E. Ignatieva - Academia.edu (original) (raw)
Papers by E. Ignatieva
Vavilovskij Žurnal Genetiki i Selekcii, 2014
By now, a huge body of experimental data on gene transcription regulation has been accumulated. T... more 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 proces...
Vavilovskij Žurnal Genetiki i Selekcii, 2014
This paper describes a RESTful Web service-based distributed software system, which focuses on th... more This paper describes a RESTful Web service-based distributed software system, which focuses on the reconstruction of gene networks by integrating data from heterogeneous data sources, including databases of molecular-genetic interactions, metabolic and signaling pathways, gene networks, etc.
Vavilov Journal of Genetics and Breeding, 2017
Molecular Biology, 2018
⎯The identification of human predisposition genes to severe forms of infectious diseases is impor... more ⎯The identification of human predisposition genes to severe forms of infectious diseases is important for understanding the mechanisms of pathogenesis, as well as for the detection of the risk groups. This will allow one to carry out targeted vaccination and preventive therapy. The most common approaches to the genetic risk estimation include conducting association studies, in which the groups of patients and control individuals are compared using both preliminarily selected candidate genes and using genome-wide analysis. To search for genetic variants predisposed to severe forms of infectious diseases, it is expedient to form a control that consists of patients with clinically proven infections with asymptomatic or mild forms of the disease. The examples of the use of these approaches to identify genetic factors that predispose one to severe forms of infections caused by viruses from the Flaviviridae family are considered in the review. At present, a number of genetic markers associated with predisposition to tick-borne encephalitis, West Nile fever, and Dengue fever have already been detected. These associations must be confirmed in independent samples. Genetic variants, for which the association with spontaneous recovery during infection with hepatitis C virus, patient's reaction on antiviral drugs, and the development of liver fibrosis was established, were also detected. The gene variants with more pronounced phenotypic effects will probably be found during further studies; they can be used in clinical practice as prognostic markers of the course and outcomes of infection with the Flaviviridae, as well as of the response to treatment.
Vavilov Journal of Genetics and Breeding, 2016
научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского ... more научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, Россия 2 Федеральное государственное бюджетное научное учреждение «Научно-исследовательский институт терапии и профилактической медицины», Новосибирск, Россия 3 Федеральное государственное автономное образовательное учреждение высшего образования «Новосибирский национальный исследовательский государственный университет», Новосибирск, Россия 4 Федеральное государственное бюджетное образовательное учреждение высшего образования «Новосибирский государственный аграрный университет», Новосибирск, Россия 5 Хэйлунцзянский университет, биологический факультет, Харбин, Хэйлунцзянская провинция, Китай
Genetika
The review describes integrated experimental and computer approaches to the investigation of the ... more 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.
Vavilov Journal of Genetics and Breeding, 2020
In recent years, using a genome-wide association study (GWAS), a number of single nucleotide poly... more In recent years, using a genome-wide association study (GWAS), a number of single nucleotide polymorphisms (SNPs) have been suggested to be associated with susceptibility to leukemia in cattle. However, all studies have been done with purebred Holstein cows and their hybrids. In this regard, it is important to confirm the functional role of polymorphisms previously identified in a GWAS study in Russian cattle breeds. The aim of this study was to verify the association between rs110861313 in the intergenic region of bovine chromosome 23 and leukemia in the Russian Black Pied cattle. Based on the levels of bovine leukemia virus (BLV)-specific antibodies detected in serum using serodiagnostic techniques, animals were divided into three groups: healthy animals (n = 115), asymptomatic virus carriers (n = 145) and animals with leukemia (n = 107). Genotyping of rs110861313 was carried out using polymerase chain reaction followed by analysis of restriction fragment length polymorphisms. A s...
Bioinformatics of Genome Regulation and Structure II, 2006
ABSTRACT The ArtSite database was developed; the database compiles the information on the structu... more ABSTRACT The ArtSite database was developed; the database compiles the information on the structures of eukaryotic transcription factor binding sites and/or their DNA-binding domains obtained from in vitro selected sequences. Current release of the database comprises 420 matrices describing specific features of binding sites or their DNA-binding domains for over 200 transcription factors. The matrices were constructed basing on alignments of representative samples of transcription factor binding sites, totally containing over 10 thousand sequences. The information compiled in ArtSite was used to compare the structures of natural and in vitro selected binding sites for USF1, SP1, YY1, RAR/RXR, and E2F/DP1 transcription factors. The structures of the natural and in vitro selected binding sites for each transcription factor analyzed were found similar, suggesting that at least for the factors in question the structures of binding sites correlated with the affinities of the corresponding factors. Insignificant differences in detected frequencies of certain nucleotides reflect the general trend, namely, a higher occurrence of moderate affinity sites in the natural population of sequences compared with the sequences obtained in vitro.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1998
GeneExpress system has been designed to integrate description, analysis, and recognition of eukar... more GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on t...
Nucleic Acids Research, 1998
Nucleic Acids Research, 2004
Biochemistry (Moscow), 2007
The development of computer-assisted methods for transcription factor binding sites (TFBS) recogn... more The development of computer-assisted methods for transcription factor binding sites (TFBS) recognition is necessary for study the DNA regulatory transcription code. There are a great number of experimental methods that enable TFBS identification in genome sequences. The experimental data can be used to elaborate multiple computer approaches to recognition of TFBS, each of which has its own advantages and limitations. A short review of the characteristics of computer methods of TFBS prediction based on various principles is presented. Methods used for experimental monitoring of predicted sites are analyzed. Data concerning DNA regulatory potential and its realization at the chromatin level, obtained using these methods, are discussed along with approaches to recognition of target genes of certain transcription factors in the genome sequences.
Briefings in Bioinformatics, 2007
Proceedings of the Xth International Scientific Congress in fur animal production
Endocrinologia experimentalis, 1990
The effects of thymic hormone thymosin (fraction 5) and tactivin on the adrenal glucocorticoid fu... more The effects of thymic hormone thymosin (fraction 5) and tactivin on the adrenal glucocorticoid function were compared in BALB/c mice. An elevation in plasma corticosterone level was found 3 h after i.p. injection of thymosin (1 microgram/mouse) which was possibly caused by an activation of neuroendocrine structures. This appeared plausible because the pretreatment with dexamethasone (10 micrograms/mouse) abolished the effect of thymosin. In contrast, tactivin produced a decrease in plasma corticosterone if administered to mice with high basal level of the hormone. Tactivin added at doses from 0.00064-2 micrograms/ml together with ACTH (1.6 microIU/ml) to isolated adrenal cells hindered the stimulatory influence of ACTH on the production of corticosterone by the adrenal cells. Thus, the thymic hormone thymosin and tactivin showed opposite influences on the adrenal glucocorticoid function which appeared to be mediated through different mechanisms.
165 Recognition of transcriptional factor binding sites in genomic sequences is a promising appro... more 165 Recognition of transcriptional factor binding sites in genomic sequences is a promising approach to deciphering the regulatory code of DNA. Today, the methods of recognition of transcriptional factor binding sites based of various principles (consensus, weight matrices, etc.) are known and widely used [1]. However, in most cases, the recognition accuracy of transcriptional factor binding sites is insufficient for analysis of extended genomic sequences [2, 3], which makes it necessary to use additional criteria that allow the percent of false predictions to be decreased [3–5]. In addition, in different situations, the existing methods of recognition of transcriptional factor binding sites may differ significantly with respect to recognition quality even within the same approach (e.g., weight matrixes) [6]. For this reason, development of new approaches to recognizing transcriptional factor binding sites remains a topical problem. Another key problem is determination whether the transcriptional factor binding sites predicted by computer methods are functional in the regulatory regions of different genes in vivo (i.e., in chromosomes in living cells).
Russian Journal of Genetics: Applied Research
Nucleic acids research, 1999
The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulat... more 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/
Vavilovskij Žurnal Genetiki i Selekcii, 2014
By now, a huge body of experimental data on gene transcription regulation has been accumulated. T... more 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 proces...
Vavilovskij Žurnal Genetiki i Selekcii, 2014
This paper describes a RESTful Web service-based distributed software system, which focuses on th... more This paper describes a RESTful Web service-based distributed software system, which focuses on the reconstruction of gene networks by integrating data from heterogeneous data sources, including databases of molecular-genetic interactions, metabolic and signaling pathways, gene networks, etc.
Vavilov Journal of Genetics and Breeding, 2017
Molecular Biology, 2018
⎯The identification of human predisposition genes to severe forms of infectious diseases is impor... more ⎯The identification of human predisposition genes to severe forms of infectious diseases is important for understanding the mechanisms of pathogenesis, as well as for the detection of the risk groups. This will allow one to carry out targeted vaccination and preventive therapy. The most common approaches to the genetic risk estimation include conducting association studies, in which the groups of patients and control individuals are compared using both preliminarily selected candidate genes and using genome-wide analysis. To search for genetic variants predisposed to severe forms of infectious diseases, it is expedient to form a control that consists of patients with clinically proven infections with asymptomatic or mild forms of the disease. The examples of the use of these approaches to identify genetic factors that predispose one to severe forms of infections caused by viruses from the Flaviviridae family are considered in the review. At present, a number of genetic markers associated with predisposition to tick-borne encephalitis, West Nile fever, and Dengue fever have already been detected. These associations must be confirmed in independent samples. Genetic variants, for which the association with spontaneous recovery during infection with hepatitis C virus, patient's reaction on antiviral drugs, and the development of liver fibrosis was established, were also detected. The gene variants with more pronounced phenotypic effects will probably be found during further studies; they can be used in clinical practice as prognostic markers of the course and outcomes of infection with the Flaviviridae, as well as of the response to treatment.
Vavilov Journal of Genetics and Breeding, 2016
научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского ... more научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, Россия 2 Федеральное государственное бюджетное научное учреждение «Научно-исследовательский институт терапии и профилактической медицины», Новосибирск, Россия 3 Федеральное государственное автономное образовательное учреждение высшего образования «Новосибирский национальный исследовательский государственный университет», Новосибирск, Россия 4 Федеральное государственное бюджетное образовательное учреждение высшего образования «Новосибирский государственный аграрный университет», Новосибирск, Россия 5 Хэйлунцзянский университет, биологический факультет, Харбин, Хэйлунцзянская провинция, Китай
Genetika
The review describes integrated experimental and computer approaches to the investigation of the ... more 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.
Vavilov Journal of Genetics and Breeding, 2020
In recent years, using a genome-wide association study (GWAS), a number of single nucleotide poly... more In recent years, using a genome-wide association study (GWAS), a number of single nucleotide polymorphisms (SNPs) have been suggested to be associated with susceptibility to leukemia in cattle. However, all studies have been done with purebred Holstein cows and their hybrids. In this regard, it is important to confirm the functional role of polymorphisms previously identified in a GWAS study in Russian cattle breeds. The aim of this study was to verify the association between rs110861313 in the intergenic region of bovine chromosome 23 and leukemia in the Russian Black Pied cattle. Based on the levels of bovine leukemia virus (BLV)-specific antibodies detected in serum using serodiagnostic techniques, animals were divided into three groups: healthy animals (n = 115), asymptomatic virus carriers (n = 145) and animals with leukemia (n = 107). Genotyping of rs110861313 was carried out using polymerase chain reaction followed by analysis of restriction fragment length polymorphisms. A s...
Bioinformatics of Genome Regulation and Structure II, 2006
ABSTRACT The ArtSite database was developed; the database compiles the information on the structu... more ABSTRACT The ArtSite database was developed; the database compiles the information on the structures of eukaryotic transcription factor binding sites and/or their DNA-binding domains obtained from in vitro selected sequences. Current release of the database comprises 420 matrices describing specific features of binding sites or their DNA-binding domains for over 200 transcription factors. The matrices were constructed basing on alignments of representative samples of transcription factor binding sites, totally containing over 10 thousand sequences. The information compiled in ArtSite was used to compare the structures of natural and in vitro selected binding sites for USF1, SP1, YY1, RAR/RXR, and E2F/DP1 transcription factors. The structures of the natural and in vitro selected binding sites for each transcription factor analyzed were found similar, suggesting that at least for the factors in question the structures of binding sites correlated with the affinities of the corresponding factors. Insignificant differences in detected frequencies of certain nucleotides reflect the general trend, namely, a higher occurrence of moderate affinity sites in the natural population of sequences compared with the sequences obtained in vitro.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1998
GeneExpress system has been designed to integrate description, analysis, and recognition of eukar... more GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on t...
Nucleic Acids Research, 1998
Nucleic Acids Research, 2004
Biochemistry (Moscow), 2007
The development of computer-assisted methods for transcription factor binding sites (TFBS) recogn... more The development of computer-assisted methods for transcription factor binding sites (TFBS) recognition is necessary for study the DNA regulatory transcription code. There are a great number of experimental methods that enable TFBS identification in genome sequences. The experimental data can be used to elaborate multiple computer approaches to recognition of TFBS, each of which has its own advantages and limitations. A short review of the characteristics of computer methods of TFBS prediction based on various principles is presented. Methods used for experimental monitoring of predicted sites are analyzed. Data concerning DNA regulatory potential and its realization at the chromatin level, obtained using these methods, are discussed along with approaches to recognition of target genes of certain transcription factors in the genome sequences.
Briefings in Bioinformatics, 2007
Proceedings of the Xth International Scientific Congress in fur animal production
Endocrinologia experimentalis, 1990
The effects of thymic hormone thymosin (fraction 5) and tactivin on the adrenal glucocorticoid fu... more The effects of thymic hormone thymosin (fraction 5) and tactivin on the adrenal glucocorticoid function were compared in BALB/c mice. An elevation in plasma corticosterone level was found 3 h after i.p. injection of thymosin (1 microgram/mouse) which was possibly caused by an activation of neuroendocrine structures. This appeared plausible because the pretreatment with dexamethasone (10 micrograms/mouse) abolished the effect of thymosin. In contrast, tactivin produced a decrease in plasma corticosterone if administered to mice with high basal level of the hormone. Tactivin added at doses from 0.00064-2 micrograms/ml together with ACTH (1.6 microIU/ml) to isolated adrenal cells hindered the stimulatory influence of ACTH on the production of corticosterone by the adrenal cells. Thus, the thymic hormone thymosin and tactivin showed opposite influences on the adrenal glucocorticoid function which appeared to be mediated through different mechanisms.
165 Recognition of transcriptional factor binding sites in genomic sequences is a promising appro... more 165 Recognition of transcriptional factor binding sites in genomic sequences is a promising approach to deciphering the regulatory code of DNA. Today, the methods of recognition of transcriptional factor binding sites based of various principles (consensus, weight matrices, etc.) are known and widely used [1]. However, in most cases, the recognition accuracy of transcriptional factor binding sites is insufficient for analysis of extended genomic sequences [2, 3], which makes it necessary to use additional criteria that allow the percent of false predictions to be decreased [3–5]. In addition, in different situations, the existing methods of recognition of transcriptional factor binding sites may differ significantly with respect to recognition quality even within the same approach (e.g., weight matrixes) [6]. For this reason, development of new approaches to recognizing transcriptional factor binding sites remains a topical problem. Another key problem is determination whether the transcriptional factor binding sites predicted by computer methods are functional in the regulatory regions of different genes in vivo (i.e., in chromosomes in living cells).
Russian Journal of Genetics: Applied Research
Nucleic acids research, 1999
The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulat... more 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/