EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES

The development of in vitro methods produced new experimental information on protein binding to DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic g...

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Main Authors: T. M. Khlebodarova, D. Yu. Oshchepkov, V. G. Levitsky, O. A. Podkolodnaya, E. V. Ignatieva, E. A. Ananko, I. L. Stepanenko, N. A. Kolchanov
Format: Article
Language:English
Published: Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders 2015-01-01
Series:Вавиловский журнал генетики и селекции
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Online Access:https://vavilov.elpub.ru/jour/article/view/317
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author T. M. Khlebodarova
D. Yu. Oshchepkov
V. G. Levitsky
O. A. Podkolodnaya
E. V. Ignatieva
E. A. Ananko
I. L. Stepanenko
N. A. Kolchanov
author_facet T. M. Khlebodarova
D. Yu. Oshchepkov
V. G. Levitsky
O. A. Podkolodnaya
E. V. Ignatieva
E. A. Ananko
I. L. Stepanenko
N. A. Kolchanov
author_sort T. M. Khlebodarova
collection DOAJ
description The development of in vitro methods produced new experimental information on protein binding to DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent sequences selected in vitro reflect the actual structures of natural transcription factor (TF) binding sites. The Kullback – Leibler divergence was applied to the comparison of frequency matrices of TF binding sites constructed on samples of artificially selected sequences and natural sites. Core sequences of natural and artificial sites showed high similarity for 80 % of all TFs studied. For 20 % of TFs, binding site sequences selected in vitro had a broader range of permissible significant nucleotides not found in natural sites. The optimum lengths of DNA sequences including natural binding sites, at which they are recognized most accurately, were estimated by the weight matrix method. For approximately 80 % of the TFs studied, the optimum binding site length notably exceeded the lengths of the core sequences, as well as the lengths of in vitro selected sites. The detected features of in vitro selected TF binding sites impose constraints on their use in the development of computer-assisted methods of the recognition of candidate sites in genomic sequences.
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institution Kabale University
issn 2500-3259
language English
publishDate 2015-01-01
publisher Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
record_format Article
series Вавиловский журнал генетики и селекции
spelling doaj-art-4deb69976220440a881ea2f3d651f5552025-02-01T09:58:01ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592015-01-01184/2876886300EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITEST. M. Khlebodarova0D. Yu. Oshchepkov1V. G. Levitsky2O. A. Podkolodnaya3E. V. Ignatieva4E. A. Ananko5I. L. Stepanenko6N. A. Kolchanov7Institute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaThe development of in vitro methods produced new experimental information on protein binding to DNA, which is accumulated in databases and used in studies of mechanisms regulating gene expression and in the development of computer-assisted methods of binding site recognition in pro- and eukaryotic genomes. However, it is still questionable to what extent sequences selected in vitro reflect the actual structures of natural transcription factor (TF) binding sites. The Kullback – Leibler divergence was applied to the comparison of frequency matrices of TF binding sites constructed on samples of artificially selected sequences and natural sites. Core sequences of natural and artificial sites showed high similarity for 80 % of all TFs studied. For 20 % of TFs, binding site sequences selected in vitro had a broader range of permissible significant nucleotides not found in natural sites. The optimum lengths of DNA sequences including natural binding sites, at which they are recognized most accurately, were estimated by the weight matrix method. For approximately 80 % of the TFs studied, the optimum binding site length notably exceeded the lengths of the core sequences, as well as the lengths of in vitro selected sites. The detected features of in vitro selected TF binding sites impose constraints on their use in the development of computer-assisted methods of the recognition of candidate sites in genomic sequences.https://vavilov.elpub.ru/jour/article/view/317transcription factorsbinding sitesfrequency and weight matricesin vitro selected sequences
spellingShingle T. M. Khlebodarova
D. Yu. Oshchepkov
V. G. Levitsky
O. A. Podkolodnaya
E. V. Ignatieva
E. A. Ananko
I. L. Stepanenko
N. A. Kolchanov
EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
Вавиловский журнал генетики и селекции
transcription factors
binding sites
frequency and weight matrices
in vitro selected sequences
title EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
title_full EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
title_fullStr EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
title_full_unstemmed EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
title_short EFFECT OF FLANKING SEQUENCES ON THE ACCURACY OF THE RECOGNITION OF TRANSCRIPTION FACTOR BINDING SITES
title_sort effect of flanking sequences on the accuracy of the recognition of transcription factor binding sites
topic transcription factors
binding sites
frequency and weight matrices
in vitro selected sequences
url https://vavilov.elpub.ru/jour/article/view/317
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