SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition

Abstract

The local DNA conformation in the region of transcription factor binding sites, determined by context, is one of the factors underlying the specificity of DNA-protein interactions. Analysis of the local conformation of a set of functional DNA sequences may allow for determination of the conservative conformational and physicochemical parameters reflecting molecular mechanisms of interaction. The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for >100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a sample proposed by a user. The resource SITECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/.

Mechanisms Regulating Escherichia Coli dps Gene Expression under Stress: Reconstruction on Kinetic Data

“…Метод заключается в выявлении набора консервативных контекстно-зависимых конформационных и физико-химических свойств, определенных для позиций выравнивания сайтов связывания ТФ и дальнейшего сравнения выявленных консервативных свойств со свойствами анализируемой последовательности [19]. Для распознавания в промоторе гена dps потенциальных сайтов ТФ, были созданы обучающие выборки экспериментально доказанных сайтов связывания ТФ Rob, PurR, MetJ, MarA, SoxS, и IscR, которые прямо или косвенно могут участвовать в ответе гена на тяжелые металлы и окислительный стресс [5,20,21].…”

“…В табл. 3 приведены результаты анализа последовательности промотора гена dps методом SITECON [19]. Дополнительно к ранее локализованным сайтам ТФ OxyR и IHF [8], в промоторе гена dps выявлены потенциальные сайты связывания трех ТФ, которые удовлетворяют описанным в разделе «Методы» ограничениям и могут участвовать в ответе гена на кадмий.…”

Guide to Genome-Wide Bacterial Transcription Factor Binding Site Prediction Using OmpR as Model

“…A factor that contributes to the specificity of the interaction between a TF and its binding site is the local conformation of the DNA site (Oshchepkov et al, 2004). Even though a TF often regulates multiple genes and the binding sites in the promoters of these genes show variations, certain conformational and physicochemical properties are conserved among these sites so that the TF can recognize the sites (Oshchepkov et al, 2004). Thus, these context-dependent TFBS properties can be used to improve the predictions of genes controlled by a TF (Oshchepkov et al, 2004).…”

“…SITECON (Oshchepkov et al, 2004) is a web application that can analyze and report 38 properties-major groove depth, bend, entropy change, to name a few-in a given set of DNA binding site sequences, and optionally, find binding sites in one or more DNA sequences using those properties. CRoSSeD (Conditional Random fields of Smoothed Structural Data) (Meysman et al, 2011) is another program that leverages structure information.…”

Transactivation by Body Burden Dioxin of Herpes Simplex Virus Genes and Cytokines Genes can Weaken the Host Antiviral Defense

“…Going along with the experimental data, multiple potentially active DRE were computationally detected and quantified in regulatory area of several human viruses [4,5]. In this study, a computational search for DRE in HSV-1 genes was performed using approach SITECON [6] designated for recognition of transcriptional factor binding sites. HSV-1 is a DNA virus causing diseases ranging from simple cold sores to lethal encephalitis [7].…”