)+Lys C cleavage simulations digesting the protein at the positions of amino acid residues from the inertial and external hydropathy groups, respectively [1]. Conclusion: To summarize, we have suggested a multivariate statistical model to suc- cessfully predict various structural and structure-driven properties of uncharacterized proteins from their post-cleavage mass spectrometry data. Availability: Complete data and test examples at http://www.nature.com/articles/ srep22286. Acknowledgements: We acknowledge the financial support by the RSF grant 15-14- 00046. References: 1. Bogachev, M. I. et al. (2016) Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage, Scientific Re- ports, 6: 22286; doi: 10.1038/srep22286. 183 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY ON THE POSSIBLE IMPACT OF EXOGENOUS 8-OXO-2’- DEOXYGUANOSINE ON DNA SYNTHESIS, DAMAGE AND REPAIR IN AGING CELL CULTURES AND ORGANISM N.V. Marmiy 1 *, G.V. Morgunova 2 , D.S. Esipov 1 , A.N. Khokhlov 2 1 Division of Bioorganic Chemistry, Biology Department, Moscow State University, Moscow, Russia 2 Evolutionary Cytogerontology Sector, Biology Department, Moscow State University, Moscow, Russia * Corresponding author: marmiynv@gmail.com Download 3.91 Kb. Do'stlaringiz bilan baham: |
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