Laboratory of Theoretical Genetics
Head N.A.Kolchanov, Dr.Biol.Sci., Prof.
Correlation between the value of helical twist angle and double strand DNA
nucleotide context (as represented in B-DNA-Video database)
A model of the DNA-protein interaction
Linear correlation between a) DNA-USF affinity and twist and b) DNA-USF affinity and minor groove depthth
A leader fragment of E. coli thrS mRNA: the secondary
structure predicted by the genetic algorithm
Fragment of the regulatory 5'-region controlling transcription of the rat
tyrosine aminotransferase gene described in the TRRD database
Fragments of gene networks of erythrocyte maturation and differentiation
Informational biology occupies a crucial and an exceptionally important position in modern biology. It provides the theoretical and computer-assisted informational background for genomic research, genetics and breeding, molecular genetics and molecular biology, gene and protein engineering, biotechnology, medical genetics, gene diagnostics, and gene therapy, in other words, sciences whose outstanding achievements confer a leading status to modern biology of the coming century. Top priority is given to the development of research in the area of informational biology throughout the world. The Institute of Cytology and Genetics (IC&G) SB RAS is also committed to the development of integrative informational biology.
The main lines of research
The main goals of the Laboratory are:
This work requires an integrated approach, i.e., theoretical and computer-assisted analyses of genetic systems and processes are executed at different levels: from molecule, cell, organism, to population.
Informational and program resources for analysis of genetic systems and processes
The current list of resources includes:
TRRD- a database on transcription regulatory regions in eukaryotic genes
ACTIVITY- for predicting the activity of functional sites on the basis of their nucleotide sequences
B-DNA Video - for investigating the physico-chemical and conformational
properties of sites and their recognition.
ConsFreq TFBSR GeneNet Leader_mRNA CRASP Nucleosome Fitness
ConsFreq- for investigating the contextual characteristics of sites and site recognition by frequency matrices and consensusi
TFBSR- for analyzing and recognizing transcription factor binding sites using methods of realizations
GeneNet- a database on eukaryotic gene nets
Leader_mRNA- for estimating the level of eukaryotic mRNA translation
CRASP- for investigating the structural organization and evolution of proteins on the basis of analysis of co-adaptive substitutions
Nucleosome- for analyzing and recognizing DNA nucleosome sites
Fitness- for RNA secondary structure prediction by genetic algorithm
We are developing the TRRD (Transcription Regulatory Regions Database), designed for accumulation of experimental data on extended transcription regulatory regions of the eukaryotic genes. The TRRD allows to describe the modular structure of transcription regulatory regions and the hierarchy of their constituent regulatory units, including cis-elements (transcription factor binding sites), composite elements formed by the pairs of neighboring sites, promoters, enhancers, silencers, and long transcription regulatory regions in the 5'- and 3'-ends of the genes or in their introns that contain all the listed above elements.
DNA conformational and physico-chemical properties underlie the function of regulatory genomic sequences (RGS) and define the specificity and efficiency of their interactions with regulatory proteins. The conformational and physico-chemical DNA properties are context-dependent. They determine the orientation of base pairs in the DNA double helix with respect to each other; physico-chemical properties of RGS; RGS dynamic characteristics significant for DNA-protein interactions.
We have developed the ACTIVITY system for revealing the conformational and physico-chemical properties of RGS. Analysis of different types of RGS demonstrates that each type is characterized by a specific set of conformational and physico-chemical properties and their activity values.
The GeneExpress system, which we are developing, is designed to integrate our and other Internet available resources on gene expression regulation.
We are developing the GeneNet database to accumulate and store information on gene networks and signal transduction pathways of the eukaryotic organisms. The following hierarchical levels of the gene network are considered: an organism, a single cell, and a single gene. The following gene networks are described in the GeneNet database: