Biochemistry (Moscow)

, Volume 72, Issue 11, pp 1187–1193

Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate genes

  • T. I. Merkulova
  • D. Yu. Oshchepkov
  • E. V. Ignatieva
  • E. A. Ananko
  • V. G. Levitsky
  • G. V. Vasiliev
  • N. V. Klimova
  • V. M. Merkulov
  • N. A. Kolchanov
Review

DOI: 10.1134/S000629790711003X

Cite this article as:
Merkulova, T.I., Oshchepkov, D.Y., Ignatieva, E.V. et al. Biochemistry Moscow (2007) 72: 1187. doi:10.1134/S000629790711003X

Abstract

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.

Key words

genome annotationrecognition of transcription factor binding sitescomputer and experimental methodsdatabasestraining samples

Abbreviations

ChIP

chromatin immunoprecipitation

EMSA

electromobility shift assay

GRE

glucocorticoid-responsive element

SAGE

serial analysis of gene expression

TF

transcription factor

TFBS

transcription factor binding site

Copyright information

© Pleiades Publishing, Ltd. 2007

Authors and Affiliations

  • T. I. Merkulova
    • 1
    • 2
  • D. Yu. Oshchepkov
    • 1
    • 2
  • E. V. Ignatieva
    • 1
    • 2
  • E. A. Ananko
    • 1
  • V. G. Levitsky
    • 1
    • 2
  • G. V. Vasiliev
    • 1
  • N. V. Klimova
    • 1
  • V. M. Merkulov
    • 1
  • N. A. Kolchanov
    • 1
    • 2
  1. 1.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia