Comparison of the structures of in vitro selected and natural binding sites of transcription factors

被引：0
|
作者：
Khlebodarova, T. M. [1 ]
Podkolodnaya, O. A. [1 ]
Ananko, E. A. [1 ]
Ignatieva, E., V [1 ]
机构：
[1] RAS, SB, Inst Cytol & Genet, Novosibirsk, Russia
来源：
Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure, Vol 1 | 2004年
关键词：
databases; transcription factor; binding sites; transcription regulation;
D O I：
暂无
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
The information compiled in TRRD_ARTSITE database was used to compare the structures natural and in vitro selected binding sites for transcription factors USF1, SP1, YY1, RAR/RXR, and E2F/DP1. 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 frequencies of certain nucleotides detected 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.
引用
收藏
页码：99 / 102
页数：4
相关论文
共 50 条
  • [21] Turnover of binding sites for transcription factors involved in early Drosophila development
    Costas, J
    Casares, F
    Vieira, J
    GENE, 2003, 310 : 215 - 220
  • [22] The characteristics of miRNA binding sites with mRNA of MYB plant transcription factors
    Rakhmetullina, A. K.
    Regnier, M.
    Ivashchenko, A. T.
    INTERNATIONAL JOURNAL OF BIOLOGY AND CHEMISTRY, 2019, 12 (01): : 60 - 67
  • [23] Facilitated dissociation of transcription factors from single DNA binding sites
    Kamar, Ramsey I.
    Banigan, Edward J.
    Erbas, Aykut
    Giuntoli, Rebecca D.
    de la Cruz, Monica Olvera
    Johnson, Reid C.
    Marko, John F.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2017, 114 (16) : E3251 - E3257
  • [24] How do transcription factors select specific binding sites in the genome?
    Yongping Pan
    Chung-Jung Tsai
    Buyong Ma
    Ruth Nussinov
    Nature Structural & Molecular Biology, 2009, 16 : 1118 - 1120
  • [25] How do transcription factors select specific binding sites in the genome?
    Pan, Yongping
    Tsai, Chung-Jung
    Ma, Buyong
    Nussinov, Ruth
    NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2009, 16 (11) : 1118 - 1120
  • [26] The role of transcription factors in autism disease, looking for binding sites enrichments
    Vilardell, M.
    Herwig, R.
    INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE, 2010, 28 (08) : 688 - 688
  • [27] Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes
    Blumberg, Amit
    Sailaja, Badi Sri
    Kundaje, Anshul
    Levin, Liron
    Dadon, Sara
    Shmorak, Shimrit
    Shaulian, Eitan
    Meshorer, Eran
    Mishmar, Dan
    GENOME BIOLOGY AND EVOLUTION, 2014, 6 (10): : 2634 - 2646
  • [28] In vitro selection of optimal AbrB-binding sites: Comparison to known in vivo sites indicates flexibility in AbrB binding and recognition of three-dimensional DNA structures
    Xu, K
    Strauch, MA
    MOLECULAR MICROBIOLOGY, 1996, 19 (01) : 145 - 158
  • [29] Functional determinants of transcription factors in Escherichia coli:: protein families and binding sites
    Babu, MM
    Teichmann, SA
    TRENDS IN GENETICS, 2003, 19 (02) : 75 - 79
  • [30] Transcription factor binding sites recognition by the regularities matrices based on the natural classification method
    Vityaev, E. E.
    Lapardin, K. A.
    Khomicheva, I., V
    Levitsky, V. G.
    PROCEEDINGS OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, VOL 1, 2006, : 199 - +
12345