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Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family

(2013) CURRENT BIOINFORMATICS. 8(4). p.483-488
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
It is well known that transcription factors can induce deformations in their DNA-binding sites upon complex formation. However, few attempts have been made to investigate the extent to which induced structural deformations in the DNA molecule are conserved between different members of the same transcription factor family. In this article, we used the CRoSSeD methodology for describing DNA structural properties to extract common features in the binding sites of different LacI-GalR family members. The most significant feature identified in this way was located at the center of the binding sites, which is also the most likely location for an induced DNA deformation following an amino acid interdigitation. This feature was related further to specific elements present in the protein structure and was used to identify and characterize deviant family members. A general family-wide binding site model was constructed and applied to screen for unknown member binding sites.
Keywords
Conditional random fields, transcription factor, CRoSSeD, DNA structure, protein-DNA interaction, LacI-GalR family, REPRESSOR, ESCHERICHIA COLI, RECOGNITION, MODEL, OPERATOR

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Citation

Please use this url to cite or link to this publication:

Chicago
Meysman, Pieter, Kathleen Marchal, and Kristof Engelen. 2013. “Identifying Common Structural DNA Properties in Transcription Factor Binding Site Sets of the LacI-GalR Family.” Current Bioinformatics 8 (4): 483–488.
APA
Meysman, P., Marchal, K., & Engelen, K. (2013). Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family. CURRENT BIOINFORMATICS, 8(4), 483–488.
Vancouver
1.
Meysman P, Marchal K, Engelen K. Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family. CURRENT BIOINFORMATICS. 2013;8(4):483–8.
MLA
Meysman, Pieter, Kathleen Marchal, and Kristof Engelen. “Identifying Common Structural DNA Properties in Transcription Factor Binding Site Sets of the LacI-GalR Family.” CURRENT BIOINFORMATICS 8.4 (2013): 483–488. Print.
@article{4180235,
  abstract     = {It is well known that transcription factors can induce deformations in their DNA-binding sites upon complex formation. However, few attempts have been made to investigate the extent to which induced structural deformations in the DNA molecule are conserved between different members of the same transcription factor family. In this article, we used the CRoSSeD methodology for describing DNA structural properties to extract common features in the binding sites of different LacI-GalR family members. The most significant feature identified in this way was located at the center of the binding sites, which is also the most likely location for an induced DNA deformation following an amino acid interdigitation. This feature was related further to specific elements present in the protein structure and was used to identify and characterize deviant family members. A general family-wide binding site model was constructed and applied to screen for unknown member binding sites.},
  author       = {Meysman, Pieter and Marchal, Kathleen and Engelen, Kristof},
  issn         = {1574-8936},
  journal      = {CURRENT BIOINFORMATICS},
  keyword      = {Conditional random fields,transcription factor,CRoSSeD,DNA structure,protein-DNA interaction,LacI-GalR family,REPRESSOR,ESCHERICHIA COLI,RECOGNITION,MODEL,OPERATOR},
  language     = {eng},
  number       = {4},
  pages        = {483--488},
  title        = {Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family},
  volume       = {8},
  year         = {2013},
}

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